Starting phenix.real_space_refine on Thu Feb 15 01:06:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lj3_4055/02_2024/5lj3_4055_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lj3_4055/02_2024/5lj3_4055.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lj3_4055/02_2024/5lj3_4055.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lj3_4055/02_2024/5lj3_4055.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lj3_4055/02_2024/5lj3_4055_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lj3_4055/02_2024/5lj3_4055_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 7 6.06 5 P 461 5.49 5 Mg 2 5.21 5 S 183 5.16 5 C 38134 2.51 5 N 11285 2.21 5 O 13089 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 177": "OE1" <-> "OE2" Residue "A GLU 204": "OE1" <-> "OE2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "A GLU 382": "OE1" <-> "OE2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A GLU 533": "OE1" <-> "OE2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 668": "NH1" <-> "NH2" Residue "A ARG 749": "NH1" <-> "NH2" Residue "A GLU 933": "OE1" <-> "OE2" Residue "A GLU 941": "OE1" <-> "OE2" Residue "A GLU 942": "OE1" <-> "OE2" Residue "A GLU 1129": "OE1" <-> "OE2" Residue "A GLU 1151": "OE1" <-> "OE2" Residue "A ARG 1163": "NH1" <-> "NH2" Residue "A GLU 1178": "OE1" <-> "OE2" Residue "A GLU 1180": "OE1" <-> "OE2" Residue "A GLU 1181": "OE1" <-> "OE2" Residue "A GLU 1354": "OE1" <-> "OE2" Residue "A GLU 1434": "OE1" <-> "OE2" Residue "A ARG 1442": "NH1" <-> "NH2" Residue "A GLU 1479": "OE1" <-> "OE2" Residue "A ARG 1650": "NH1" <-> "NH2" Residue "A GLU 1708": "OE1" <-> "OE2" Residue "A GLU 1817": "OE1" <-> "OE2" Residue "A GLU 1867": "OE1" <-> "OE2" Residue "A GLU 1927": "OE1" <-> "OE2" Residue "A ARG 1962": "NH1" <-> "NH2" Residue "A GLU 2052": "OE1" <-> "OE2" Residue "A GLU 2062": "OE1" <-> "OE2" Residue "A GLU 2078": "OE1" <-> "OE2" Residue "D ARG 25": "NH1" <-> "NH2" Residue "D ARG 42": "NH1" <-> "NH2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C GLU 368": "OE1" <-> "OE2" Residue "C ARG 401": "NH1" <-> "NH2" Residue "C ARG 430": "NH1" <-> "NH2" Residue "C ARG 500": "NH1" <-> "NH2" Residue "C GLU 786": "OE1" <-> "OE2" Residue "C ARG 938": "NH1" <-> "NH2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G ARG 31": "NH1" <-> "NH2" Residue "G GLU 72": "OE1" <-> "OE2" Residue "G GLU 77": "OE1" <-> "OE2" Residue "H ARG 349": "NH1" <-> "NH2" Residue "H GLU 374": "OE1" <-> "OE2" Residue "H ARG 382": "NH1" <-> "NH2" Residue "H GLU 395": "OE1" <-> "OE2" Residue "H ARG 439": "NH1" <-> "NH2" Residue "H GLU 456": "OE1" <-> "OE2" Residue "J ARG 114": "NH1" <-> "NH2" Residue "J GLU 202": "OE1" <-> "OE2" Residue "J GLU 212": "OE1" <-> "OE2" Residue "J GLU 348": "OE1" <-> "OE2" Residue "J GLU 391": "OE1" <-> "OE2" Residue "K ARG 47": "NH1" <-> "NH2" Residue "K ARG 88": "NH1" <-> "NH2" Residue "K GLU 162": "OE1" <-> "OE2" Residue "K GLU 183": "OE1" <-> "OE2" Residue "K ARG 220": "NH1" <-> "NH2" Residue "L ARG 3": "NH1" <-> "NH2" Residue "L ARG 7": "NH1" <-> "NH2" Residue "L ARG 8": "NH1" <-> "NH2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L ARG 61": "NH1" <-> "NH2" Residue "L ARG 107": "NH1" <-> "NH2" Residue "M ARG 63": "NH1" <-> "NH2" Residue "M GLU 96": "OE1" <-> "OE2" Residue "M GLU 97": "OE1" <-> "OE2" Residue "M GLU 107": "OE1" <-> "OE2" Residue "M ARG 121": "NH1" <-> "NH2" Residue "M ARG 131": "NH1" <-> "NH2" Residue "M GLU 157": "OE1" <-> "OE2" Residue "M ARG 161": "NH1" <-> "NH2" Residue "M ARG 166": "NH1" <-> "NH2" Residue "M GLU 177": "OE1" <-> "OE2" Residue "N GLU 14": "OE1" <-> "OE2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 111": "NH1" <-> "NH2" Residue "N PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 257": "OE1" <-> "OE2" Residue "N ARG 261": "NH1" <-> "NH2" Residue "N GLU 323": "OE1" <-> "OE2" Residue "O GLU 17": "OE1" <-> "OE2" Residue "O GLU 49": "OE1" <-> "OE2" Residue "O GLU 145": "OE1" <-> "OE2" Residue "O ARG 158": "NH1" <-> "NH2" Residue "O ARG 169": "NH1" <-> "NH2" Residue "O GLU 178": "OE1" <-> "OE2" Residue "O GLU 184": "OE1" <-> "OE2" Residue "O GLU 242": "OE1" <-> "OE2" Residue "R ARG 22": "NH1" <-> "NH2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "S GLU 41": "OE1" <-> "OE2" Residue "S GLU 77": "OE1" <-> "OE2" Residue "S ARG 82": "NH1" <-> "NH2" Residue "S GLU 109": "OE1" <-> "OE2" Residue "S GLU 176": "OE1" <-> "OE2" Residue "S GLU 259": "OE1" <-> "OE2" Residue "S GLU 261": "OE1" <-> "OE2" Residue "S GLU 272": "OE1" <-> "OE2" Residue "b ARG 11": "NH1" <-> "NH2" Residue "b GLU 90": "OE1" <-> "OE2" Residue "d ASP 38": "OD1" <-> "OD2" Residue "d GLU 51": "OE1" <-> "OE2" Residue "f ARG 82": "NH1" <-> "NH2" Residue "g ARG 30": "NH1" <-> "NH2" Residue "h ARG 88": "NH1" <-> "NH2" Residue "j ARG 63": "NH1" <-> "NH2" Residue "j GLU 70": "OE1" <-> "OE2" Residue "j ARG 97": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 63161 Number of models: 1 Model: "" Number of chains: 45 Chain: "U" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2999 Classifications: {'RNA': 141} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 8, 'rna3p_pur': 60, 'rna3p_pyr': 60} Link IDs: {'rna2p': 20, 'rna3p': 120} Chain breaks: 2 Chain: "E" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 346 Classifications: {'RNA': 16} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 3} Link IDs: {'rna2p': 5, 'rna3p': 10} Chain: "I" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 693 Classifications: {'RNA': 33} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 13, 'rna3p_pyr': 15} Link IDs: {'rna2p': 5, 'rna3p': 27} Chain breaks: 1 Chain: "Z" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3610 Classifications: {'RNA': 171} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 14, 'rna3p_pur': 69, 'rna3p_pyr': 82} Link IDs: {'rna2p': 20, 'rna3p': 150} Chain breaks: 8 Chain: "V" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 2066 Classifications: {'RNA': 97} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 47, 'rna3p_pyr': 35} Link IDs: {'rna2p': 15, 'rna3p': 81} Chain breaks: 2 Chain: "A" Number of atoms: 15704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1922, 15704 Classifications: {'peptide': 1922} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 2, 'PTRANS': 96, 'TRANS': 1823} Chain breaks: 2 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 11, 'GLU:plan': 23, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 147 Chain: "D" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 912 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 106} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 321 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 1, 'TRANS': 44} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 6756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 882, 6756 Classifications: {'peptide': 882} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 49, 'TRANS': 832} Chain breaks: 4 Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 17, 'GLU:plan': 30, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 224 Chain: "G" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 823 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 2639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2639 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 187} Link IDs: {'PTRANS': 6, 'TRANS': 392} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 657 Unresolved non-hydrogen angles: 839 Unresolved non-hydrogen dihedrals: 533 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 10, 'TYR:plan': 4, 'ASN:plan1': 12, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 7, 'GLU:plan': 14, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 329 Chain: "J" Number of atoms: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2556 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1289 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 152} Chain breaks: 3 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1270 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 150} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 2010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2010 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 241} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1658 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 199} Chain breaks: 6 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1645 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 275 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 33} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 550 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain breaks: 2 Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 290 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 8, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 12, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 157 Chain: "S" Number of atoms: 3120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3120 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 219} Link IDs: {'PTRANS': 7, 'TRANS': 456} Chain breaks: 15 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 927 Unresolved non-hydrogen angles: 1186 Unresolved non-hydrogen dihedrals: 804 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 12, 'TYR:plan': 17, 'ASN:plan1': 6, 'TRP:plan': 8, 'ASP:plan': 14, 'PHE:plan': 13, 'GLU:plan': 25, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 552 Chain: "T" Number of atoms: 2946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 2946 Classifications: {'peptide': 592} Incomplete info: {'truncation_to_alanine': 547} Link IDs: {'PTRANS': 14, 'TRANS': 577} Chain breaks: 29 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 2169 Unresolved non-hydrogen angles: 2790 Unresolved non-hydrogen dihedrals: 1871 Unresolved non-hydrogen chiralities: 168 Planarities with less than four sites: {'GLN:plan1': 23, 'HIS:plan': 7, 'TYR:plan': 34, 'ASN:plan1': 23, 'TRP:plan': 19, 'ASP:plan': 29, 'PHE:plan': 30, 'GLU:plan': 59, 'ARG:plan': 34} Unresolved non-hydrogen planarities: 1278 Chain: "b" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 631 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "d" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 625 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "e" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "f" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 573 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 69} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "g" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 529 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "h" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain breaks: 1 Chain: "j" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 741 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "W" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 816 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 541 Unresolved non-hydrogen angles: 694 Unresolved non-hydrogen dihedrals: 429 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 14, 'TYR:plan': 4, 'ASN:plan1': 14, 'HIS:plan': 7, 'PHE:plan': 4, 'GLU:plan': 8, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 294 Chain: "Y" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 416 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 345 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 1, 'PHE:plan': 8, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 145 Chain: "k" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 396 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 253 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 121 Chain: "l" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 392 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 101 Chain: "m" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 467 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 400 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'HIS:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 164 Chain: "n" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 404 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 77} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 114 Chain: "p" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 369 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 100 Chain: "q" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 354 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 2, 'TRANS': 69} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 8, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 136 Chain: "r" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 340 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 93 Chain: "x" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 660 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 132} Link IDs: {'TRANS': 131} Chain breaks: 4 Unresolved non-hydrogen bonds: 264 Unresolved non-hydrogen angles: 396 Unresolved non-hydrogen dihedrals: 132 Planarities with less than four sites: {'UNK:plan-1': 132} Unresolved non-hydrogen planarities: 132 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 25822 SG CYS D 51 89.848 100.052 127.560 1.00145.50 S ATOM 25845 SG CYS D 54 92.838 97.940 128.737 1.00179.20 S ATOM 26134 SG CYS D 88 92.595 101.317 127.080 1.00153.57 S ATOM 26158 SG CYS D 91 92.850 98.516 126.780 1.00175.64 S ATOM 41594 SG CYS L 104 147.721 160.908 111.074 1.00 60.22 S ATOM 41600 SG CYS L 105 144.204 160.852 113.670 1.00 78.67 S ATOM 41625 SG CYS L 108 147.173 158.151 113.194 1.00 56.51 S ATOM 41935 SG CYS L 148 144.921 158.978 110.762 1.00 79.52 S ATOM 41594 SG CYS L 104 147.721 160.908 111.074 1.00 60.22 S ATOM 41724 SG CYS L 122 150.535 158.681 111.350 1.00 73.02 S ATOM 41945 SG CYS L 150 147.756 157.783 109.145 1.00 94.12 S ATOM 41966 SG CYS L 153 150.732 162.139 109.979 1.00 81.33 S ATOM 41625 SG CYS L 108 147.173 158.151 113.194 1.00 56.51 S ATOM 41710 SG CYS L 120 149.754 155.622 112.789 1.00 53.53 S ATOM 41724 SG CYS L 122 150.535 158.681 111.350 1.00 73.02 S ATOM 41912 SG CYS L 145 146.429 155.546 111.092 1.00 97.07 S ATOM 41945 SG CYS L 150 147.756 157.783 109.145 1.00 94.12 S ATOM 42543 SG CYS M 73 140.633 136.474 99.659 1.00 66.53 S ATOM 42605 SG CYS M 81 139.796 139.511 97.927 1.00 73.03 S ATOM 42645 SG CYS M 87 142.607 139.649 100.118 1.00 90.21 S ATOM 44212 SG CYS N 34 141.447 123.748 126.987 1.00108.86 S ATOM 44235 SG CYS N 37 141.642 122.516 127.632 1.00 84.16 S ATOM 44434 SG CYS N 61 144.529 123.066 128.643 1.00 93.20 S ATOM 44054 SG CYS N 13 158.282 125.572 118.460 1.00122.51 S ATOM 44078 SG CYS N 16 154.932 128.671 118.664 1.00118.15 S ATOM 44512 SG CYS N 71 155.174 126.013 120.067 1.00116.24 S ATOM 44533 SG CYS N 74 155.496 125.879 116.621 1.00108.05 S Time building chain proxies: 24.66, per 1000 atoms: 0.39 Number of scatterers: 63161 At special positions: 0 Unit cell: (210.21, 265.98, 270.27, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 S 183 16.00 P 461 15.00 Mg 2 11.99 O 13089 8.00 N 11285 7.00 C 38134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 23.94 Conformation dependent library (CDL) restraints added in 7.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1001 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 91 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 54 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 51 " pdb=" ZN L1000 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 148 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 104 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 108 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 105 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 104 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 122 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 150 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 153 " pdb=" ZN M1000 " pdb="ZN ZN M1000 " - pdb=" SG CYS M 81 " pdb="ZN ZN M1000 " - pdb=" SG CYS M 73 " pdb="ZN ZN M1000 " - pdb=" SG CYS M 87 " pdb="ZN ZN M1000 " - pdb=" NE2 HIS M 91 " pdb=" ZN N 401 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 61 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 37 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 34 " pdb=" ZN N 402 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 71 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 74 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 13 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 16 " Number of angles added : 27 14178 Ramachandran restraints generated. 7089 Oldfield, 0 Emsley, 7089 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14246 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 272 helices and 62 sheets defined 44.5% alpha, 9.2% beta 139 base pairs and 216 stacking pairs defined. Time for finding SS restraints: 22.37 Creating SS restraints... Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 155 through 177 removed outlier: 3.567A pdb=" N LEU A 165 " --> pdb=" O PHE A 161 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LYS A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TYR A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 210 through 230 Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 305 through 319 Proline residue: A 317 - end of helix Processing helix chain 'A' and resid 326 through 328 No H-bonds generated for 'chain 'A' and resid 326 through 328' Processing helix chain 'A' and resid 333 through 342 Processing helix chain 'A' and resid 381 through 386 removed outlier: 3.741A pdb=" N VAL A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 381 through 386' Processing helix chain 'A' and resid 388 through 391 No H-bonds generated for 'chain 'A' and resid 388 through 391' Processing helix chain 'A' and resid 473 through 481 Processing helix chain 'A' and resid 484 through 487 No H-bonds generated for 'chain 'A' and resid 484 through 487' Processing helix chain 'A' and resid 503 through 507 Processing helix chain 'A' and resid 516 through 534 Processing helix chain 'A' and resid 547 through 553 Processing helix chain 'A' and resid 564 through 586 Processing helix chain 'A' and resid 607 through 612 Processing helix chain 'A' and resid 619 through 640 Processing helix chain 'A' and resid 646 through 663 removed outlier: 5.686A pdb=" N GLY A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N GLN A 662 " --> pdb=" O ASN A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 691 Processing helix chain 'A' and resid 705 through 734 removed outlier: 3.618A pdb=" N GLY A 717 " --> pdb=" O ASN A 713 " (cutoff:3.500A) Proline residue: A 720 - end of helix Processing helix chain 'A' and resid 750 through 769 Processing helix chain 'A' and resid 775 through 795 removed outlier: 3.582A pdb=" N ARG A 780 " --> pdb=" O GLN A 776 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR A 781 " --> pdb=" O LYS A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 836 Processing helix chain 'A' and resid 842 through 869 Processing helix chain 'A' and resid 876 through 893 Processing helix chain 'A' and resid 908 through 923 removed outlier: 3.845A pdb=" N TYR A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 945 Processing helix chain 'A' and resid 947 through 960 Processing helix chain 'A' and resid 986 through 1006 removed outlier: 4.001A pdb=" N THR A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1034 Processing helix chain 'A' and resid 1063 through 1073 removed outlier: 3.507A pdb=" N ILE A1073 " --> pdb=" O LEU A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1086 Processing helix chain 'A' and resid 1108 through 1126 removed outlier: 3.919A pdb=" N SER A1111 " --> pdb=" O LYS A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1135 Processing helix chain 'A' and resid 1150 through 1155 Processing helix chain 'A' and resid 1176 through 1189 Processing helix chain 'A' and resid 1219 through 1233 Processing helix chain 'A' and resid 1306 through 1320 Processing helix chain 'A' and resid 1328 through 1345 Processing helix chain 'A' and resid 1348 through 1350 No H-bonds generated for 'chain 'A' and resid 1348 through 1350' Processing helix chain 'A' and resid 1354 through 1374 Processing helix chain 'A' and resid 1385 through 1389 removed outlier: 3.655A pdb=" N TYR A1389 " --> pdb=" O ALA A1386 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1394 No H-bonds generated for 'chain 'A' and resid 1392 through 1394' Processing helix chain 'A' and resid 1412 through 1415 No H-bonds generated for 'chain 'A' and resid 1412 through 1415' Processing helix chain 'A' and resid 1440 through 1443 Processing helix chain 'A' and resid 1447 through 1471 Processing helix chain 'A' and resid 1491 through 1493 No H-bonds generated for 'chain 'A' and resid 1491 through 1493' Processing helix chain 'A' and resid 1499 through 1502 No H-bonds generated for 'chain 'A' and resid 1499 through 1502' Processing helix chain 'A' and resid 1509 through 1518 removed outlier: 4.226A pdb=" N GLN A1516 " --> pdb=" O ARG A1512 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N TYR A1517 " --> pdb=" O GLU A1513 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER A1518 " --> pdb=" O PHE A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1530 through 1533 No H-bonds generated for 'chain 'A' and resid 1530 through 1533' Processing helix chain 'A' and resid 1540 through 1549 removed outlier: 3.785A pdb=" N ILE A1547 " --> pdb=" O ARG A1543 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN A1548 " --> pdb=" O THR A1544 " (cutoff:3.500A) Processing helix chain 'A' and resid 1553 through 1559 Processing helix chain 'A' and resid 1603 through 1609 removed outlier: 3.619A pdb=" N LEU A1608 " --> pdb=" O ARG A1604 " (cutoff:3.500A) Processing helix chain 'A' and resid 1611 through 1614 No H-bonds generated for 'chain 'A' and resid 1611 through 1614' Processing helix chain 'A' and resid 1639 through 1648 removed outlier: 4.131A pdb=" N ILE A1643 " --> pdb=" O PRO A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1671 Processing helix chain 'A' and resid 1688 through 1692 removed outlier: 4.035A pdb=" N SER A1691 " --> pdb=" O PRO A1688 " (cutoff:3.500A) Processing helix chain 'A' and resid 1748 through 1761 removed outlier: 3.911A pdb=" N THR A1761 " --> pdb=" O LEU A1757 " (cutoff:3.500A) Processing helix chain 'A' and resid 1794 through 1807 Processing helix chain 'A' and resid 1810 through 1823 Processing helix chain 'A' and resid 1841 through 1844 removed outlier: 3.623A pdb=" N PHE A1844 " --> pdb=" O ALA A1841 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1841 through 1844' Processing helix chain 'A' and resid 1896 through 1899 Processing helix chain 'A' and resid 1905 through 1923 Processing helix chain 'A' and resid 1938 through 1949 removed outlier: 3.757A pdb=" N LEU A1941 " --> pdb=" O LYS A1938 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ASP A1942 " --> pdb=" O ALA A1939 " (cutoff:3.500A) Proline residue: A1943 - end of helix removed outlier: 3.625A pdb=" N LEU A1949 " --> pdb=" O VAL A1946 " (cutoff:3.500A) Processing helix chain 'A' and resid 1964 through 1968 Processing helix chain 'A' and resid 1972 through 1979 Processing helix chain 'A' and resid 2001 through 2017 Processing helix chain 'A' and resid 2019 through 2026 Processing helix chain 'A' and resid 2045 through 2067 Processing helix chain 'A' and resid 2075 through 2083 removed outlier: 4.123A pdb=" N LYS A2080 " --> pdb=" O GLN A2076 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A2081 " --> pdb=" O THR A2077 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 29 removed outlier: 3.831A pdb=" N LYS D 29 " --> pdb=" O ARG D 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 9 No H-bonds generated for 'chain 'F' and resid 7 through 9' Processing helix chain 'F' and resid 17 through 47 Processing helix chain 'C' and resid 120 through 128 Processing helix chain 'C' and resid 146 through 157 Processing helix chain 'C' and resid 166 through 170 Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 247 through 258 Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 281 through 298 Processing helix chain 'C' and resid 324 through 331 Processing helix chain 'C' and resid 338 through 349 removed outlier: 3.870A pdb=" N ILE C 341 " --> pdb=" O SER C 338 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP C 342 " --> pdb=" O SER C 339 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TRP C 349 " --> pdb=" O THR C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 376 Processing helix chain 'C' and resid 378 through 390 Processing helix chain 'C' and resid 393 through 402 Processing helix chain 'C' and resid 410 through 413 No H-bonds generated for 'chain 'C' and resid 410 through 413' Processing helix chain 'C' and resid 417 through 428 Processing helix chain 'C' and resid 434 through 444 Processing helix chain 'C' and resid 448 through 456 Processing helix chain 'C' and resid 504 through 506 No H-bonds generated for 'chain 'C' and resid 504 through 506' Processing helix chain 'C' and resid 508 through 517 Processing helix chain 'C' and resid 583 through 588 Processing helix chain 'C' and resid 612 through 628 Proline residue: C 616 - end of helix Processing helix chain 'C' and resid 649 through 661 Processing helix chain 'C' and resid 717 through 724 Processing helix chain 'C' and resid 745 through 756 Processing helix chain 'C' and resid 760 through 765 Processing helix chain 'C' and resid 793 through 804 Processing helix chain 'C' and resid 831 through 852 removed outlier: 3.636A pdb=" N LYS C 835 " --> pdb=" O ILE C 831 " (cutoff:3.500A) Proline residue: C 840 - end of helix removed outlier: 3.759A pdb=" N LYS C 843 " --> pdb=" O ILE C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 882 removed outlier: 3.656A pdb=" N LEU C 873 " --> pdb=" O ALA C 870 " (cutoff:3.500A) Proline residue: C 874 - end of helix Processing helix chain 'C' and resid 915 through 921 Processing helix chain 'C' and resid 962 through 974 Processing helix chain 'C' and resid 989 through 997 removed outlier: 3.689A pdb=" N ILE C 993 " --> pdb=" O LEU C 989 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 8 No H-bonds generated for 'chain 'G' and resid 5 through 8' Processing helix chain 'G' and resid 11 through 22 Processing helix chain 'G' and resid 44 through 65 Processing helix chain 'G' and resid 73 through 92 removed outlier: 3.554A pdb=" N ASP G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 31 Proline residue: H 27 - end of helix Processing helix chain 'H' and resid 37 through 46 Processing helix chain 'H' and resid 53 through 65 Processing helix chain 'H' and resid 73 through 86 Processing helix chain 'H' and resid 88 through 108 Processing helix chain 'H' and resid 111 through 126 Processing helix chain 'H' and resid 132 through 144 Processing helix chain 'H' and resid 148 through 157 removed outlier: 4.333A pdb=" N ALA H 153 " --> pdb=" O ARG H 149 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL H 154 " --> pdb=" O LEU H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 165 Processing helix chain 'H' and resid 167 through 182 Processing helix chain 'H' and resid 188 through 203 Processing helix chain 'H' and resid 248 through 261 Processing helix chain 'H' and resid 290 through 300 Processing helix chain 'H' and resid 305 through 315 Processing helix chain 'H' and resid 322 through 335 Processing helix chain 'H' and resid 341 through 353 Processing helix chain 'H' and resid 355 through 371 Processing helix chain 'H' and resid 378 through 394 removed outlier: 3.956A pdb=" N TYR H 394 " --> pdb=" O HIS H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 415 through 431 Processing helix chain 'H' and resid 433 through 442 Processing helix chain 'H' and resid 458 through 467 Processing helix chain 'H' and resid 473 through 480 Processing helix chain 'J' and resid 112 through 120 removed outlier: 3.844A pdb=" N LYS J 117 " --> pdb=" O ASN J 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 37 Processing helix chain 'K' and resid 40 through 42 No H-bonds generated for 'chain 'K' and resid 40 through 42' Processing helix chain 'K' and resid 60 through 84 Processing helix chain 'K' and resid 160 through 163 No H-bonds generated for 'chain 'K' and resid 160 through 163' Processing helix chain 'K' and resid 199 through 224 removed outlier: 4.127A pdb=" N SER K 205 " --> pdb=" O PHE K 201 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 33 removed outlier: 4.393A pdb=" N GLU L 17 " --> pdb=" O ASP L 14 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS L 20 " --> pdb=" O GLU L 17 " (cutoff:3.500A) Proline residue: L 21 - end of helix removed outlier: 3.785A pdb=" N THR L 24 " --> pdb=" O PRO L 21 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE L 26 " --> pdb=" O LEU L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 67 Processing helix chain 'L' and resid 75 through 83 Processing helix chain 'L' and resid 89 through 96 Processing helix chain 'L' and resid 106 through 108 No H-bonds generated for 'chain 'L' and resid 106 through 108' Processing helix chain 'L' and resid 121 through 123 No H-bonds generated for 'chain 'L' and resid 121 through 123' Processing helix chain 'L' and resid 126 through 136 Processing helix chain 'M' and resid 4 through 7 No H-bonds generated for 'chain 'M' and resid 4 through 7' Processing helix chain 'M' and resid 55 through 58 No H-bonds generated for 'chain 'M' and resid 55 through 58' Processing helix chain 'M' and resid 63 through 67 Processing helix chain 'M' and resid 74 through 78 Processing helix chain 'M' and resid 84 through 86 No H-bonds generated for 'chain 'M' and resid 84 through 86' Processing helix chain 'M' and resid 96 through 101 Processing helix chain 'M' and resid 105 through 107 No H-bonds generated for 'chain 'M' and resid 105 through 107' Processing helix chain 'M' and resid 142 through 145 No H-bonds generated for 'chain 'M' and resid 142 through 145' Processing helix chain 'M' and resid 153 through 167 removed outlier: 3.731A pdb=" N ARG M 166 " --> pdb=" O PHE M 162 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU M 167 " --> pdb=" O VAL M 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 199 Processing helix chain 'M' and resid 232 through 253 Processing helix chain 'N' and resid 14 through 17 No H-bonds generated for 'chain 'N' and resid 14 through 17' Processing helix chain 'N' and resid 62 through 68 Processing helix chain 'N' and resid 84 through 93 Processing helix chain 'N' and resid 109 through 116 Processing helix chain 'N' and resid 123 through 127 Processing helix chain 'N' and resid 129 through 143 Processing helix chain 'N' and resid 216 through 226 Processing helix chain 'N' and resid 256 through 265 removed outlier: 3.721A pdb=" N SER N 264 " --> pdb=" O GLU N 260 " (cutoff:3.500A) Processing helix chain 'N' and resid 307 through 323 Processing helix chain 'O' and resid 15 through 27 Processing helix chain 'O' and resid 35 through 39 Processing helix chain 'O' and resid 45 through 54 Processing helix chain 'O' and resid 67 through 79 Processing helix chain 'O' and resid 84 through 91 Processing helix chain 'O' and resid 95 through 104 Processing helix chain 'O' and resid 145 through 160 Processing helix chain 'O' and resid 166 through 190 removed outlier: 3.556A pdb=" N ILE O 171 " --> pdb=" O ALA O 167 " (cutoff:3.500A) Processing helix chain 'O' and resid 229 through 246 removed outlier: 3.563A pdb=" N PHE O 241 " --> pdb=" O ILE O 237 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 33 Proline residue: R 32 - end of helix Processing helix chain 'R' and resid 37 through 46 Processing helix chain 'R' and resid 65 through 86 Processing helix chain 'R' and resid 92 through 109 Processing helix chain 'S' and resid 40 through 60 removed outlier: 3.587A pdb=" N ARG S 60 " --> pdb=" O GLY S 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 66 through 78 Processing helix chain 'S' and resid 81 through 94 Processing helix chain 'S' and resid 99 through 111 Processing helix chain 'S' and resid 115 through 128 Processing helix chain 'S' and resid 134 through 146 Processing helix chain 'S' and resid 149 through 162 removed outlier: 3.668A pdb=" N LEU S 162 " --> pdb=" O LYS S 158 " (cutoff:3.500A) Processing helix chain 'S' and resid 166 through 178 Processing helix chain 'S' and resid 185 through 195 Processing helix chain 'S' and resid 199 through 211 Processing helix chain 'S' and resid 215 through 231 Processing helix chain 'S' and resid 240 through 256 Processing helix chain 'S' and resid 261 through 272 Processing helix chain 'S' and resid 278 through 290 Processing helix chain 'S' and resid 296 through 314 Processing helix chain 'S' and resid 321 through 331 Processing helix chain 'S' and resid 335 through 348 Processing helix chain 'S' and resid 357 through 376 Processing helix chain 'S' and resid 382 through 394 Processing helix chain 'S' and resid 404 through 415 Processing helix chain 'S' and resid 420 through 431 Processing helix chain 'S' and resid 440 through 449 Processing helix chain 'S' and resid 453 through 466 Processing helix chain 'S' and resid 471 through 482 Processing helix chain 'S' and resid 486 through 499 Processing helix chain 'S' and resid 508 through 520 Processing helix chain 'S' and resid 531 through 540 Processing helix chain 'S' and resid 546 through 555 Processing helix chain 'T' and resid 22 through 32 Processing helix chain 'T' and resid 38 through 47 removed outlier: 3.935A pdb=" N TYR T 46 " --> pdb=" O ARG T 42 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TRP T 47 " --> pdb=" O TYR T 43 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 67 Processing helix chain 'T' and resid 72 through 82 Processing helix chain 'T' and resid 90 through 101 Processing helix chain 'T' and resid 108 through 120 removed outlier: 3.577A pdb=" N SER T 114 " --> pdb=" O ARG T 110 " (cutoff:3.500A) Processing helix chain 'T' and resid 128 through 138 Processing helix chain 'T' and resid 146 through 158 Proline residue: T 150 - end of helix removed outlier: 3.609A pdb=" N VAL T 155 " --> pdb=" O VAL T 151 " (cutoff:3.500A) Processing helix chain 'T' and resid 175 through 190 Processing helix chain 'T' and resid 210 through 217 Processing helix chain 'T' and resid 225 through 237 Processing helix chain 'T' and resid 241 through 250 Processing helix chain 'T' and resid 271 through 281 Processing helix chain 'T' and resid 285 through 295 Processing helix chain 'T' and resid 300 through 313 Processing helix chain 'T' and resid 318 through 331 Processing helix chain 'T' and resid 340 through 364 Processing helix chain 'T' and resid 374 through 404 removed outlier: 3.774A pdb=" N TYR T 392 " --> pdb=" O LEU T 388 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASP T 393 " --> pdb=" O ILE T 389 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ILE T 394 " --> pdb=" O ASN T 390 " (cutoff:3.500A) Processing helix chain 'T' and resid 408 through 418 Processing helix chain 'T' and resid 424 through 432 Processing helix chain 'T' and resid 436 through 439 No H-bonds generated for 'chain 'T' and resid 436 through 439' Processing helix chain 'T' and resid 449 through 460 removed outlier: 3.508A pdb=" N LEU T 456 " --> pdb=" O SER T 452 " (cutoff:3.500A) Processing helix chain 'T' and resid 463 through 475 Processing helix chain 'T' and resid 484 through 496 Processing helix chain 'T' and resid 514 through 521 Proline residue: T 518 - end of helix Processing helix chain 'T' and resid 542 through 554 Processing helix chain 'T' and resid 567 through 580 Processing helix chain 'T' and resid 586 through 597 removed outlier: 3.571A pdb=" N ASN T 597 " --> pdb=" O LEU T 593 " (cutoff:3.500A) Processing helix chain 'T' and resid 601 through 614 Proline residue: T 613 - end of helix Processing helix chain 'T' and resid 617 through 633 Processing helix chain 'T' and resid 642 through 654 Processing helix chain 'T' and resid 662 through 674 Processing helix chain 'T' and resid 682 through 692 Processing helix chain 'T' and resid 703 through 717 Processing helix chain 'T' and resid 725 through 735 Processing helix chain 'T' and resid 744 through 752 Processing helix chain 'T' and resid 761 through 770 Processing helix chain 'T' and resid 778 through 789 Processing helix chain 'b' and resid 13 through 15 No H-bonds generated for 'chain 'b' and resid 13 through 15' Processing helix chain 'd' and resid 6 through 14 Processing helix chain 'd' and resid 76 through 79 Processing helix chain 'e' and resid 13 through 23 Processing helix chain 'e' and resid 84 through 86 No H-bonds generated for 'chain 'e' and resid 84 through 86' Processing helix chain 'f' and resid 15 through 21 Processing helix chain 'h' and resid 3 through 9 Processing helix chain 'h' and resid 103 through 107 Processing helix chain 'j' and resid 16 through 28 Processing helix chain 'j' and resid 32 through 40 Processing helix chain 'W' and resid 5 through 10 Processing helix chain 'W' and resid 43 through 45 No H-bonds generated for 'chain 'W' and resid 43 through 45' Processing helix chain 'W' and resid 112 through 115 Processing helix chain 'W' and resid 140 through 147 Processing helix chain 'W' and resid 161 through 166 Processing helix chain 'Y' and resid 41 through 52 Processing helix chain 'Y' and resid 79 through 88 Processing helix chain 'l' and resid 4 through 9 Processing helix chain 'm' and resid 16 through 28 removed outlier: 3.828A pdb=" N GLU m 22 " --> pdb=" O LEU m 18 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU m 23 " --> pdb=" O GLU m 19 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE m 24 " --> pdb=" O GLU m 20 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU m 25 " --> pdb=" O LEU m 21 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE m 26 " --> pdb=" O GLU m 22 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS m 27 " --> pdb=" O GLU m 23 " (cutoff:3.500A) Processing helix chain 'm' and resid 30 through 39 removed outlier: 4.161A pdb=" N LEU m 33 " --> pdb=" O PRO m 30 " (cutoff:3.500A) Processing helix chain 'n' and resid 6 through 13 Processing helix chain 'p' and resid 13 through 23 removed outlier: 3.531A pdb=" N ILE p 17 " --> pdb=" O PRO p 13 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE p 18 " --> pdb=" O ILE p 14 " (cutoff:3.500A) Processing helix chain 'q' and resid 15 through 22 Processing helix chain 'q' and resid 60 through 62 No H-bonds generated for 'chain 'q' and resid 60 through 62' Processing helix chain 'x' and resid 2 through 35 Processing helix chain 'x' and resid 38 through 53 Processing helix chain 'x' and resid 56 through 86 Processing helix chain 'x' and resid 89 through 109 Processing helix chain 'x' and resid 112 through 131 Processing sheet with id= A, first strand: chain 'A' and resid 557 through 563 Processing sheet with id= B, first strand: chain 'A' and resid 300 through 302 Processing sheet with id= C, first strand: chain 'A' and resid 591 through 593 Processing sheet with id= D, first strand: chain 'A' and resid 968 through 972 removed outlier: 3.758A pdb=" N ASP A 968 " --> pdb=" O SER A 983 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1247 through 1251 removed outlier: 3.504A pdb=" N LEU A1160 " --> pdb=" O LEU A1171 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N HIS A1173 " --> pdb=" O ILE A1158 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ILE A1158 " --> pdb=" O HIS A1173 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1089 through 1092 Processing sheet with id= G, first strand: chain 'A' and resid 1257 through 1262 Processing sheet with id= H, first strand: chain 'A' and resid 1624 through 1626 Processing sheet with id= I, first strand: chain 'A' and resid 1783 through 1788 Processing sheet with id= J, first strand: chain 'A' and resid 1709 through 1711 Processing sheet with id= K, first strand: chain 'A' and resid 1880 through 1882 removed outlier: 3.546A pdb=" N PHE A1880 " --> pdb=" O ASP A1853 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLN A1932 " --> pdb=" O LEU A1850 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL A1852 " --> pdb=" O GLN A1932 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE A1934 " --> pdb=" O VAL A1852 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA A1955 " --> pdb=" O ILE A1933 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL A1935 " --> pdb=" O ALA A1955 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG A1957 " --> pdb=" O VAL A1935 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1859 through 1861 removed outlier: 4.553A pdb=" N ARG A1859 " --> pdb=" O ILE A1875 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 1877 through 1879 removed outlier: 3.537A pdb=" N LYS A1892 " --> pdb=" O ILE A1879 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 39 through 44 removed outlier: 7.433A pdb=" N ASN D 65 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N SER D 87 " --> pdb=" O ASN D 65 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 49 through 51 Processing sheet with id= P, first strand: chain 'C' and resid 133 through 135 removed outlier: 9.107A pdb=" N ILE C 134 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N MET C 209 " --> pdb=" O ILE C 134 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 238 through 240 removed outlier: 6.640A pdb=" N VAL C 266 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE C 312 " --> pdb=" O ILE C 267 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 536 through 538 removed outlier: 3.528A pdb=" N LEU C 468 " --> pdb=" O SER C 579 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N HIS C 471 " --> pdb=" O ILE C 488 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ILE C 488 " --> pdb=" O HIS C 471 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN C 560 " --> pdb=" O ILE C 488 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 474 through 476 Processing sheet with id= T, first strand: chain 'C' and resid 542 through 546 removed outlier: 3.791A pdb=" N ILE C 542 " --> pdb=" O VAL C 553 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 668 through 670 Processing sheet with id= V, first strand: chain 'C' and resid 678 through 681 Processing sheet with id= W, first strand: chain 'C' and resid 775 through 777 Processing sheet with id= X, first strand: chain 'C' and resid 929 through 931 removed outlier: 3.797A pdb=" N LYS C 890 " --> pdb=" O ARG C 903 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLN C 905 " --> pdb=" O ILE C 888 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ILE C 888 " --> pdb=" O GLN C 905 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'J' and resid 154 through 158 removed outlier: 3.523A pdb=" N LYS J 165 " --> pdb=" O THR J 157 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR J 176 " --> pdb=" O VAL J 166 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ASP J 168 " --> pdb=" O LEU J 174 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU J 174 " --> pdb=" O ASP J 168 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'J' and resid 206 through 210 Processing sheet with id= AA, first strand: chain 'J' and resid 227 through 232 removed outlier: 6.849A pdb=" N ALA J 242 " --> pdb=" O ARG J 228 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL J 230 " --> pdb=" O ALA J 240 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA J 240 " --> pdb=" O VAL J 230 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ILE J 232 " --> pdb=" O LEU J 238 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU J 238 " --> pdb=" O ILE J 232 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE J 248 " --> pdb=" O LEU J 262 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE J 260 " --> pdb=" O LEU J 250 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASP J 252 " --> pdb=" O PRO J 258 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 314 through 316 Processing sheet with id= AC, first strand: chain 'J' and resid 363 through 366 removed outlier: 6.221A pdb=" N ASP J 377 " --> pdb=" O LYS J 383 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LYS J 383 " --> pdb=" O ASP J 377 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 130 through 134 removed outlier: 6.505A pdb=" N ILE J 425 " --> pdb=" O SER J 132 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL J 134 " --> pdb=" O ILE J 423 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE J 423 " --> pdb=" O VAL J 134 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER J 422 " --> pdb=" O GLU J 418 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'J' and resid 290 through 294 removed outlier: 4.943A pdb=" N ASP J 294 " --> pdb=" O THR J 300 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N THR J 300 " --> pdb=" O ASP J 294 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'J' and resid 332 through 335 removed outlier: 5.409A pdb=" N GLY J 335 " --> pdb=" O LEU J 341 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU J 341 " --> pdb=" O GLY J 335 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'K' and resid 105 through 107 Processing sheet with id= AH, first strand: chain 'M' and resid 29 through 31 removed outlier: 3.741A pdb=" N LYS M 36 " --> pdb=" O ASN M 31 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'M' and resid 222 through 225 Processing sheet with id= AJ, first strand: chain 'N' and resid 25 through 28 Processing sheet with id= AK, first strand: chain 'b' and resid 77 through 83 removed outlier: 6.075A pdb=" N CYS b 48 " --> pdb=" O LEU b 82 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ARG b 21 " --> pdb=" O VAL b 97 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N VAL b 97 " --> pdb=" O ARG b 21 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU b 23 " --> pdb=" O THR b 95 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N THR b 95 " --> pdb=" O LEU b 23 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'b' and resid 43 through 45 Processing sheet with id= AM, first strand: chain 'd' and resid 56 through 59 removed outlier: 3.603A pdb=" N ARG d 30 " --> pdb=" O ILE d 48 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'd' and resid 61 through 64 removed outlier: 3.708A pdb=" N GLU d 35 " --> pdb=" O GLN d 43 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ARG d 45 " --> pdb=" O LEU d 33 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU d 33 " --> pdb=" O ARG d 45 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'e' and resid 26 through 30 Processing sheet with id= AP, first strand: chain 'e' and resid 52 through 54 removed outlier: 3.628A pdb=" N VAL e 52 " --> pdb=" O LEU e 82 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'f' and resid 66 through 69 removed outlier: 3.954A pdb=" N GLY f 66 " --> pdb=" O GLU f 58 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ALA f 56 " --> pdb=" O LEU f 68 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS f 30 " --> pdb=" O TYR f 80 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR f 80 " --> pdb=" O LYS f 30 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'f' and resid 71 through 73 removed outlier: 3.594A pdb=" N GLN f 52 " --> pdb=" O SER f 44 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER f 44 " --> pdb=" O GLN f 52 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ASN f 54 " --> pdb=" O LEU f 42 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LEU f 42 " --> pdb=" O ASN f 54 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'g' and resid 23 through 25 Processing sheet with id= AT, first strand: chain 'g' and resid 60 through 63 removed outlier: 6.255A pdb=" N ASP g 41 " --> pdb=" O LEU g 29 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU g 29 " --> pdb=" O ASP g 41 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'h' and resid 79 through 82 removed outlier: 3.735A pdb=" N GLU h 13 " --> pdb=" O LEU h 29 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR h 16 " --> pdb=" O ILE h 96 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'h' and resid 84 through 87 removed outlier: 3.500A pdb=" N ILE h 85 " --> pdb=" O LEU h 40 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR h 41 " --> pdb=" O LEU h 29 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LEU h 29 " --> pdb=" O THR h 41 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'j' and resid 43 through 46 removed outlier: 3.577A pdb=" N ARG j 89 " --> pdb=" O GLU j 74 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'j' and resid 67 through 70 Processing sheet with id= AY, first strand: chain 'Y' and resid 30 through 32 removed outlier: 3.846A pdb=" N ALA Y 72 " --> pdb=" O VAL Y 32 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'Y' and resid 92 through 94 removed outlier: 3.921A pdb=" N GLU Y 92 " --> pdb=" O LEU Y 99 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS Y 97 " --> pdb=" O PHE Y 94 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'k' and resid 32 through 34 removed outlier: 3.852A pdb=" N TYR k 18 " --> pdb=" O LEU k 34 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS k 19 " --> pdb=" O ASP k 99 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP k 99 " --> pdb=" O LYS k 19 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ARG k 21 " --> pdb=" O VAL k 97 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N VAL k 97 " --> pdb=" O ARG k 21 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU k 23 " --> pdb=" O THR k 95 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR k 95 " --> pdb=" O LEU k 23 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'm' and resid 43 through 47 removed outlier: 3.974A pdb=" N ARG m 89 " --> pdb=" O GLU m 74 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TRP m 76 " --> pdb=" O ARG m 87 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG m 87 " --> pdb=" O TRP m 76 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'm' and resid 57 through 60 removed outlier: 7.054A pdb=" N VAL m 68 " --> pdb=" O LYS m 59 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'n' and resid 19 through 21 removed outlier: 3.660A pdb=" N GLY n 31 " --> pdb=" O VAL n 19 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR n 28 " --> pdb=" O THR n 50 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG n 30 " --> pdb=" O ILE n 48 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'n' and resid 43 through 45 removed outlier: 3.829A pdb=" N ILE n 62 " --> pdb=" O LEU n 44 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'p' and resid 37 through 40 Processing sheet with id= BG, first strand: chain 'p' and resid 52 through 54 removed outlier: 3.905A pdb=" N VAL p 52 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU p 82 " --> pdb=" O VAL p 52 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'q' and resid 57 through 59 removed outlier: 3.906A pdb=" N HIS q 25 " --> pdb=" O LEU q 42 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS q 30 " --> pdb=" O TYR q 80 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR q 80 " --> pdb=" O LYS q 30 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'q' and resid 71 through 73 removed outlier: 3.785A pdb=" N GLN q 52 " --> pdb=" O SER q 44 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER q 44 " --> pdb=" O GLN q 52 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASN q 54 " --> pdb=" O LEU q 42 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU q 42 " --> pdb=" O ASN q 54 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'r' and resid 26 through 28 removed outlier: 3.539A pdb=" N ILE r 15 " --> pdb=" O GLY r 27 " (cutoff:3.500A) 2512 hydrogen bonds defined for protein. 7116 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 337 hydrogen bonds 606 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 216 stacking parallelities Total time for adding SS restraints: 40.64 Time building geometry restraints manager: 25.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 10248 1.32 - 1.45: 19306 1.45 - 1.58: 34379 1.58 - 1.71: 895 1.71 - 1.84: 304 Bond restraints: 65132 Sorted by residual: bond pdb=" N ILE A 632 " pdb=" CA ILE A 632 " ideal model delta sigma weight residual 1.460 1.521 -0.062 1.21e-02 6.83e+03 2.60e+01 bond pdb=" C5 GTP C1101 " pdb=" C6 GTP C1101 " ideal model delta sigma weight residual 1.390 1.471 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" N GLY H 471 " pdb=" CA GLY H 471 " ideal model delta sigma weight residual 1.443 1.476 -0.033 8.60e-03 1.35e+04 1.43e+01 bond pdb=" CA ILE N 91 " pdb=" CB ILE N 91 " ideal model delta sigma weight residual 1.540 1.582 -0.042 1.17e-02 7.31e+03 1.31e+01 bond pdb=" CA ASN A1369 " pdb=" C ASN A1369 " ideal model delta sigma weight residual 1.522 1.474 0.049 1.36e-02 5.41e+03 1.27e+01 ... (remaining 65127 not shown) Histogram of bond angle deviations from ideal: 98.94 - 106.37: 3913 106.37 - 113.80: 36088 113.80 - 121.22: 29945 121.22 - 128.65: 19846 128.65 - 136.08: 818 Bond angle restraints: 90610 Sorted by residual: angle pdb=" C ILE H 87 " pdb=" N PRO H 88 " pdb=" CA PRO H 88 " ideal model delta sigma weight residual 118.85 134.45 -15.60 1.09e+00 8.42e-01 2.05e+02 angle pdb=" CA ILE T 612 " pdb=" C ILE T 612 " pdb=" N PRO T 613 " ideal model delta sigma weight residual 120.83 114.28 6.55 6.10e-01 2.69e+00 1.15e+02 angle pdb=" C PHE T 615 " pdb=" N PRO T 616 " pdb=" CA PRO T 616 " ideal model delta sigma weight residual 120.38 131.39 -11.01 1.03e+00 9.43e-01 1.14e+02 angle pdb=" C SER l 33 " pdb=" N PRO l 34 " pdb=" CA PRO l 34 " ideal model delta sigma weight residual 119.05 130.02 -10.97 1.11e+00 8.12e-01 9.76e+01 angle pdb=" N PHE C 106 " pdb=" CA PHE C 106 " pdb=" C PHE C 106 " ideal model delta sigma weight residual 109.24 124.05 -14.81 1.51e+00 4.39e-01 9.62e+01 ... (remaining 90605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.22: 37335 34.22 - 68.44: 2212 68.44 - 102.66: 192 102.66 - 136.88: 11 136.88 - 171.10: 5 Dihedral angle restraints: 39755 sinusoidal: 17990 harmonic: 21765 Sorted by residual: dihedral pdb=" CA SER A1325 " pdb=" C SER A1325 " pdb=" N THR A1326 " pdb=" CA THR A1326 " ideal model delta harmonic sigma weight residual -180.00 -134.19 -45.81 0 5.00e+00 4.00e-02 8.39e+01 dihedral pdb=" O4' C U 79 " pdb=" C1' C U 79 " pdb=" N1 C U 79 " pdb=" C2 C U 79 " ideal model delta sinusoidal sigma weight residual 200.00 73.47 126.53 1 1.50e+01 4.44e-03 6.81e+01 dihedral pdb=" C5' A U 45 " pdb=" C4' A U 45 " pdb=" C3' A U 45 " pdb=" O3' A U 45 " ideal model delta sinusoidal sigma weight residual 147.00 90.43 56.57 1 8.00e+00 1.56e-02 6.74e+01 ... (remaining 39752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.220: 10711 0.220 - 0.439: 257 0.439 - 0.659: 8 0.659 - 0.879: 0 0.879 - 1.098: 1 Chirality restraints: 10977 Sorted by residual: chirality pdb=" C4' A V 35 " pdb=" C5' A V 35 " pdb=" O4' A V 35 " pdb=" C3' A V 35 " both_signs ideal model delta sigma weight residual False -2.50 -1.40 -1.10 2.00e-01 2.50e+01 3.02e+01 chirality pdb=" CA PHE A 506 " pdb=" N PHE A 506 " pdb=" C PHE A 506 " pdb=" CB PHE A 506 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.48e+00 chirality pdb=" C3' U Z 118 " pdb=" C4' U Z 118 " pdb=" O3' U Z 118 " pdb=" C2' U Z 118 " both_signs ideal model delta sigma weight residual False -2.74 -2.24 -0.50 2.00e-01 2.50e+01 6.37e+00 ... (remaining 10974 not shown) Planarity restraints: 9985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA d 81 " -0.094 5.00e-02 4.00e+02 1.44e-01 3.34e+01 pdb=" N PRO d 82 " 0.250 5.00e-02 4.00e+02 pdb=" CA PRO d 82 " -0.088 5.00e-02 4.00e+02 pdb=" CD PRO d 82 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS H 413 " -0.077 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO H 414 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO H 414 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO H 414 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 379 " -0.064 5.00e-02 4.00e+02 9.64e-02 1.49e+01 pdb=" N PRO C 380 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO C 380 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 380 " -0.052 5.00e-02 4.00e+02 ... (remaining 9982 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 13 2.28 - 2.94: 25281 2.94 - 3.59: 101592 3.59 - 4.25: 145187 4.25 - 4.90: 238788 Nonbonded interactions: 510861 Sorted by model distance: nonbonded pdb=" P G I 1 " pdb=" O2' A I 70 " model vdw 1.631 3.400 nonbonded pdb=" N1 A U 45 " pdb=" O4 U U 74 " model vdw 1.649 2.496 nonbonded pdb=" SG CYS D 88 " pdb=" O CYS D 91 " model vdw 1.731 3.400 nonbonded pdb=" SG CYS L 120 " pdb="ZN ZN L1002 " model vdw 2.111 2.590 nonbonded pdb=" OP2 A V 76 " pdb=" NH2 ARG A 749 " model vdw 2.210 2.520 ... (remaining 510856 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'b' and ((resid 4 through 26 and (name N or name CA or name C or name O o \ r name CB )) or resid 27 or (resid 28 through 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 or (resid 33 through 82 and (name N or nam \ e CA or name C or name O or name CB )) or resid 83 or (resid 84 through 88 and ( \ name N or name CA or name C or name O or name CB )) or resid 89 or (resid 90 thr \ ough 102 and (name N or name CA or name C or name O or name CB )))) selection = chain 'k' } ncs_group { reference = (chain 'd' and ((resid 4 and (name N or name CA or name C or name O or name CB ) \ ) or resid 5 or (resid 6 through 15 and (name N or name CA or name C or name O o \ r name CB )) or resid 16 or (resid 17 through 25 and (name N or name CA or name \ C or name O or name CB )) or (resid 26 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 31 or (resid 32 through 53 and (name N or na \ me CA or name C or name O or name CB )) or (resid 54 through 65 and (name N or n \ ame CA or name C or name O or name CB )) or resid 66 or (resid 67 through 85 and \ (name N or name CA or name C or name O or name CB )))) selection = chain 'n' } ncs_group { reference = (chain 'e' and ((resid 10 through 35 and (name N or name CA or name C or name O \ or name CB )) or resid 36 or (resid 37 through 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 or (resid 42 through 44 and (name N or na \ me CA or name C or name O or name CB )) or resid 45 or (resid 46 through 73 and \ (name N or name CA or name C or name O or name CB )) or resid 74 or (resid 75 th \ rough 77 and (name N or name CA or name C or name O or name CB )) or resid 78 or \ (resid 79 through 83 and (name N or name CA or name C or name O or name CB )) o \ r resid 84 or (resid 85 through 92 and (name N or name CA or name C or name O or \ name CB )))) selection = chain 'p' } ncs_group { reference = (chain 'f' and ((resid 12 through 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 or (resid 22 through 27 and (name N or name CA or name \ C or name O or name CB )) or resid 28 or (resid 29 through 39 and (name N or na \ me CA or name C or name O or name CB )) or resid 40 or (resid 41 through 61 and \ (name N or name CA or name C or name O or name CB )) or resid 62 or (resid 63 th \ rough 65 and (name N or name CA or name C or name O or name CB )) or resid 66 or \ (resid 67 through 68 and (name N or name CA or name C or name O or name CB )) o \ r resid 69 or (resid 70 through 83 and (name N or name CA or name C or name O or \ name CB )))) selection = chain 'q' } ncs_group { reference = (chain 'g' and ((resid 2 through 20 and (name N or name CA or name C or name O o \ r name CB )) or resid 21 or (resid 22 through 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 or (resid 28 through 30 and (name N or nam \ e CA or name C or name O or name CB )) or resid 31 or (resid 32 through 57 and ( \ name N or name CA or name C or name O or name CB )) or resid 58 or (resid 59 thr \ ough 64 and (name N or name CA or name C or name O or name CB )) or resid 65 or \ (resid 66 through 76 and (name N or name CA or name C or name O or name CB )))) selection = chain 'r' } ncs_group { reference = (chain 'h' and ((resid 1 through 21 and (name N or name CA or name C or name O o \ r name CB )) or resid 22 or (resid 23 through 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 or (resid 28 through 88 and (name N or nam \ e CA or name C or name O or name CB )) or resid 89 or (resid 90 through 106 and \ (name N or name CA or name C or name O or name CB )))) selection = chain 'l' } ncs_group { reference = (chain 'j' and ((resid 15 through 28 and (name N or name CA or name C or name O \ or name CB )) or resid 29 or (resid 30 through 80 and (name N or name CA or name \ C or name O or name CB )) or resid 81 or (resid 82 through 97 and (name N or na \ me CA or name C or name O or name CB )) or resid 98 or (resid 99 through 108 and \ (name N or name CA or name C or name O or name CB )))) selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 16.380 Check model and map are aligned: 0.690 Set scattering table: 0.430 Process input model: 169.440 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 195.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 65132 Z= 0.490 Angle : 1.455 15.596 90610 Z= 1.057 Chirality : 0.089 1.098 10977 Planarity : 0.006 0.144 9985 Dihedral : 19.669 171.096 25509 Min Nonbonded Distance : 1.631 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 1.18 % Allowed : 8.14 % Favored : 90.68 % Rotamer: Outliers : 8.54 % Allowed : 11.22 % Favored : 80.24 % Cbeta Deviations : 0.56 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.36 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.09), residues: 7089 helix: 1.07 (0.07), residues: 3215 sheet: -3.08 (0.15), residues: 777 loop : -3.11 (0.09), residues: 3097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 823 HIS 0.012 0.002 HIS L 56 PHE 0.047 0.003 PHE J 198 TYR 0.022 0.003 TYR J 376 ARG 0.011 0.001 ARG H 382 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14178 Ramachandran restraints generated. 7089 Oldfield, 0 Emsley, 7089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14178 Ramachandran restraints generated. 7089 Oldfield, 0 Emsley, 7089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1761 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 402 poor density : 1359 time to evaluate : 4.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 TYR cc_start: 0.7725 (OUTLIER) cc_final: 0.6893 (t80) REVERT: A 153 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8488 (tpt) REVERT: A 155 ASN cc_start: 0.9018 (t0) cc_final: 0.8789 (t0) REVERT: A 165 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9002 (mm) REVERT: A 183 TRP cc_start: 0.8771 (p-90) cc_final: 0.8519 (p-90) REVERT: A 204 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7748 (tm-30) REVERT: A 205 THR cc_start: 0.9516 (OUTLIER) cc_final: 0.9176 (t) REVERT: A 272 ASP cc_start: 0.7264 (t0) cc_final: 0.6898 (t70) REVERT: A 281 TYR cc_start: 0.8501 (m-80) cc_final: 0.8102 (m-80) REVERT: A 325 LYS cc_start: 0.9430 (tttp) cc_final: 0.9125 (tttt) REVERT: A 392 ASN cc_start: 0.8837 (t0) cc_final: 0.8565 (t0) REVERT: A 425 ASP cc_start: 0.7364 (OUTLIER) cc_final: 0.7049 (t0) REVERT: A 479 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8901 (mt) REVERT: A 492 LYS cc_start: 0.9355 (mtpp) cc_final: 0.9083 (ptpt) REVERT: A 495 ARG cc_start: 0.8493 (mtm180) cc_final: 0.8104 (mtm110) REVERT: A 507 LEU cc_start: 0.9426 (mt) cc_final: 0.9221 (mt) REVERT: A 528 ASN cc_start: 0.8897 (m-40) cc_final: 0.8618 (t0) REVERT: A 553 ASN cc_start: 0.9084 (m-40) cc_final: 0.8871 (m-40) REVERT: A 555 LYS cc_start: 0.9499 (OUTLIER) cc_final: 0.9111 (pttt) REVERT: A 625 LEU cc_start: 0.9481 (mt) cc_final: 0.9236 (mp) REVERT: A 633 VAL cc_start: 0.9375 (t) cc_final: 0.8929 (p) REVERT: A 664 THR cc_start: 0.9323 (m) cc_final: 0.8829 (m) REVERT: A 682 ASP cc_start: 0.8322 (m-30) cc_final: 0.7763 (m-30) REVERT: A 723 GLU cc_start: 0.9033 (tt0) cc_final: 0.8792 (mt-10) REVERT: A 726 ILE cc_start: 0.9481 (OUTLIER) cc_final: 0.8984 (tt) REVERT: A 813 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8279 (tt0) REVERT: A 821 ASP cc_start: 0.8970 (OUTLIER) cc_final: 0.8597 (m-30) REVERT: A 852 LEU cc_start: 0.9620 (OUTLIER) cc_final: 0.9394 (tt) REVERT: A 873 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7643 (mt-10) REVERT: A 918 ASP cc_start: 0.9008 (m-30) cc_final: 0.8590 (m-30) REVERT: A 921 ASP cc_start: 0.8492 (t0) cc_final: 0.8175 (m-30) REVERT: A 933 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8112 (mt-10) REVERT: A 965 LYS cc_start: 0.9037 (mtmt) cc_final: 0.8326 (mttt) REVERT: A 985 ASP cc_start: 0.8823 (t70) cc_final: 0.8141 (t0) REVERT: A 988 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8306 (mp0) REVERT: A 1004 ASP cc_start: 0.9049 (OUTLIER) cc_final: 0.8690 (t0) REVERT: A 1019 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8181 (mp0) REVERT: A 1037 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8278 (pt0) REVERT: A 1057 MET cc_start: 0.8768 (tmm) cc_final: 0.8339 (tmm) REVERT: A 1099 ASN cc_start: 0.9182 (OUTLIER) cc_final: 0.8678 (t0) REVERT: A 1101 TYR cc_start: 0.9003 (t80) cc_final: 0.8591 (t80) REVERT: A 1119 LEU cc_start: 0.9456 (tp) cc_final: 0.9082 (tp) REVERT: A 1122 ASP cc_start: 0.8876 (m-30) cc_final: 0.8457 (m-30) REVERT: A 1140 ASN cc_start: 0.8755 (t0) cc_final: 0.8200 (p0) REVERT: A 1153 GLU cc_start: 0.8437 (tt0) cc_final: 0.8211 (tm-30) REVERT: A 1163 ARG cc_start: 0.8846 (ttp80) cc_final: 0.8645 (ttp80) REVERT: A 1171 LEU cc_start: 0.9527 (tp) cc_final: 0.9157 (tp) REVERT: A 1203 ASN cc_start: 0.8984 (t0) cc_final: 0.8441 (p0) REVERT: A 1212 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8533 (ptp-170) REVERT: A 1213 MET cc_start: 0.8548 (tmt) cc_final: 0.7779 (tmm) REVERT: A 1291 GLU cc_start: 0.9199 (mt-10) cc_final: 0.8968 (tp30) REVERT: A 1310 LYS cc_start: 0.9203 (mttt) cc_final: 0.8798 (mttt) REVERT: A 1314 SER cc_start: 0.9111 (m) cc_final: 0.8869 (p) REVERT: A 1315 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7591 (ttm-80) REVERT: A 1344 THR cc_start: 0.8859 (p) cc_final: 0.8521 (p) REVERT: A 1347 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.7978 (mpt-90) REVERT: A 1348 GLU cc_start: 0.8716 (tt0) cc_final: 0.8430 (tt0) REVERT: A 1379 MET cc_start: 0.9360 (OUTLIER) cc_final: 0.8875 (ttm) REVERT: A 1405 ILE cc_start: 0.9244 (mt) cc_final: 0.8854 (mt) REVERT: A 1461 TYR cc_start: 0.7895 (t80) cc_final: 0.7606 (t80) REVERT: A 1471 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8671 (tt0) REVERT: A 1472 ASN cc_start: 0.8223 (m-40) cc_final: 0.7955 (t0) REVERT: A 1485 ASP cc_start: 0.8825 (m-30) cc_final: 0.8432 (p0) REVERT: A 1520 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7168 (tm-30) REVERT: A 1523 SER cc_start: 0.8734 (t) cc_final: 0.8234 (m) REVERT: A 1558 GLU cc_start: 0.8991 (tp30) cc_final: 0.8625 (tp30) REVERT: A 1585 MET cc_start: 0.8189 (tpt) cc_final: 0.7369 (tpp) REVERT: A 1586 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.6976 (pm20) REVERT: A 1589 LYS cc_start: 0.3810 (OUTLIER) cc_final: 0.3007 (pttt) REVERT: A 1594 GLN cc_start: 0.5142 (OUTLIER) cc_final: 0.4838 (mm-40) REVERT: A 1600 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.6960 (mm110) REVERT: A 1603 ASN cc_start: 0.8980 (OUTLIER) cc_final: 0.8407 (p0) REVERT: A 1618 ASN cc_start: 0.8621 (m-40) cc_final: 0.8357 (m-40) REVERT: A 1647 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7997 (tp40) REVERT: A 1659 GLU cc_start: 0.9099 (tt0) cc_final: 0.8893 (tm-30) REVERT: A 1732 MET cc_start: 0.7847 (mmm) cc_final: 0.7600 (tpp) REVERT: A 1766 MET cc_start: 0.7691 (mmm) cc_final: 0.6944 (ptm) REVERT: A 1781 TYR cc_start: 0.9153 (m-80) cc_final: 0.8609 (m-80) REVERT: A 1803 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8600 (ttp-110) REVERT: A 1806 MET cc_start: 0.9256 (mpp) cc_final: 0.8705 (mmp) REVERT: A 1880 PHE cc_start: 0.9206 (t80) cc_final: 0.8393 (t80) REVERT: A 1894 ILE cc_start: 0.8839 (mm) cc_final: 0.8392 (mp) REVERT: A 1907 GLN cc_start: 0.8980 (tt0) cc_final: 0.8609 (mm110) REVERT: A 1990 ASN cc_start: 0.8236 (m-40) cc_final: 0.7699 (t0) REVERT: A 2048 TRP cc_start: 0.6995 (OUTLIER) cc_final: 0.6435 (m100) REVERT: D 2 SER cc_start: 0.9353 (p) cc_final: 0.9137 (p) REVERT: D 5 LYS cc_start: 0.9399 (mttt) cc_final: 0.9168 (mtmm) REVERT: D 16 ASN cc_start: 0.8876 (m-40) cc_final: 0.8061 (t0) REVERT: D 19 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8322 (mm-30) REVERT: D 49 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7507 (pmm) REVERT: D 61 SER cc_start: 0.9044 (m) cc_final: 0.8322 (p) REVERT: D 73 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8394 (mp0) REVERT: D 83 ARG cc_start: 0.7955 (mtp180) cc_final: 0.7742 (ttm110) REVERT: D 85 THR cc_start: 0.8835 (m) cc_final: 0.8202 (p) REVERT: D 90 ARG cc_start: 0.8978 (ttm-80) cc_final: 0.8007 (ttt180) REVERT: D 93 ASN cc_start: 0.8915 (t0) cc_final: 0.8694 (t0) REVERT: D 114 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8055 (tmm160) REVERT: F 8 LEU cc_start: 0.9168 (tp) cc_final: 0.8471 (tp) REVERT: C 132 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7888 (mtp85) REVERT: C 176 ARG cc_start: 0.8992 (mtm-85) cc_final: 0.8518 (ptp-110) REVERT: C 183 GLN cc_start: 0.8046 (tt0) cc_final: 0.7735 (tt0) REVERT: C 222 MET cc_start: 0.8859 (mmm) cc_final: 0.8272 (mmm) REVERT: C 238 VAL cc_start: 0.9643 (t) cc_final: 0.9397 (m) REVERT: C 261 VAL cc_start: 0.9516 (OUTLIER) cc_final: 0.8818 (m) REVERT: C 291 ILE cc_start: 0.9427 (mt) cc_final: 0.9224 (mm) REVERT: C 312 ILE cc_start: 0.9527 (mt) cc_final: 0.9294 (mp) REVERT: C 334 HIS cc_start: 0.8423 (m-70) cc_final: 0.7965 (t-90) REVERT: C 488 ILE cc_start: 0.9576 (mp) cc_final: 0.9339 (mt) REVERT: C 493 LEU cc_start: 0.9236 (tt) cc_final: 0.8993 (mt) REVERT: C 537 CYS cc_start: 0.8616 (m) cc_final: 0.8362 (m) REVERT: C 586 MET cc_start: 0.8395 (tmt) cc_final: 0.7988 (tmm) REVERT: C 611 LEU cc_start: 0.9330 (mt) cc_final: 0.8687 (mm) REVERT: C 654 CYS cc_start: 0.8700 (m) cc_final: 0.8180 (m) REVERT: C 774 LEU cc_start: 0.6406 (OUTLIER) cc_final: 0.6110 (mt) REVERT: C 837 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.6954 (pp30) REVERT: C 861 ILE cc_start: 0.9373 (OUTLIER) cc_final: 0.8911 (mt) REVERT: C 880 MET cc_start: 0.9261 (mmm) cc_final: 0.8404 (mmm) REVERT: C 889 TYR cc_start: 0.8640 (m-80) cc_final: 0.8333 (m-10) REVERT: C 927 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8632 (tpp) REVERT: C 965 ASP cc_start: 0.9139 (OUTLIER) cc_final: 0.8920 (p0) REVERT: C 968 MET cc_start: 0.8933 (mmm) cc_final: 0.8712 (mmp) REVERT: G 13 VAL cc_start: 0.9256 (t) cc_final: 0.9022 (t) REVERT: G 29 TYR cc_start: 0.8882 (m-80) cc_final: 0.8070 (m-10) REVERT: G 33 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.7766 (mt0) REVERT: G 36 ARG cc_start: 0.9104 (tpt-90) cc_final: 0.8873 (tmt170) REVERT: G 45 LYS cc_start: 0.8610 (mmtm) cc_final: 0.8232 (tttm) REVERT: G 46 GLU cc_start: 0.8890 (tt0) cc_final: 0.8075 (tp30) REVERT: G 57 GLU cc_start: 0.9428 (tp30) cc_final: 0.8917 (tp30) REVERT: G 65 ILE cc_start: 0.6028 (pp) cc_final: 0.5772 (pt) REVERT: G 68 PRO cc_start: 0.8138 (Cg_endo) cc_final: 0.7386 (Cg_exo) REVERT: G 73 MET cc_start: 0.8647 (tpt) cc_final: 0.8284 (tpp) REVERT: G 74 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.6854 (pm20) REVERT: G 77 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8556 (mt-10) REVERT: G 88 GLU cc_start: 0.8980 (tp30) cc_final: 0.8494 (tp30) REVERT: G 91 ARG cc_start: 0.8788 (mtt180) cc_final: 0.7554 (mmp-170) REVERT: H 336 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8025 (mt-10) REVERT: H 343 TYR cc_start: 0.8444 (m-80) cc_final: 0.7894 (m-80) REVERT: H 348 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8362 (tp30) REVERT: H 349 ARG cc_start: 0.9256 (mmp80) cc_final: 0.8888 (mmt-90) REVERT: H 357 TRP cc_start: 0.8986 (OUTLIER) cc_final: 0.8470 (m-90) REVERT: H 376 TYR cc_start: 0.9024 (m-80) cc_final: 0.8747 (m-80) REVERT: H 379 ASP cc_start: 0.8655 (m-30) cc_final: 0.8365 (p0) REVERT: H 391 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8786 (mt) REVERT: H 421 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8952 (pttm) REVERT: H 425 GLN cc_start: 0.9296 (tt0) cc_final: 0.9048 (tt0) REVERT: H 429 ASN cc_start: 0.9258 (m-40) cc_final: 0.8992 (m110) REVERT: H 448 MET cc_start: 0.8390 (mmm) cc_final: 0.8021 (mtp) REVERT: H 454 ASP cc_start: 0.8417 (t70) cc_final: 0.8103 (m-30) REVERT: H 477 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7701 (ptp) REVERT: J 119 LEU cc_start: 0.7963 (mt) cc_final: 0.7662 (tp) REVERT: J 164 MET cc_start: 0.8990 (ptp) cc_final: 0.8754 (ptp) REVERT: J 183 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8527 (mtm) REVERT: J 184 THR cc_start: 0.9409 (p) cc_final: 0.9121 (p) REVERT: J 212 GLU cc_start: 0.8540 (mp0) cc_final: 0.8315 (mm-30) REVERT: J 215 GLN cc_start: 0.9209 (OUTLIER) cc_final: 0.8996 (mm-40) REVERT: J 218 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7184 (mtt-85) REVERT: J 245 ASP cc_start: 0.8825 (m-30) cc_final: 0.8494 (m-30) REVERT: J 253 MET cc_start: 0.8995 (mtm) cc_final: 0.8518 (mtm) REVERT: J 346 GLU cc_start: 0.9196 (mt-10) cc_final: 0.8846 (mt-10) REVERT: J 373 LEU cc_start: 0.9578 (mp) cc_final: 0.9377 (mp) REVERT: J 404 CYS cc_start: 0.9286 (t) cc_final: 0.8868 (t) REVERT: K 33 GLN cc_start: 0.6796 (OUTLIER) cc_final: 0.6018 (mp10) REVERT: K 48 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7913 (pp30) REVERT: K 62 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8817 (tm-30) REVERT: K 73 TYR cc_start: 0.9424 (t80) cc_final: 0.9089 (t80) REVERT: K 77 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8583 (tt) REVERT: K 106 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7313 (mp) REVERT: K 116 SER cc_start: 0.9088 (t) cc_final: 0.8768 (p) REVERT: K 118 GLN cc_start: 0.8615 (mt0) cc_final: 0.8137 (pm20) REVERT: K 149 MET cc_start: 0.8600 (mmm) cc_final: 0.8399 (mmm) REVERT: K 162 GLU cc_start: 0.9345 (tt0) cc_final: 0.9137 (pt0) REVERT: K 216 ARG cc_start: 0.8474 (mmm-85) cc_final: 0.7930 (mpt180) REVERT: L 10 LYS cc_start: 0.9321 (mmtp) cc_final: 0.8884 (ptmm) REVERT: L 37 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8603 (mmtp) REVERT: L 70 ARG cc_start: 0.8948 (mtp-110) cc_final: 0.8630 (mmt-90) REVERT: L 76 ASP cc_start: 0.9289 (t70) cc_final: 0.9049 (p0) REVERT: L 79 ASP cc_start: 0.9367 (t70) cc_final: 0.9148 (m-30) REVERT: L 142 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.7738 (p90) REVERT: M 38 SER cc_start: 0.9337 (OUTLIER) cc_final: 0.9134 (m) REVERT: M 80 MET cc_start: 0.9143 (ptm) cc_final: 0.8721 (ptt) REVERT: M 95 ASP cc_start: 0.7998 (p0) cc_final: 0.7753 (p0) REVERT: M 107 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8685 (tp30) REVERT: M 116 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8945 (mtpt) REVERT: M 127 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8600 (pt) REVERT: M 132 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8320 (tptp) REVERT: M 136 THR cc_start: 0.9234 (OUTLIER) cc_final: 0.8845 (p) REVERT: M 172 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8751 (ptm160) REVERT: M 188 TYR cc_start: 0.8613 (m-80) cc_final: 0.7904 (m-10) REVERT: M 214 ASP cc_start: 0.9158 (m-30) cc_final: 0.8607 (t0) REVERT: M 227 ASN cc_start: 0.8694 (t0) cc_final: 0.8214 (p0) REVERT: M 241 GLU cc_start: 0.9294 (tm-30) cc_final: 0.8980 (mm-30) REVERT: N 20 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8330 (mp0) REVERT: N 24 ARG cc_start: 0.9041 (ttp80) cc_final: 0.8720 (ttm-80) REVERT: N 30 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8491 (mp10) REVERT: N 44 TYR cc_start: 0.9355 (m-80) cc_final: 0.8952 (m-80) REVERT: N 60 ILE cc_start: 0.9208 (pt) cc_final: 0.8930 (tp) REVERT: N 88 ASP cc_start: 0.8817 (m-30) cc_final: 0.8466 (m-30) REVERT: N 93 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8135 (tt) REVERT: N 318 LYS cc_start: 0.9027 (mttt) cc_final: 0.8809 (tmtt) REVERT: O 18 ASP cc_start: 0.8911 (t70) cc_final: 0.8685 (t0) REVERT: O 53 ASN cc_start: 0.8857 (OUTLIER) cc_final: 0.8586 (t0) REVERT: O 84 TRP cc_start: 0.9105 (m100) cc_final: 0.8719 (m100) REVERT: O 100 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8939 (mp0) REVERT: O 151 MET cc_start: 0.8479 (ptm) cc_final: 0.8156 (ptt) REVERT: O 154 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8458 (mt-10) REVERT: O 170 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7493 (tttt) REVERT: O 184 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8317 (tp30) REVERT: O 234 ASP cc_start: 0.8857 (m-30) cc_final: 0.8386 (m-30) REVERT: P 16 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7650 (ptmt) REVERT: P 29 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8748 (mmt90) REVERT: P 30 LEU cc_start: 0.9454 (tp) cc_final: 0.9238 (tp) REVERT: R 15 SER cc_start: 0.9349 (OUTLIER) cc_final: 0.8693 (m) REVERT: S 45 GLU cc_start: 0.8767 (tp30) cc_final: 0.8398 (tp30) REVERT: S 60 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8190 (mtt90) REVERT: S 73 GLN cc_start: 0.8936 (mt0) cc_final: 0.8696 (tm-30) REVERT: S 117 HIS cc_start: 0.8925 (OUTLIER) cc_final: 0.8437 (m90) REVERT: S 122 MET cc_start: 0.9301 (mtm) cc_final: 0.8801 (mtp) REVERT: S 126 ILE cc_start: 0.9338 (mm) cc_final: 0.8999 (mm) REVERT: S 156 TYR cc_start: 0.8744 (OUTLIER) cc_final: 0.7742 (t80) REVERT: S 163 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8336 (tm-30) REVERT: S 189 TYR cc_start: 0.9114 (OUTLIER) cc_final: 0.7647 (t80) REVERT: S 201 THR cc_start: 0.9263 (m) cc_final: 0.8949 (p) REVERT: S 234 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7977 (p0) REVERT: b 11 ARG cc_start: 0.4306 (mtt180) cc_final: 0.3277 (mtm180) REVERT: b 14 ASN cc_start: 0.8023 (m-40) cc_final: 0.7603 (m-40) REVERT: b 35 MET cc_start: 0.8565 (mtp) cc_final: 0.8235 (mmp) REVERT: b 39 LYS cc_start: 0.8104 (ttpt) cc_final: 0.7852 (mmtt) REVERT: b 41 MET cc_start: 0.9001 (mmm) cc_final: 0.8756 (mmp) REVERT: b 45 LEU cc_start: 0.9051 (mt) cc_final: 0.8761 (tp) REVERT: b 46 ASN cc_start: 0.8476 (t0) cc_final: 0.8249 (t0) REVERT: b 47 GLU cc_start: 0.8379 (tm-30) cc_final: 0.7989 (pm20) REVERT: b 78 GLU cc_start: 0.6512 (tm-30) cc_final: 0.6250 (tm-30) REVERT: b 86 ILE cc_start: 0.9047 (mt) cc_final: 0.8787 (mt) REVERT: b 93 LEU cc_start: 0.8359 (mt) cc_final: 0.7998 (mt) REVERT: b 94 SER cc_start: 0.9302 (p) cc_final: 0.9058 (t) REVERT: b 97 VAL cc_start: 0.8632 (t) cc_final: 0.7971 (p) REVERT: d 21 LEU cc_start: 0.8744 (tp) cc_final: 0.8489 (mp) REVERT: d 79 LYS cc_start: 0.9403 (ttmt) cc_final: 0.9063 (tmmt) REVERT: e 18 PHE cc_start: 0.7574 (m-80) cc_final: 0.7174 (m-80) REVERT: e 32 PHE cc_start: 0.8250 (t80) cc_final: 0.7641 (t80) REVERT: e 37 ILE cc_start: 0.8337 (mt) cc_final: 0.7981 (mm) REVERT: e 38 ARG cc_start: 0.6139 (mtt180) cc_final: 0.5791 (ptt180) REVERT: e 47 ASP cc_start: 0.7344 (t70) cc_final: 0.6935 (m-30) REVERT: e 82 LEU cc_start: 0.7552 (tt) cc_final: 0.7058 (tp) REVERT: f 25 HIS cc_start: 0.8366 (t-90) cc_final: 0.8116 (m90) REVERT: f 70 GLU cc_start: 0.7891 (tt0) cc_final: 0.7682 (tt0) REVERT: g 5 PRO cc_start: 0.7283 (Cg_exo) cc_final: 0.6493 (Cg_endo) REVERT: g 7 LEU cc_start: 0.7755 (mt) cc_final: 0.7544 (mp) REVERT: g 11 MET cc_start: 0.5318 (mmm) cc_final: 0.5056 (mmm) REVERT: g 14 LYS cc_start: 0.8958 (tttp) cc_final: 0.8709 (tptp) REVERT: g 17 LEU cc_start: 0.7249 (mp) cc_final: 0.6748 (tp) REVERT: g 23 ARG cc_start: 0.6493 (mtm180) cc_final: 0.5894 (mtp-110) REVERT: g 24 LYS cc_start: 0.7995 (mttp) cc_final: 0.7564 (tmtt) REVERT: g 56 GLN cc_start: 0.8150 (tt0) cc_final: 0.7718 (tm-30) REVERT: g 59 LEU cc_start: 0.7031 (mm) cc_final: 0.6729 (tp) REVERT: g 72 GLU cc_start: 0.5729 (tm-30) cc_final: 0.5297 (tm-30) REVERT: h 4 VAL cc_start: 0.9013 (t) cc_final: 0.8776 (t) REVERT: h 17 ILE cc_start: 0.8178 (mt) cc_final: 0.7914 (tp) REVERT: h 44 LYS cc_start: 0.9048 (ttpp) cc_final: 0.8762 (mmtm) REVERT: h 84 TYR cc_start: 0.5710 (t80) cc_final: 0.4789 (t80) REVERT: h 90 ASN cc_start: 0.7981 (p0) cc_final: 0.7497 (p0) REVERT: h 91 THR cc_start: 0.8366 (p) cc_final: 0.8127 (p) REVERT: h 102 ASN cc_start: 0.8168 (m-40) cc_final: 0.7904 (t0) REVERT: j 28 HIS cc_start: 0.7979 (m90) cc_final: 0.7450 (t-90) REVERT: j 70 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7665 (tp30) REVERT: j 75 LEU cc_start: 0.8245 (mt) cc_final: 0.8021 (mp) REVERT: j 82 LYS cc_start: 0.5075 (OUTLIER) cc_final: 0.4848 (mmmt) REVERT: j 92 SER cc_start: 0.9332 (m) cc_final: 0.8863 (t) REVERT: j 94 LEU cc_start: 0.7792 (tt) cc_final: 0.7460 (tp) REVERT: j 96 LEU cc_start: 0.8857 (tp) cc_final: 0.8310 (pp) outliers start: 402 outliers final: 110 residues processed: 1650 average time/residue: 0.6195 time to fit residues: 1685.3867 Evaluate side-chains 1012 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 828 time to evaluate : 4.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 755 ASP Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 944 TYR Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1019 GLU Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1099 ASN Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1212 ARG Chi-restraints excluded: chain A residue 1315 ARG Chi-restraints excluded: chain A residue 1337 THR Chi-restraints excluded: chain A residue 1346 PHE Chi-restraints excluded: chain A residue 1347 ARG Chi-restraints excluded: chain A residue 1356 LEU Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain A residue 1382 ARG Chi-restraints excluded: chain A residue 1433 ASP Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1491 ILE Chi-restraints excluded: chain A residue 1520 GLU Chi-restraints excluded: chain A residue 1586 GLN Chi-restraints excluded: chain A residue 1589 LYS Chi-restraints excluded: chain A residue 1590 LEU Chi-restraints excluded: chain A residue 1594 GLN Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1600 GLN Chi-restraints excluded: chain A residue 1603 ASN Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1647 GLN Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1803 ARG Chi-restraints excluded: chain A residue 2048 TRP Chi-restraints excluded: chain D residue 47 PHE Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 114 ARG Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 590 LYS Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain C residue 791 TYR Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 837 GLN Chi-restraints excluded: chain C residue 861 ILE Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 927 MET Chi-restraints excluded: chain C residue 965 ASP Chi-restraints excluded: chain G residue 31 ARG Chi-restraints excluded: chain G residue 33 GLN Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 348 GLU Chi-restraints excluded: chain H residue 357 TRP Chi-restraints excluded: chain H residue 373 ILE Chi-restraints excluded: chain H residue 391 LEU Chi-restraints excluded: chain H residue 421 LYS Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 477 MET Chi-restraints excluded: chain J residue 143 ARG Chi-restraints excluded: chain J residue 151 ASP Chi-restraints excluded: chain J residue 183 MET Chi-restraints excluded: chain J residue 194 HIS Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 215 GLN Chi-restraints excluded: chain J residue 218 ARG Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 248 ILE Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 334 TRP Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 423 ILE Chi-restraints excluded: chain K residue 33 GLN Chi-restraints excluded: chain K residue 48 GLN Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 66 CYS Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 111 HIS Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 197 ILE Chi-restraints excluded: chain K residue 203 LYS Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain L residue 3 ARG Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain L residue 84 GLU Chi-restraints excluded: chain L residue 142 PHE Chi-restraints excluded: chain M residue 10 LYS Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 38 SER Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain M residue 116 LYS Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 132 LYS Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 172 ARG Chi-restraints excluded: chain N residue 20 GLU Chi-restraints excluded: chain N residue 30 GLN Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 254 GLN Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 53 ASN Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 170 LYS Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain O residue 189 ARG Chi-restraints excluded: chain O residue 205 LYS Chi-restraints excluded: chain O residue 206 LYS Chi-restraints excluded: chain P residue 8 GLN Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 16 LYS Chi-restraints excluded: chain P residue 29 ARG Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain S residue 60 ARG Chi-restraints excluded: chain S residue 87 ILE Chi-restraints excluded: chain S residue 117 HIS Chi-restraints excluded: chain S residue 143 GLU Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 156 TYR Chi-restraints excluded: chain S residue 158 LYS Chi-restraints excluded: chain S residue 173 VAL Chi-restraints excluded: chain S residue 188 ILE Chi-restraints excluded: chain S residue 189 TYR Chi-restraints excluded: chain S residue 234 ASN Chi-restraints excluded: chain S residue 257 GLN Chi-restraints excluded: chain d residue 20 SER Chi-restraints excluded: chain e residue 79 LYS Chi-restraints excluded: chain j residue 82 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 773 random chunks: chunk 652 optimal weight: 4.9990 chunk 585 optimal weight: 30.0000 chunk 325 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 395 optimal weight: 1.9990 chunk 313 optimal weight: 5.9990 chunk 605 optimal weight: 5.9990 chunk 234 optimal weight: 8.9990 chunk 368 optimal weight: 5.9990 chunk 450 optimal weight: 0.4980 chunk 701 optimal weight: 9.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS A 265 ASN A 310 ASN A 326 ASN A 344 ASN A 508 GLN A 509 HIS A 705 GLN A 733 GLN ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A 948 HIS A 997 GLN A1097 HIS A1115 GLN A1128 GLN A1368 GLN A1417 GLN A1449 ASN A1568 ASN A1687 HIS A1799 GLN A1907 GLN A2018 ASN A2068 ASN ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 ASN C 194 ASN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 GLN C 260 ASN C 355 HIS C 418 GLN C 557 HIS C 608 GLN C 794 GLN C 869 HIS G 9 ASN G 33 GLN G 60 GLN H 260 GLN H 368 ASN ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 233 HIS J 273 GLN J 280 GLN J 443 ASN K 33 GLN K 64 GLN K 210 ASN ** K 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 GLN L 115 ASN M 31 ASN ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 85 GLN ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 ASN ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 47 GLN S 61 ASN S 78 GLN S 79 HIS S 214 ASN S 234 ASN d 4 ASN d 41 ASN e 24 GLN e 86 ASN f 24 ASN g 18 ASN g 66 ASN Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.129 65132 Z= 0.314 Angle : 0.729 13.986 90610 Z= 0.373 Chirality : 0.044 0.324 10977 Planarity : 0.005 0.102 9985 Dihedral : 19.290 177.599 15275 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.57 % Favored : 95.23 % Rotamer: Outliers : 7.48 % Allowed : 16.81 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.10), residues: 7089 helix: 3.24 (0.09), residues: 3222 sheet: -2.53 (0.16), residues: 763 loop : -2.49 (0.10), residues: 3104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP J 293 HIS 0.007 0.001 HIS N 45 PHE 0.047 0.002 PHE j 26 TYR 0.025 0.002 TYR H 369 ARG 0.010 0.001 ARG K 47 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14178 Ramachandran restraints generated. 7089 Oldfield, 0 Emsley, 7089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14178 Ramachandran restraints generated. 7089 Oldfield, 0 Emsley, 7089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1239 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 352 poor density : 887 time to evaluate : 5.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 TYR cc_start: 0.7952 (OUTLIER) cc_final: 0.6785 (t80) REVERT: A 165 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9105 (mm) REVERT: A 272 ASP cc_start: 0.7036 (t0) cc_final: 0.6533 (t70) REVERT: A 275 TYR cc_start: 0.8861 (m-80) cc_final: 0.8638 (m-80) REVERT: A 304 ASP cc_start: 0.8812 (m-30) cc_final: 0.8611 (m-30) REVERT: A 325 LYS cc_start: 0.9362 (tttp) cc_final: 0.9147 (tttt) REVERT: A 392 ASN cc_start: 0.8993 (t0) cc_final: 0.8474 (t0) REVERT: A 479 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8814 (mt) REVERT: A 514 TYR cc_start: 0.9180 (OUTLIER) cc_final: 0.8577 (m-80) REVERT: A 528 ASN cc_start: 0.8921 (m-40) cc_final: 0.8521 (t0) REVERT: A 553 ASN cc_start: 0.9091 (m-40) cc_final: 0.8864 (m-40) REVERT: A 625 LEU cc_start: 0.9553 (mt) cc_final: 0.9266 (mp) REVERT: A 634 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.7883 (t70) REVERT: A 682 ASP cc_start: 0.8330 (m-30) cc_final: 0.7934 (m-30) REVERT: A 726 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.8778 (tt) REVERT: A 743 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8956 (tptm) REVERT: A 763 MET cc_start: 0.8757 (tpt) cc_final: 0.8537 (tpp) REVERT: A 769 MET cc_start: 0.9086 (mmt) cc_final: 0.8785 (mmm) REVERT: A 813 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8239 (tt0) REVERT: A 821 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8350 (m-30) REVERT: A 873 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7967 (mp0) REVERT: A 933 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8023 (mt-10) REVERT: A 965 LYS cc_start: 0.8758 (mtmt) cc_final: 0.8098 (mttt) REVERT: A 968 ASP cc_start: 0.9075 (t0) cc_final: 0.8814 (t0) REVERT: A 1004 ASP cc_start: 0.9031 (OUTLIER) cc_final: 0.8691 (t0) REVERT: A 1019 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8073 (mp0) REVERT: A 1056 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8815 (mt-10) REVERT: A 1057 MET cc_start: 0.9043 (tmm) cc_final: 0.8745 (tmm) REVERT: A 1101 TYR cc_start: 0.8911 (t80) cc_final: 0.8017 (t80) REVERT: A 1140 ASN cc_start: 0.8783 (t0) cc_final: 0.8204 (p0) REVERT: A 1162 THR cc_start: 0.9468 (OUTLIER) cc_final: 0.9057 (m) REVERT: A 1167 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8287 (tpt-90) REVERT: A 1171 LEU cc_start: 0.9330 (tp) cc_final: 0.9100 (tp) REVERT: A 1212 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.7839 (ptp90) REVERT: A 1261 SER cc_start: 0.8633 (t) cc_final: 0.8256 (p) REVERT: A 1291 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8954 (tp30) REVERT: A 1315 ARG cc_start: 0.8209 (ttm110) cc_final: 0.7730 (tpp-160) REVERT: A 1321 MET cc_start: 0.8977 (mmm) cc_final: 0.8721 (mmm) REVERT: A 1347 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8823 (mtt90) REVERT: A 1348 GLU cc_start: 0.8644 (tt0) cc_final: 0.8289 (tt0) REVERT: A 1379 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8822 (ttm) REVERT: A 1445 THR cc_start: 0.9254 (OUTLIER) cc_final: 0.9051 (p) REVERT: A 1448 GLU cc_start: 0.9009 (tt0) cc_final: 0.8807 (tt0) REVERT: A 1485 ASP cc_start: 0.8813 (m-30) cc_final: 0.8472 (p0) REVERT: A 1520 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7001 (tm-30) REVERT: A 1558 GLU cc_start: 0.9099 (tp30) cc_final: 0.8896 (tp30) REVERT: A 1585 MET cc_start: 0.7595 (tpt) cc_final: 0.7326 (tpt) REVERT: A 1586 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7435 (pm20) REVERT: A 1589 LYS cc_start: 0.4032 (OUTLIER) cc_final: 0.3755 (ptpt) REVERT: A 1600 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.7063 (mm110) REVERT: A 1603 ASN cc_start: 0.8961 (OUTLIER) cc_final: 0.8229 (p0) REVERT: A 1618 ASN cc_start: 0.8475 (m-40) cc_final: 0.8222 (m-40) REVERT: A 1632 ILE cc_start: 0.9592 (mt) cc_final: 0.9217 (mt) REVERT: A 1803 ARG cc_start: 0.9220 (OUTLIER) cc_final: 0.8697 (ttp-110) REVERT: A 1806 MET cc_start: 0.9310 (mpp) cc_final: 0.8948 (mmp) REVERT: A 1880 PHE cc_start: 0.9279 (t80) cc_final: 0.8115 (t80) REVERT: A 1907 GLN cc_start: 0.8951 (tt0) cc_final: 0.8643 (mm110) REVERT: A 1920 LEU cc_start: 0.8751 (tt) cc_final: 0.8539 (mm) REVERT: A 1940 MET cc_start: 0.7774 (tpt) cc_final: 0.6721 (tpp) REVERT: A 2019 GLU cc_start: 0.7881 (pm20) cc_final: 0.7662 (pm20) REVERT: A 2024 MET cc_start: 0.7662 (mtm) cc_final: 0.7391 (mtm) REVERT: A 2048 TRP cc_start: 0.6849 (OUTLIER) cc_final: 0.6413 (m100) REVERT: D 15 TYR cc_start: 0.8909 (t80) cc_final: 0.8360 (t80) REVERT: D 16 ASN cc_start: 0.8785 (m-40) cc_final: 0.8118 (t0) REVERT: D 19 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8459 (mm-30) REVERT: D 44 MET cc_start: 0.8948 (mtm) cc_final: 0.8709 (mtm) REVERT: D 53 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8281 (tm-30) REVERT: D 61 SER cc_start: 0.8602 (m) cc_final: 0.7922 (p) REVERT: D 73 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8534 (mp0) REVERT: D 85 THR cc_start: 0.8784 (m) cc_final: 0.8333 (p) REVERT: D 90 ARG cc_start: 0.8853 (ttm-80) cc_final: 0.7823 (ttt180) REVERT: D 114 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7652 (ttt180) REVERT: F 8 LEU cc_start: 0.9266 (tp) cc_final: 0.8646 (tp) REVERT: C 183 GLN cc_start: 0.8283 (tt0) cc_final: 0.8081 (tt0) REVERT: C 222 MET cc_start: 0.8804 (mmm) cc_final: 0.8572 (mmm) REVERT: C 225 THR cc_start: 0.9334 (p) cc_final: 0.8872 (p) REVERT: C 238 VAL cc_start: 0.9644 (t) cc_final: 0.9396 (m) REVERT: C 334 HIS cc_start: 0.8407 (m-70) cc_final: 0.7854 (t-90) REVERT: C 488 ILE cc_start: 0.9542 (mp) cc_final: 0.9261 (mt) REVERT: C 493 LEU cc_start: 0.9133 (tt) cc_final: 0.8846 (mt) REVERT: C 586 MET cc_start: 0.8488 (tmt) cc_final: 0.8074 (tmm) REVERT: C 590 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8553 (pmmt) REVERT: C 600 GLU cc_start: 0.9391 (tp30) cc_final: 0.8577 (tm-30) REVERT: C 652 MET cc_start: 0.8975 (mmm) cc_final: 0.8743 (tpp) REVERT: C 654 CYS cc_start: 0.8603 (m) cc_final: 0.8370 (m) REVERT: C 658 ASP cc_start: 0.8769 (m-30) cc_final: 0.8566 (m-30) REVERT: C 719 MET cc_start: 0.8855 (tpp) cc_final: 0.8545 (tpp) REVERT: C 861 ILE cc_start: 0.9426 (OUTLIER) cc_final: 0.9190 (mp) REVERT: C 927 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8653 (tpp) REVERT: G 16 GLN cc_start: 0.9274 (mm-40) cc_final: 0.8811 (mp10) REVERT: G 18 GLN cc_start: 0.8553 (tt0) cc_final: 0.7877 (tp40) REVERT: G 29 TYR cc_start: 0.8692 (m-80) cc_final: 0.8468 (m-80) REVERT: G 33 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8026 (pp30) REVERT: G 36 ARG cc_start: 0.9016 (tpt-90) cc_final: 0.8761 (tmt170) REVERT: G 45 LYS cc_start: 0.8317 (mmtm) cc_final: 0.7830 (tttm) REVERT: G 46 GLU cc_start: 0.9002 (tt0) cc_final: 0.8600 (mp0) REVERT: G 49 GLU cc_start: 0.9461 (mm-30) cc_final: 0.9140 (mm-30) REVERT: G 57 GLU cc_start: 0.9380 (tp30) cc_final: 0.8759 (tp30) REVERT: G 77 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8685 (mt-10) REVERT: G 88 GLU cc_start: 0.9084 (tp30) cc_final: 0.8607 (tp30) REVERT: G 91 ARG cc_start: 0.8694 (mtt180) cc_final: 0.7583 (mmp-170) REVERT: H 315 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9262 (mm) REVERT: H 317 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8092 (pp) REVERT: H 348 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8214 (tp30) REVERT: H 379 ASP cc_start: 0.8864 (m-30) cc_final: 0.8432 (p0) REVERT: H 380 GLN cc_start: 0.8607 (mt0) cc_final: 0.8327 (tt0) REVERT: H 425 GLN cc_start: 0.9377 (tt0) cc_final: 0.9099 (tt0) REVERT: H 429 ASN cc_start: 0.9503 (m-40) cc_final: 0.9261 (m110) REVERT: H 448 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7854 (mtp) REVERT: H 454 ASP cc_start: 0.8151 (t70) cc_final: 0.7893 (m-30) REVERT: J 212 GLU cc_start: 0.8775 (mp0) cc_final: 0.8428 (mm-30) REVERT: J 218 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8443 (ptp90) REVERT: J 231 SER cc_start: 0.9258 (t) cc_final: 0.8867 (t) REVERT: J 332 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8601 (mmt90) REVERT: J 404 CYS cc_start: 0.9069 (t) cc_final: 0.8486 (t) REVERT: J 443 ASN cc_start: 0.8917 (m-40) cc_final: 0.8643 (t0) REVERT: K 36 LYS cc_start: 0.6845 (OUTLIER) cc_final: 0.6119 (ptpt) REVERT: K 62 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8820 (tm-30) REVERT: K 66 CYS cc_start: 0.9331 (OUTLIER) cc_final: 0.8919 (t) REVERT: K 106 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7385 (mp) REVERT: K 118 GLN cc_start: 0.8614 (mt0) cc_final: 0.8183 (pm20) REVERT: K 162 GLU cc_start: 0.9322 (tt0) cc_final: 0.8986 (pt0) REVERT: K 212 ASP cc_start: 0.8953 (t0) cc_final: 0.8684 (t0) REVERT: K 213 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8126 (mtpt) REVERT: K 216 ARG cc_start: 0.8112 (mmm-85) cc_final: 0.7765 (mpt180) REVERT: K 219 ILE cc_start: 0.7745 (mt) cc_final: 0.7503 (mt) REVERT: L 10 LYS cc_start: 0.9391 (mmtp) cc_final: 0.8917 (pttp) REVERT: L 37 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8565 (mmtp) REVERT: L 142 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.7734 (p90) REVERT: M 80 MET cc_start: 0.9086 (ptm) cc_final: 0.8858 (ptp) REVERT: M 114 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7300 (ppt-90) REVERT: M 136 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8751 (p) REVERT: M 214 ASP cc_start: 0.9258 (m-30) cc_final: 0.8655 (t0) REVERT: M 235 GLN cc_start: 0.8802 (tp-100) cc_final: 0.8509 (tp-100) REVERT: M 239 GLN cc_start: 0.9133 (tp-100) cc_final: 0.8908 (mt0) REVERT: N 24 ARG cc_start: 0.9032 (ttp80) cc_final: 0.8760 (ttm-80) REVERT: N 30 GLN cc_start: 0.8853 (mt0) cc_final: 0.8454 (mt0) REVERT: N 43 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8748 (tt) REVERT: N 93 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7960 (tt) REVERT: N 318 LYS cc_start: 0.8989 (mttt) cc_final: 0.8788 (tmtt) REVERT: O 18 ASP cc_start: 0.8948 (t70) cc_final: 0.8598 (t0) REVERT: O 35 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8235 (mttm) REVERT: O 90 MET cc_start: 0.8808 (mmm) cc_final: 0.8555 (mmm) REVERT: O 151 MET cc_start: 0.8510 (ptm) cc_final: 0.8234 (ptm) REVERT: O 154 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8570 (mt-10) REVERT: O 158 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8526 (mmm-85) REVERT: O 184 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8534 (tp30) REVERT: O 189 ARG cc_start: 0.9377 (OUTLIER) cc_final: 0.8875 (mtt-85) REVERT: O 207 TYR cc_start: 0.7769 (m-10) cc_final: 0.7515 (m-10) REVERT: O 224 MET cc_start: 0.8722 (ttm) cc_final: 0.8388 (ttm) REVERT: O 234 ASP cc_start: 0.8896 (m-30) cc_final: 0.8340 (m-30) REVERT: O 244 PHE cc_start: 0.6123 (t80) cc_final: 0.5900 (t80) REVERT: R 15 SER cc_start: 0.9291 (OUTLIER) cc_final: 0.9014 (m) REVERT: S 73 GLN cc_start: 0.8883 (mt0) cc_final: 0.8561 (tm-30) REVERT: S 117 HIS cc_start: 0.8983 (OUTLIER) cc_final: 0.8616 (m170) REVERT: S 122 MET cc_start: 0.9302 (mtm) cc_final: 0.8965 (mtp) REVERT: S 126 ILE cc_start: 0.9271 (mm) cc_final: 0.8835 (mm) REVERT: S 156 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.7864 (t80) REVERT: S 163 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8412 (tm-30) REVERT: S 189 TYR cc_start: 0.8992 (OUTLIER) cc_final: 0.7554 (t80) REVERT: S 218 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7949 (p) REVERT: b 11 ARG cc_start: 0.4317 (mtt180) cc_final: 0.3298 (mtm180) REVERT: b 14 ASN cc_start: 0.7785 (m-40) cc_final: 0.7233 (m-40) REVERT: b 35 MET cc_start: 0.8577 (mtp) cc_final: 0.8026 (mmm) REVERT: b 39 LYS cc_start: 0.8198 (ttpt) cc_final: 0.7663 (mmtt) REVERT: b 41 MET cc_start: 0.9151 (mmm) cc_final: 0.8833 (mmp) REVERT: b 46 ASN cc_start: 0.8495 (t0) cc_final: 0.8206 (t0) REVERT: b 47 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8010 (pm20) REVERT: b 86 ILE cc_start: 0.8974 (mt) cc_final: 0.8722 (mt) REVERT: b 93 LEU cc_start: 0.8349 (mt) cc_final: 0.7929 (mt) REVERT: b 94 SER cc_start: 0.9263 (p) cc_final: 0.8955 (m) REVERT: b 97 VAL cc_start: 0.8676 (t) cc_final: 0.8370 (p) REVERT: d 76 ASP cc_start: 0.8784 (t70) cc_final: 0.8575 (t0) REVERT: e 38 ARG cc_start: 0.6681 (mtt180) cc_final: 0.6138 (ptt180) REVERT: e 47 ASP cc_start: 0.7162 (t70) cc_final: 0.6747 (m-30) REVERT: e 50 MET cc_start: 0.6343 (tpp) cc_final: 0.5454 (ttm) REVERT: f 25 HIS cc_start: 0.8153 (t-90) cc_final: 0.7947 (m90) REVERT: g 17 LEU cc_start: 0.7553 (mp) cc_final: 0.6637 (tp) REVERT: g 23 ARG cc_start: 0.6190 (mtm180) cc_final: 0.5575 (mtm110) REVERT: g 56 GLN cc_start: 0.8512 (tt0) cc_final: 0.7811 (tm-30) REVERT: g 59 LEU cc_start: 0.6979 (mm) cc_final: 0.6715 (tp) REVERT: g 72 GLU cc_start: 0.5557 (tm-30) cc_final: 0.5144 (tm-30) REVERT: h 1 MET cc_start: 0.6048 (ptp) cc_final: 0.5582 (pmm) REVERT: h 90 ASN cc_start: 0.8082 (p0) cc_final: 0.7523 (p0) REVERT: h 102 ASN cc_start: 0.8180 (m-40) cc_final: 0.7931 (t0) REVERT: j 24 PHE cc_start: 0.7967 (t80) cc_final: 0.7625 (t80) REVERT: j 28 HIS cc_start: 0.7970 (m90) cc_final: 0.7462 (t70) REVERT: j 70 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7612 (tp30) REVERT: j 77 THR cc_start: 0.6081 (OUTLIER) cc_final: 0.5836 (t) REVERT: j 82 LYS cc_start: 0.5440 (OUTLIER) cc_final: 0.5050 (mmmt) REVERT: j 89 ARG cc_start: 0.7264 (ttp-170) cc_final: 0.6422 (mpt180) REVERT: j 92 SER cc_start: 0.9399 (m) cc_final: 0.9000 (p) outliers start: 352 outliers final: 169 residues processed: 1152 average time/residue: 0.6067 time to fit residues: 1183.1211 Evaluate side-chains 922 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 697 time to evaluate : 4.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 755 ASP Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 944 TYR Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1019 GLU Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1082 ILE Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1167 ARG Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1205 LYS Chi-restraints excluded: chain A residue 1212 ARG Chi-restraints excluded: chain A residue 1317 ARG Chi-restraints excluded: chain A residue 1346 PHE Chi-restraints excluded: chain A residue 1347 ARG Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain A residue 1431 HIS Chi-restraints excluded: chain A residue 1433 ASP Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1445 THR Chi-restraints excluded: chain A residue 1498 ASP Chi-restraints excluded: chain A residue 1520 GLU Chi-restraints excluded: chain A residue 1586 GLN Chi-restraints excluded: chain A residue 1589 LYS Chi-restraints excluded: chain A residue 1590 LEU Chi-restraints excluded: chain A residue 1600 GLN Chi-restraints excluded: chain A residue 1603 ASN Chi-restraints excluded: chain A residue 1619 VAL Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1646 ILE Chi-restraints excluded: chain A residue 1648 ILE Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1803 ARG Chi-restraints excluded: chain A residue 1881 THR Chi-restraints excluded: chain A residue 2048 TRP Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 47 PHE Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 114 ARG Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 590 LYS Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 681 CYS Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 837 GLN Chi-restraints excluded: chain C residue 861 ILE Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 927 MET Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 33 GLN Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 315 LEU Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 348 GLU Chi-restraints excluded: chain H residue 352 THR Chi-restraints excluded: chain H residue 373 ILE Chi-restraints excluded: chain H residue 394 TYR Chi-restraints excluded: chain H residue 436 LEU Chi-restraints excluded: chain H residue 448 MET Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 477 MET Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 151 ASP Chi-restraints excluded: chain J residue 194 HIS Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 218 ARG Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 246 SER Chi-restraints excluded: chain J residue 248 ILE Chi-restraints excluded: chain J residue 263 VAL Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 280 GLN Chi-restraints excluded: chain J residue 286 THR Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 332 ARG Chi-restraints excluded: chain J residue 334 TRP Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 358 ILE Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 397 GLU Chi-restraints excluded: chain J residue 423 ILE Chi-restraints excluded: chain K residue 36 LYS Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 66 CYS Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 111 HIS Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 196 THR Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain K residue 213 LYS Chi-restraints excluded: chain L residue 3 ARG Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 138 THR Chi-restraints excluded: chain L residue 142 PHE Chi-restraints excluded: chain M residue 10 LYS Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 111 CYS Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 85 GLN Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 158 ARG Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain O residue 189 ARG Chi-restraints excluded: chain O residue 200 ILE Chi-restraints excluded: chain O residue 206 LYS Chi-restraints excluded: chain O residue 212 ASP Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 117 HIS Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 143 GLU Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 156 TYR Chi-restraints excluded: chain S residue 158 LYS Chi-restraints excluded: chain S residue 173 VAL Chi-restraints excluded: chain S residue 188 ILE Chi-restraints excluded: chain S residue 189 TYR Chi-restraints excluded: chain S residue 218 THR Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 257 GLN Chi-restraints excluded: chain S residue 263 SER Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain e residue 81 LEU Chi-restraints excluded: chain f residue 31 LEU Chi-restraints excluded: chain f residue 47 ASN Chi-restraints excluded: chain f residue 58 GLU Chi-restraints excluded: chain f residue 78 VAL Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 75 ASP Chi-restraints excluded: chain j residue 21 LEU Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 77 THR Chi-restraints excluded: chain j residue 82 LYS Chi-restraints excluded: chain j residue 100 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 773 random chunks: chunk 390 optimal weight: 0.3980 chunk 217 optimal weight: 7.9990 chunk 584 optimal weight: 30.0000 chunk 477 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 703 optimal weight: 50.0000 chunk 759 optimal weight: 40.0000 chunk 626 optimal weight: 2.9990 chunk 697 optimal weight: 50.0000 chunk 239 optimal weight: 4.9990 chunk 564 optimal weight: 40.0000 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 HIS A 216 GLN A 265 ASN A 497 GLN A 638 GLN ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 ASN ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 ASN A1548 GLN A1929 GLN C 158 HIS C 180 ASN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 GLN C 776 ASN ** C 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 260 GLN H 358 GLN H 362 ASN H 368 ASN ** H 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 121 GLN ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN K 174 ASN ** K 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 128 GLN L 144 GLN ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 321 GLN ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 73 GLN ** b 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 71 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 65132 Z= 0.396 Angle : 0.733 13.664 90610 Z= 0.373 Chirality : 0.044 0.495 10977 Planarity : 0.005 0.103 9985 Dihedral : 19.035 169.030 15098 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.14 % Favored : 93.68 % Rotamer: Outliers : 8.10 % Allowed : 18.55 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.10), residues: 7089 helix: 2.73 (0.09), residues: 3237 sheet: -2.28 (0.17), residues: 755 loop : -2.20 (0.10), residues: 3097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 183 HIS 0.010 0.002 HIS A1652 PHE 0.026 0.002 PHE A1851 TYR 0.027 0.002 TYR D 75 ARG 0.018 0.001 ARG K 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14178 Ramachandran restraints generated. 7089 Oldfield, 0 Emsley, 7089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14178 Ramachandran restraints generated. 7089 Oldfield, 0 Emsley, 7089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1118 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 381 poor density : 737 time to evaluate : 4.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 TYR cc_start: 0.7929 (OUTLIER) cc_final: 0.6817 (t80) REVERT: A 149 MET cc_start: 0.8612 (ptp) cc_final: 0.8336 (ptp) REVERT: A 224 MET cc_start: 0.8482 (mtm) cc_final: 0.8073 (mtp) REVERT: A 392 ASN cc_start: 0.9081 (t0) cc_final: 0.8440 (t0) REVERT: A 415 GLU cc_start: 0.4917 (OUTLIER) cc_final: 0.4154 (tm-30) REVERT: A 514 TYR cc_start: 0.9077 (OUTLIER) cc_final: 0.8552 (m-80) REVERT: A 528 ASN cc_start: 0.8722 (m-40) cc_final: 0.8306 (t0) REVERT: A 553 ASN cc_start: 0.9125 (m-40) cc_final: 0.8880 (m-40) REVERT: A 610 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.8530 (ttm-80) REVERT: A 625 LEU cc_start: 0.9603 (mt) cc_final: 0.9381 (mp) REVERT: A 634 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.7869 (t70) REVERT: A 749 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.7751 (ttp-170) REVERT: A 763 MET cc_start: 0.8607 (tpt) cc_final: 0.8284 (tpp) REVERT: A 770 MET cc_start: 0.8991 (pmt) cc_final: 0.8654 (pmm) REVERT: A 813 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8435 (tt0) REVERT: A 821 ASP cc_start: 0.8847 (OUTLIER) cc_final: 0.8491 (m-30) REVERT: A 873 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7944 (mp0) REVERT: A 933 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8127 (mt-10) REVERT: A 969 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8284 (pt) REVERT: A 1004 ASP cc_start: 0.9043 (OUTLIER) cc_final: 0.8581 (t0) REVERT: A 1019 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8284 (mp0) REVERT: A 1056 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8799 (mt-10) REVERT: A 1057 MET cc_start: 0.9095 (tmm) cc_final: 0.8780 (tmm) REVERT: A 1069 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9235 (mm) REVERT: A 1072 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8964 (mp) REVERT: A 1101 TYR cc_start: 0.8848 (t80) cc_final: 0.8194 (t80) REVERT: A 1140 ASN cc_start: 0.8927 (t0) cc_final: 0.8324 (p0) REVERT: A 1162 THR cc_start: 0.9525 (OUTLIER) cc_final: 0.9315 (m) REVERT: A 1167 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8315 (tpt-90) REVERT: A 1171 LEU cc_start: 0.9338 (tp) cc_final: 0.9072 (tp) REVERT: A 1212 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7589 (ptp90) REVERT: A 1347 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8804 (mpp80) REVERT: A 1379 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8875 (ttm) REVERT: A 1445 THR cc_start: 0.9265 (OUTLIER) cc_final: 0.8844 (p) REVERT: A 1558 GLU cc_start: 0.9126 (tp30) cc_final: 0.8789 (tp30) REVERT: A 1585 MET cc_start: 0.7692 (tpt) cc_final: 0.7461 (tpt) REVERT: A 1586 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7576 (pm20) REVERT: A 1594 GLN cc_start: 0.4110 (OUTLIER) cc_final: 0.3598 (mm-40) REVERT: A 1600 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7641 (mm110) REVERT: A 1603 ASN cc_start: 0.9026 (OUTLIER) cc_final: 0.8239 (p0) REVERT: A 1618 ASN cc_start: 0.8514 (m-40) cc_final: 0.8283 (m-40) REVERT: A 1632 ILE cc_start: 0.9574 (mt) cc_final: 0.9286 (mt) REVERT: A 1664 ASP cc_start: 0.8024 (m-30) cc_final: 0.7740 (m-30) REVERT: A 1803 ARG cc_start: 0.9288 (OUTLIER) cc_final: 0.8701 (ttp-110) REVERT: A 1806 MET cc_start: 0.9335 (OUTLIER) cc_final: 0.9076 (mmm) REVERT: A 1880 PHE cc_start: 0.9284 (t80) cc_final: 0.8034 (t80) REVERT: A 1907 GLN cc_start: 0.9070 (tt0) cc_final: 0.8799 (mm110) REVERT: A 1940 MET cc_start: 0.8160 (tpt) cc_final: 0.7807 (tpp) REVERT: A 2048 TRP cc_start: 0.6619 (m100) cc_final: 0.6243 (m100) REVERT: D 15 TYR cc_start: 0.9103 (t80) cc_final: 0.8790 (t80) REVERT: D 16 ASN cc_start: 0.8730 (m-40) cc_final: 0.8237 (t0) REVERT: D 47 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.8047 (m-80) REVERT: D 53 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8306 (tm-30) REVERT: D 73 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8528 (mp0) REVERT: D 85 THR cc_start: 0.8757 (m) cc_final: 0.8251 (p) REVERT: D 90 ARG cc_start: 0.8848 (ttm-80) cc_final: 0.7881 (ttt180) REVERT: F 8 LEU cc_start: 0.9332 (tp) cc_final: 0.8618 (tp) REVERT: C 222 MET cc_start: 0.8820 (mmm) cc_final: 0.8526 (mmm) REVERT: C 334 HIS cc_start: 0.8409 (m-70) cc_final: 0.7880 (t-90) REVERT: C 396 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8897 (tt) REVERT: C 540 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8461 (mp0) REVERT: C 586 MET cc_start: 0.8540 (tmt) cc_final: 0.8125 (tmm) REVERT: C 600 GLU cc_start: 0.9416 (tp30) cc_final: 0.8703 (tm-30) REVERT: C 652 MET cc_start: 0.9118 (mmm) cc_final: 0.8881 (tpp) REVERT: C 658 ASP cc_start: 0.8682 (m-30) cc_final: 0.8398 (m-30) REVERT: C 719 MET cc_start: 0.9057 (tpp) cc_final: 0.8733 (tpp) REVERT: C 760 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6611 (tt) REVERT: C 837 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.6919 (pp30) REVERT: C 842 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8640 (ttm) REVERT: C 927 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8742 (tpp) REVERT: G 36 ARG cc_start: 0.9016 (tpt-90) cc_final: 0.8754 (tmt170) REVERT: G 49 GLU cc_start: 0.9459 (mm-30) cc_final: 0.9083 (mm-30) REVERT: G 57 GLU cc_start: 0.9455 (tp30) cc_final: 0.8749 (tp30) REVERT: G 88 GLU cc_start: 0.9310 (tp30) cc_final: 0.8878 (tp30) REVERT: H 317 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7919 (pp) REVERT: H 379 ASP cc_start: 0.8911 (m-30) cc_final: 0.8610 (p0) REVERT: H 380 GLN cc_start: 0.8562 (mt0) cc_final: 0.8345 (mt0) REVERT: H 425 GLN cc_start: 0.9435 (tt0) cc_final: 0.9065 (tt0) REVERT: H 429 ASN cc_start: 0.9503 (m-40) cc_final: 0.9259 (m110) REVERT: H 448 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.8020 (mtt) REVERT: H 454 ASP cc_start: 0.8241 (t70) cc_final: 0.8038 (m-30) REVERT: H 477 MET cc_start: 0.8051 (ptm) cc_final: 0.7507 (ptt) REVERT: J 212 GLU cc_start: 0.8929 (mp0) cc_final: 0.8585 (mm-30) REVERT: J 218 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8016 (mtt-85) REVERT: J 231 SER cc_start: 0.9210 (t) cc_final: 0.8894 (t) REVERT: J 332 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8526 (mmt90) REVERT: J 404 CYS cc_start: 0.9096 (t) cc_final: 0.8759 (t) REVERT: J 443 ASN cc_start: 0.8908 (m-40) cc_final: 0.8368 (t0) REVERT: K 36 LYS cc_start: 0.6976 (OUTLIER) cc_final: 0.6300 (ptpt) REVERT: K 47 ARG cc_start: 0.6543 (mmm160) cc_final: 0.6107 (mmm160) REVERT: K 62 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.8828 (tm-30) REVERT: K 64 GLN cc_start: 0.8869 (mt0) cc_final: 0.8624 (mt0) REVERT: K 106 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7437 (mp) REVERT: K 118 GLN cc_start: 0.8629 (mt0) cc_final: 0.8242 (pm20) REVERT: K 174 ASN cc_start: 0.9240 (OUTLIER) cc_final: 0.8972 (t0) REVERT: K 199 ASP cc_start: 0.9020 (m-30) cc_final: 0.8738 (t0) REVERT: K 213 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8285 (mtpt) REVERT: L 10 LYS cc_start: 0.9397 (mmtp) cc_final: 0.8915 (ttpp) REVERT: L 130 GLU cc_start: 0.9147 (pt0) cc_final: 0.8662 (mm-30) REVERT: L 142 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.7685 (p90) REVERT: M 188 TYR cc_start: 0.8752 (m-10) cc_final: 0.8420 (m-10) REVERT: M 213 ASP cc_start: 0.9140 (m-30) cc_final: 0.8491 (p0) REVERT: M 214 ASP cc_start: 0.9300 (m-30) cc_final: 0.8861 (t0) REVERT: M 241 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8557 (mm-30) REVERT: N 30 GLN cc_start: 0.9005 (mt0) cc_final: 0.8692 (mt0) REVERT: N 43 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8693 (tt) REVERT: N 93 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7961 (tt) REVERT: N 105 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7793 (pttm) REVERT: N 318 LYS cc_start: 0.8926 (mttt) cc_final: 0.8663 (tmtt) REVERT: O 35 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.7866 (mttm) REVERT: O 62 PHE cc_start: 0.8733 (t80) cc_final: 0.8401 (m-80) REVERT: O 90 MET cc_start: 0.8655 (mmm) cc_final: 0.8441 (mmm) REVERT: O 151 MET cc_start: 0.8497 (ptm) cc_final: 0.8248 (ptm) REVERT: O 154 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8460 (mt-10) REVERT: O 158 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8589 (mmm-85) REVERT: O 184 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8246 (tp30) REVERT: O 189 ARG cc_start: 0.9324 (OUTLIER) cc_final: 0.8851 (mtt-85) REVERT: O 219 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.7925 (m-80) REVERT: P 8 GLN cc_start: 0.7940 (pp30) cc_final: 0.7693 (pp30) REVERT: S 73 GLN cc_start: 0.8850 (mt0) cc_final: 0.8567 (tm-30) REVERT: S 95 ASP cc_start: 0.8940 (t0) cc_final: 0.8682 (t0) REVERT: S 117 HIS cc_start: 0.9207 (OUTLIER) cc_final: 0.8765 (m170) REVERT: S 122 MET cc_start: 0.9318 (mtm) cc_final: 0.8715 (mtp) REVERT: S 126 ILE cc_start: 0.9255 (mm) cc_final: 0.8891 (mm) REVERT: S 156 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.7874 (t80) REVERT: S 163 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8591 (tm-30) REVERT: S 189 TYR cc_start: 0.9122 (OUTLIER) cc_final: 0.7462 (t80) REVERT: S 201 THR cc_start: 0.9405 (m) cc_final: 0.9118 (p) REVERT: b 11 ARG cc_start: 0.3457 (mtt180) cc_final: 0.2717 (mpp-170) REVERT: b 14 ASN cc_start: 0.7379 (m-40) cc_final: 0.6693 (m110) REVERT: b 25 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7422 (pm20) REVERT: b 35 MET cc_start: 0.8607 (mtp) cc_final: 0.8046 (mmm) REVERT: b 39 LYS cc_start: 0.8405 (ttpt) cc_final: 0.7960 (mmtt) REVERT: b 41 MET cc_start: 0.9072 (mmm) cc_final: 0.8802 (mmp) REVERT: b 47 GLU cc_start: 0.8343 (tm-30) cc_final: 0.7906 (pm20) REVERT: b 93 LEU cc_start: 0.8064 (mt) cc_final: 0.7757 (mt) REVERT: b 94 SER cc_start: 0.9389 (p) cc_final: 0.9083 (m) REVERT: b 97 VAL cc_start: 0.8562 (t) cc_final: 0.8353 (p) REVERT: e 47 ASP cc_start: 0.7162 (t70) cc_final: 0.6603 (m-30) REVERT: g 11 MET cc_start: 0.5845 (mmm) cc_final: 0.5266 (mmm) REVERT: g 13 LYS cc_start: 0.7849 (ttmt) cc_final: 0.7487 (mtpt) REVERT: g 17 LEU cc_start: 0.7193 (mp) cc_final: 0.6809 (tt) REVERT: g 23 ARG cc_start: 0.6166 (mtm180) cc_final: 0.5837 (mtm180) REVERT: g 59 LEU cc_start: 0.6775 (mm) cc_final: 0.6560 (tp) REVERT: g 69 ILE cc_start: 0.8355 (mm) cc_final: 0.7904 (mt) REVERT: g 72 GLU cc_start: 0.5174 (tm-30) cc_final: 0.4693 (tm-30) REVERT: g 75 ASP cc_start: 0.6139 (OUTLIER) cc_final: 0.5800 (p0) REVERT: h 1 MET cc_start: 0.6064 (ptp) cc_final: 0.5417 (pmm) REVERT: h 2 LYS cc_start: 0.7546 (mttm) cc_final: 0.6975 (tppt) REVERT: h 36 MET cc_start: 0.8376 (mtt) cc_final: 0.8105 (mtp) REVERT: h 42 ASP cc_start: 0.8990 (t0) cc_final: 0.8627 (t0) REVERT: h 44 LYS cc_start: 0.8849 (ttpp) cc_final: 0.8530 (mmtt) REVERT: h 90 ASN cc_start: 0.7897 (p0) cc_final: 0.7536 (p0) REVERT: h 102 ASN cc_start: 0.8242 (m-40) cc_final: 0.7988 (t0) REVERT: j 24 PHE cc_start: 0.7751 (t80) cc_final: 0.7515 (t80) REVERT: j 28 HIS cc_start: 0.8015 (m90) cc_final: 0.7466 (t70) REVERT: j 70 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7787 (tp30) REVERT: j 75 LEU cc_start: 0.8474 (tp) cc_final: 0.8270 (tp) REVERT: j 82 LYS cc_start: 0.5274 (OUTLIER) cc_final: 0.5007 (mmmt) REVERT: j 89 ARG cc_start: 0.7341 (ttp-170) cc_final: 0.6694 (mpt180) REVERT: j 92 SER cc_start: 0.9441 (m) cc_final: 0.9077 (p) outliers start: 381 outliers final: 223 residues processed: 1032 average time/residue: 0.5837 time to fit residues: 1029.9088 Evaluate side-chains 903 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 626 time to evaluate : 4.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 610 ARG Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 749 ARG Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 944 TYR Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1019 GLU Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1167 ARG Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1205 LYS Chi-restraints excluded: chain A residue 1212 ARG Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1317 ARG Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1346 PHE Chi-restraints excluded: chain A residue 1347 ARG Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain A residue 1420 THR Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1431 HIS Chi-restraints excluded: chain A residue 1433 ASP Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1445 THR Chi-restraints excluded: chain A residue 1452 LEU Chi-restraints excluded: chain A residue 1491 ILE Chi-restraints excluded: chain A residue 1498 ASP Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1586 GLN Chi-restraints excluded: chain A residue 1589 LYS Chi-restraints excluded: chain A residue 1594 GLN Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1600 GLN Chi-restraints excluded: chain A residue 1603 ASN Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1646 ILE Chi-restraints excluded: chain A residue 1648 ILE Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1774 MET Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1803 ARG Chi-restraints excluded: chain A residue 1806 MET Chi-restraints excluded: chain A residue 1881 THR Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 47 PHE Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 114 ARG Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 500 ARG Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 681 CYS Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 837 GLN Chi-restraints excluded: chain C residue 842 MET Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 927 MET Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 4 ASN Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain H residue 293 LYS Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 352 THR Chi-restraints excluded: chain H residue 373 ILE Chi-restraints excluded: chain H residue 392 ILE Chi-restraints excluded: chain H residue 448 MET Chi-restraints excluded: chain H residue 457 HIS Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 184 THR Chi-restraints excluded: chain J residue 194 HIS Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 218 ARG Chi-restraints excluded: chain J residue 232 ILE Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 246 SER Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 248 ILE Chi-restraints excluded: chain J residue 263 VAL Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 286 THR Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 332 ARG Chi-restraints excluded: chain J residue 334 TRP Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 358 ILE Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 397 GLU Chi-restraints excluded: chain J residue 423 ILE Chi-restraints excluded: chain K residue 36 LYS Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 50 ASN Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 111 HIS Chi-restraints excluded: chain K residue 174 ASN Chi-restraints excluded: chain K residue 196 THR Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain K residue 213 LYS Chi-restraints excluded: chain L residue 3 ARG Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 138 THR Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain L residue 142 PHE Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 111 CYS Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 147 ASN Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 189 GLN Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 94 VAL Chi-restraints excluded: chain N residue 105 LYS Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain N residue 205 PHE Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 158 ARG Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain O residue 189 ARG Chi-restraints excluded: chain O residue 200 ILE Chi-restraints excluded: chain O residue 206 LYS Chi-restraints excluded: chain O residue 212 ASP Chi-restraints excluded: chain O residue 219 TYR Chi-restraints excluded: chain O residue 237 ILE Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 117 HIS Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 143 GLU Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 146 LEU Chi-restraints excluded: chain S residue 156 TYR Chi-restraints excluded: chain S residue 158 LYS Chi-restraints excluded: chain S residue 173 VAL Chi-restraints excluded: chain S residue 188 ILE Chi-restraints excluded: chain S residue 189 TYR Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 263 SER Chi-restraints excluded: chain b residue 25 GLN Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain d residue 20 SER Chi-restraints excluded: chain e residue 79 LYS Chi-restraints excluded: chain f residue 31 LEU Chi-restraints excluded: chain f residue 78 VAL Chi-restraints excluded: chain g residue 34 ILE Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain g residue 66 ASN Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 75 ASP Chi-restraints excluded: chain h residue 87 ILE Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 61 PHE Chi-restraints excluded: chain j residue 82 LYS Chi-restraints excluded: chain j residue 96 LEU Chi-restraints excluded: chain j residue 100 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 773 random chunks: chunk 694 optimal weight: 40.0000 chunk 528 optimal weight: 3.9990 chunk 364 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 335 optimal weight: 3.9990 chunk 472 optimal weight: 1.9990 chunk 705 optimal weight: 40.0000 chunk 747 optimal weight: 30.0000 chunk 368 optimal weight: 8.9990 chunk 668 optimal weight: 0.4980 chunk 201 optimal weight: 9.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN A 570 GLN A 848 ASN ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN A1600 GLN C 180 ASN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 ASN ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 HIS M 201 ASN N 15 GLN ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 73 GLN S 212 HIS b 8 HIS ** b 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 15 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 65132 Z= 0.300 Angle : 0.655 13.511 90610 Z= 0.331 Chirality : 0.041 0.276 10977 Planarity : 0.005 0.081 9985 Dihedral : 18.865 167.288 15050 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.04 % Favored : 94.77 % Rotamer: Outliers : 7.44 % Allowed : 20.36 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.10), residues: 7089 helix: 2.57 (0.09), residues: 3241 sheet: -2.18 (0.17), residues: 808 loop : -1.99 (0.11), residues: 3040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 823 HIS 0.007 0.001 HIS f 25 PHE 0.023 0.002 PHE j 26 TYR 0.036 0.002 TYR G 29 ARG 0.009 0.001 ARG K 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14178 Ramachandran restraints generated. 7089 Oldfield, 0 Emsley, 7089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14178 Ramachandran restraints generated. 7089 Oldfield, 0 Emsley, 7089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1082 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 350 poor density : 732 time to evaluate : 5.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 TYR cc_start: 0.8143 (OUTLIER) cc_final: 0.6987 (t80) REVERT: A 149 MET cc_start: 0.8918 (ptp) cc_final: 0.8691 (ptp) REVERT: A 183 TRP cc_start: 0.9304 (p90) cc_final: 0.8792 (p90) REVERT: A 224 MET cc_start: 0.8378 (mtm) cc_final: 0.7925 (mtp) REVERT: A 308 MET cc_start: 0.9056 (tpp) cc_final: 0.8525 (mmm) REVERT: A 331 PHE cc_start: 0.9429 (OUTLIER) cc_final: 0.8420 (t80) REVERT: A 392 ASN cc_start: 0.8994 (t0) cc_final: 0.8480 (t0) REVERT: A 415 GLU cc_start: 0.5010 (OUTLIER) cc_final: 0.4329 (tm-30) REVERT: A 477 MET cc_start: 0.9290 (mtm) cc_final: 0.8806 (mtp) REVERT: A 514 TYR cc_start: 0.8964 (OUTLIER) cc_final: 0.8420 (m-80) REVERT: A 528 ASN cc_start: 0.8725 (m-40) cc_final: 0.8284 (t0) REVERT: A 553 ASN cc_start: 0.9088 (m-40) cc_final: 0.8832 (m-40) REVERT: A 610 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8605 (ttm-80) REVERT: A 625 LEU cc_start: 0.9589 (mt) cc_final: 0.9372 (mp) REVERT: A 634 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7845 (t70) REVERT: A 682 ASP cc_start: 0.8235 (m-30) cc_final: 0.7958 (m-30) REVERT: A 770 MET cc_start: 0.8893 (pmt) cc_final: 0.8418 (pmm) REVERT: A 813 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8418 (tt0) REVERT: A 933 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8083 (mt-10) REVERT: A 936 GLU cc_start: 0.9166 (tt0) cc_final: 0.8571 (tt0) REVERT: A 969 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8210 (pt) REVERT: A 971 MET cc_start: 0.8666 (mmt) cc_final: 0.7931 (mmt) REVERT: A 1004 ASP cc_start: 0.9059 (OUTLIER) cc_final: 0.8547 (t0) REVERT: A 1014 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8321 (tppt) REVERT: A 1019 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8246 (mp0) REVERT: A 1056 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8841 (mt-10) REVERT: A 1057 MET cc_start: 0.9181 (tmm) cc_final: 0.8529 (tmm) REVERT: A 1069 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9217 (mm) REVERT: A 1114 PHE cc_start: 0.9350 (t80) cc_final: 0.8869 (t80) REVERT: A 1140 ASN cc_start: 0.8950 (t0) cc_final: 0.8305 (p0) REVERT: A 1162 THR cc_start: 0.9519 (OUTLIER) cc_final: 0.9265 (m) REVERT: A 1283 GLU cc_start: 0.7551 (tp30) cc_final: 0.7146 (tp30) REVERT: A 1379 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8767 (ttm) REVERT: A 1558 GLU cc_start: 0.9178 (tp30) cc_final: 0.8929 (tp30) REVERT: A 1586 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7632 (pm20) REVERT: A 1589 LYS cc_start: 0.3396 (OUTLIER) cc_final: 0.3168 (ptpt) REVERT: A 1603 ASN cc_start: 0.9028 (OUTLIER) cc_final: 0.8260 (p0) REVERT: A 1802 MET cc_start: 0.9140 (mmm) cc_final: 0.8635 (mmm) REVERT: A 1803 ARG cc_start: 0.9328 (OUTLIER) cc_final: 0.8703 (ttp-110) REVERT: A 1806 MET cc_start: 0.9238 (mpp) cc_final: 0.8640 (mmm) REVERT: A 1880 PHE cc_start: 0.9207 (t80) cc_final: 0.8068 (t80) REVERT: A 1907 GLN cc_start: 0.9054 (tt0) cc_final: 0.8797 (mm-40) REVERT: A 2048 TRP cc_start: 0.6510 (m100) cc_final: 0.6111 (m100) REVERT: A 2063 TYR cc_start: 0.5597 (t80) cc_final: 0.5009 (t80) REVERT: D 15 TYR cc_start: 0.9138 (t80) cc_final: 0.8918 (t80) REVERT: D 16 ASN cc_start: 0.8602 (m-40) cc_final: 0.8285 (t0) REVERT: D 19 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8684 (mm-30) REVERT: D 53 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8324 (tm-30) REVERT: D 73 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8565 (mp0) REVERT: D 85 THR cc_start: 0.8721 (m) cc_final: 0.8182 (p) REVERT: D 90 ARG cc_start: 0.8800 (ttm-80) cc_final: 0.7774 (ttt180) REVERT: C 116 THR cc_start: 0.9187 (OUTLIER) cc_final: 0.8982 (m) REVERT: C 222 MET cc_start: 0.8736 (mmm) cc_final: 0.8264 (mmm) REVERT: C 282 MET cc_start: 0.8620 (tpt) cc_final: 0.8284 (tpp) REVERT: C 334 HIS cc_start: 0.8379 (m-70) cc_final: 0.7832 (t-90) REVERT: C 364 PHE cc_start: 0.7837 (t80) cc_final: 0.7458 (t80) REVERT: C 396 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8872 (tt) REVERT: C 540 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8518 (mp0) REVERT: C 586 MET cc_start: 0.8592 (tmt) cc_final: 0.8181 (tmm) REVERT: C 600 GLU cc_start: 0.9399 (tp30) cc_final: 0.8686 (tm-30) REVERT: C 658 ASP cc_start: 0.8620 (m-30) cc_final: 0.8357 (m-30) REVERT: C 719 MET cc_start: 0.9118 (tpp) cc_final: 0.8851 (tpp) REVERT: C 760 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6558 (tt) REVERT: C 808 LEU cc_start: 0.9412 (mt) cc_final: 0.9139 (mt) REVERT: C 837 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.6785 (pp30) REVERT: C 931 TYR cc_start: 0.9256 (p90) cc_final: 0.8958 (p90) REVERT: C 965 ASP cc_start: 0.9372 (OUTLIER) cc_final: 0.8983 (p0) REVERT: G 18 GLN cc_start: 0.8648 (tt0) cc_final: 0.7913 (tp40) REVERT: G 29 TYR cc_start: 0.8765 (m-80) cc_final: 0.8476 (m-10) REVERT: G 57 GLU cc_start: 0.9514 (tp30) cc_final: 0.8972 (tp30) REVERT: G 88 GLU cc_start: 0.9196 (tp30) cc_final: 0.8774 (tp30) REVERT: H 315 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9236 (mm) REVERT: H 317 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.8020 (pp) REVERT: H 379 ASP cc_start: 0.8914 (m-30) cc_final: 0.8354 (p0) REVERT: H 425 GLN cc_start: 0.9374 (tt0) cc_final: 0.9083 (tt0) REVERT: H 429 ASN cc_start: 0.9441 (m-40) cc_final: 0.9219 (m110) REVERT: H 477 MET cc_start: 0.8082 (ptm) cc_final: 0.7745 (ptp) REVERT: J 212 GLU cc_start: 0.8866 (mp0) cc_final: 0.8517 (mm-30) REVERT: J 218 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7714 (mtt-85) REVERT: J 231 SER cc_start: 0.9141 (t) cc_final: 0.8811 (t) REVERT: J 332 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8399 (mmt90) REVERT: J 404 CYS cc_start: 0.9068 (t) cc_final: 0.8657 (t) REVERT: J 443 ASN cc_start: 0.8904 (m-40) cc_final: 0.8615 (t0) REVERT: K 62 GLU cc_start: 0.9259 (OUTLIER) cc_final: 0.8813 (tm-30) REVERT: K 73 TYR cc_start: 0.9429 (t80) cc_final: 0.9105 (t80) REVERT: K 106 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7541 (mp) REVERT: K 118 GLN cc_start: 0.8591 (mt0) cc_final: 0.8243 (pm20) REVERT: K 199 ASP cc_start: 0.9173 (m-30) cc_final: 0.8957 (t0) REVERT: K 213 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8154 (mtpt) REVERT: L 10 LYS cc_start: 0.9398 (mmtp) cc_final: 0.8934 (ttpp) REVERT: L 47 GLU cc_start: 0.9150 (tp30) cc_final: 0.8892 (tp30) REVERT: L 50 TRP cc_start: 0.8803 (m-10) cc_final: 0.8484 (m-10) REVERT: L 126 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.7066 (ttt180) REVERT: L 130 GLU cc_start: 0.9070 (pt0) cc_final: 0.8724 (pp20) REVERT: L 142 PHE cc_start: 0.9142 (OUTLIER) cc_final: 0.7520 (p90) REVERT: M 38 SER cc_start: 0.9150 (p) cc_final: 0.8850 (p) REVERT: M 44 ASN cc_start: 0.7578 (OUTLIER) cc_final: 0.7346 (p0) REVERT: M 78 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8729 (mttp) REVERT: M 114 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7056 (ppt-90) REVERT: M 188 TYR cc_start: 0.8732 (m-10) cc_final: 0.8498 (m-10) REVERT: M 214 ASP cc_start: 0.9293 (m-30) cc_final: 0.8703 (t0) REVERT: M 241 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8487 (mm-30) REVERT: N 30 GLN cc_start: 0.9054 (mt0) cc_final: 0.8726 (mt0) REVERT: N 43 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8926 (tt) REVERT: N 93 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8100 (tt) REVERT: N 105 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7643 (pttm) REVERT: N 318 LYS cc_start: 0.8984 (mttt) cc_final: 0.8769 (tmtt) REVERT: O 18 ASP cc_start: 0.8904 (t0) cc_final: 0.8485 (t0) REVERT: O 35 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.7904 (mttm) REVERT: O 62 PHE cc_start: 0.8698 (t80) cc_final: 0.8385 (m-80) REVERT: O 151 MET cc_start: 0.8334 (ptm) cc_final: 0.8089 (ptt) REVERT: O 154 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8449 (mt-10) REVERT: O 184 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8228 (tp30) REVERT: O 189 ARG cc_start: 0.9312 (OUTLIER) cc_final: 0.8883 (mtt-85) REVERT: O 219 TYR cc_start: 0.8402 (OUTLIER) cc_final: 0.7802 (m-80) REVERT: O 228 TYR cc_start: 0.6927 (t80) cc_final: 0.6660 (t80) REVERT: O 233 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8327 (tm-30) REVERT: P 8 GLN cc_start: 0.8110 (pp30) cc_final: 0.7850 (pp30) REVERT: R 9 LYS cc_start: 0.8592 (ttpp) cc_final: 0.8358 (ptmt) REVERT: S 73 GLN cc_start: 0.8840 (mt0) cc_final: 0.8577 (tm-30) REVERT: S 95 ASP cc_start: 0.8969 (t0) cc_final: 0.8696 (t0) REVERT: S 117 HIS cc_start: 0.9195 (OUTLIER) cc_final: 0.8778 (m170) REVERT: S 122 MET cc_start: 0.9209 (mtm) cc_final: 0.9001 (mtm) REVERT: S 126 ILE cc_start: 0.9264 (mm) cc_final: 0.8885 (mm) REVERT: S 156 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.7991 (t80) REVERT: S 163 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8698 (pp20) REVERT: S 189 TYR cc_start: 0.9164 (OUTLIER) cc_final: 0.7643 (t80) REVERT: S 201 THR cc_start: 0.9425 (m) cc_final: 0.9033 (p) REVERT: S 218 THR cc_start: 0.7971 (OUTLIER) cc_final: 0.7699 (p) REVERT: b 11 ARG cc_start: 0.3696 (mtt180) cc_final: 0.2909 (mpp-170) REVERT: b 35 MET cc_start: 0.8701 (mtp) cc_final: 0.8249 (mmp) REVERT: b 39 LYS cc_start: 0.8486 (ttpt) cc_final: 0.7969 (mmtt) REVERT: b 41 MET cc_start: 0.9101 (mmm) cc_final: 0.8830 (mmp) REVERT: b 45 LEU cc_start: 0.8224 (tp) cc_final: 0.7973 (tp) REVERT: b 46 ASN cc_start: 0.8665 (t0) cc_final: 0.8351 (t0) REVERT: b 47 GLU cc_start: 0.8423 (tm-30) cc_final: 0.7881 (pm20) REVERT: b 93 LEU cc_start: 0.8346 (mt) cc_final: 0.7960 (mt) REVERT: b 94 SER cc_start: 0.9359 (p) cc_final: 0.9070 (m) REVERT: d 22 GLU cc_start: 0.8684 (mp0) cc_final: 0.8136 (tp30) REVERT: e 10 MET cc_start: 0.7091 (mpp) cc_final: 0.6671 (ppp) REVERT: e 47 ASP cc_start: 0.7106 (t70) cc_final: 0.6590 (m-30) REVERT: g 8 LYS cc_start: 0.8683 (mptt) cc_final: 0.8173 (tppt) REVERT: g 11 MET cc_start: 0.6312 (mmm) cc_final: 0.5864 (mmm) REVERT: g 14 LYS cc_start: 0.9105 (tttp) cc_final: 0.8902 (tppt) REVERT: g 17 LEU cc_start: 0.7171 (mp) cc_final: 0.6767 (tt) REVERT: g 23 ARG cc_start: 0.6330 (mtm180) cc_final: 0.6085 (mtm180) REVERT: g 59 LEU cc_start: 0.6843 (mm) cc_final: 0.6624 (tp) REVERT: g 72 GLU cc_start: 0.5426 (tm-30) cc_final: 0.4917 (tm-30) REVERT: h 1 MET cc_start: 0.6110 (ptp) cc_final: 0.5509 (pmm) REVERT: h 2 LYS cc_start: 0.8021 (mttm) cc_final: 0.7511 (tppt) REVERT: h 36 MET cc_start: 0.8318 (mtt) cc_final: 0.8076 (mtp) REVERT: h 42 ASP cc_start: 0.9066 (t0) cc_final: 0.8697 (t0) REVERT: h 44 LYS cc_start: 0.8862 (ttpp) cc_final: 0.8542 (mmtt) REVERT: h 90 ASN cc_start: 0.8289 (p0) cc_final: 0.7902 (p0) REVERT: h 102 ASN cc_start: 0.8124 (m-40) cc_final: 0.7866 (t0) REVERT: j 24 PHE cc_start: 0.7724 (t80) cc_final: 0.7472 (t80) REVERT: j 28 HIS cc_start: 0.8080 (m90) cc_final: 0.7571 (t70) REVERT: j 70 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7652 (tp30) REVERT: j 89 ARG cc_start: 0.7230 (ttp-170) cc_final: 0.6615 (mpt180) REVERT: j 92 SER cc_start: 0.9470 (m) cc_final: 0.9094 (p) outliers start: 350 outliers final: 239 residues processed: 999 average time/residue: 0.5663 time to fit residues: 974.2117 Evaluate side-chains 928 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 644 time to evaluate : 4.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 497 GLN Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 610 ARG Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 749 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 944 TYR Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1014 LYS Chi-restraints excluded: chain A residue 1019 GLU Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1314 SER Chi-restraints excluded: chain A residue 1317 ARG Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1346 PHE Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain A residue 1387 VAL Chi-restraints excluded: chain A residue 1431 HIS Chi-restraints excluded: chain A residue 1433 ASP Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1452 LEU Chi-restraints excluded: chain A residue 1491 ILE Chi-restraints excluded: chain A residue 1498 ASP Chi-restraints excluded: chain A residue 1586 GLN Chi-restraints excluded: chain A residue 1589 LYS Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1603 ASN Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1646 ILE Chi-restraints excluded: chain A residue 1648 ILE Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1789 ASN Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1803 ARG Chi-restraints excluded: chain A residue 1881 THR Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 114 ARG Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 681 CYS Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 837 GLN Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain C residue 965 ASP Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 4 ASN Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain H residue 293 LYS Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 306 ASP Chi-restraints excluded: chain H residue 315 LEU Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 352 THR Chi-restraints excluded: chain H residue 368 ASN Chi-restraints excluded: chain H residue 373 ILE Chi-restraints excluded: chain H residue 394 TYR Chi-restraints excluded: chain H residue 457 HIS Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 184 THR Chi-restraints excluded: chain J residue 194 HIS Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 218 ARG Chi-restraints excluded: chain J residue 232 ILE Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 248 ILE Chi-restraints excluded: chain J residue 263 VAL Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 286 THR Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 332 ARG Chi-restraints excluded: chain J residue 334 TRP Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 358 ILE Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 397 GLU Chi-restraints excluded: chain J residue 423 ILE Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 50 ASN Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 87 ASN Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 111 HIS Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 176 ASN Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 196 THR Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain K residue 213 LYS Chi-restraints excluded: chain L residue 3 ARG Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 36 ASP Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 38 SER Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 126 ARG Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain L residue 142 PHE Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 44 ASN Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 111 CYS Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 147 ASN Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 254 ILE Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 94 VAL Chi-restraints excluded: chain N residue 105 LYS Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain N residue 241 ILE Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 158 ARG Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain O residue 189 ARG Chi-restraints excluded: chain O residue 200 ILE Chi-restraints excluded: chain O residue 206 LYS Chi-restraints excluded: chain O residue 219 TYR Chi-restraints excluded: chain O residue 237 ILE Chi-restraints excluded: chain S residue 43 LEU Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 117 HIS Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 143 GLU Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 146 LEU Chi-restraints excluded: chain S residue 156 TYR Chi-restraints excluded: chain S residue 158 LYS Chi-restraints excluded: chain S residue 188 ILE Chi-restraints excluded: chain S residue 189 TYR Chi-restraints excluded: chain S residue 218 THR Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 263 SER Chi-restraints excluded: chain S residue 266 LEU Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain d residue 77 LEU Chi-restraints excluded: chain e residue 79 LYS Chi-restraints excluded: chain f residue 31 LEU Chi-restraints excluded: chain f residue 78 VAL Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 34 ILE Chi-restraints excluded: chain g residue 66 ASN Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain h residue 16 THR Chi-restraints excluded: chain h residue 87 ILE Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 61 PHE Chi-restraints excluded: chain j residue 96 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 773 random chunks: chunk 622 optimal weight: 5.9990 chunk 424 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 556 optimal weight: 10.0000 chunk 308 optimal weight: 0.8980 chunk 637 optimal weight: 2.9990 chunk 516 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 381 optimal weight: 0.9990 chunk 670 optimal weight: 20.0000 chunk 188 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 514 GLN ** C 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 380 GLN ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 360 GLN K 33 GLN ** K 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 155 GLN ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 214 ASN ** b 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 34 ASN j 52 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 65132 Z= 0.365 Angle : 0.682 13.420 90610 Z= 0.345 Chirality : 0.042 0.265 10977 Planarity : 0.005 0.152 9985 Dihedral : 18.808 168.177 15018 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.14 % Favored : 93.69 % Rotamer: Outliers : 8.14 % Allowed : 21.25 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.10), residues: 7089 helix: 2.29 (0.09), residues: 3236 sheet: -2.02 (0.17), residues: 801 loop : -1.93 (0.11), residues: 3052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 823 HIS 0.007 0.001 HIS A1652 PHE 0.020 0.002 PHE A1734 TYR 0.030 0.002 TYR D 75 ARG 0.015 0.001 ARG K 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14178 Ramachandran restraints generated. 7089 Oldfield, 0 Emsley, 7089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14178 Ramachandran restraints generated. 7089 Oldfield, 0 Emsley, 7089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1073 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 383 poor density : 690 time to evaluate : 5.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 TYR cc_start: 0.7879 (OUTLIER) cc_final: 0.6669 (t80) REVERT: A 308 MET cc_start: 0.9092 (tpp) cc_final: 0.8579 (mmm) REVERT: A 331 PHE cc_start: 0.9410 (OUTLIER) cc_final: 0.8424 (t80) REVERT: A 392 ASN cc_start: 0.8961 (t0) cc_final: 0.8491 (t0) REVERT: A 477 MET cc_start: 0.9336 (mtm) cc_final: 0.8882 (mtp) REVERT: A 514 TYR cc_start: 0.8920 (OUTLIER) cc_final: 0.8387 (m-80) REVERT: A 553 ASN cc_start: 0.9091 (m-40) cc_final: 0.8837 (m-40) REVERT: A 610 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8633 (ttm-80) REVERT: A 625 LEU cc_start: 0.9595 (mt) cc_final: 0.9361 (mp) REVERT: A 634 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7810 (t70) REVERT: A 749 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.7405 (ttp-170) REVERT: A 770 MET cc_start: 0.8969 (pmt) cc_final: 0.8569 (pmm) REVERT: A 813 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8416 (tt0) REVERT: A 969 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8222 (pt) REVERT: A 971 MET cc_start: 0.8722 (mmt) cc_final: 0.7985 (mmt) REVERT: A 1004 ASP cc_start: 0.9122 (OUTLIER) cc_final: 0.8541 (t0) REVERT: A 1056 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8878 (mt-10) REVERT: A 1057 MET cc_start: 0.9137 (tmm) cc_final: 0.8503 (tmm) REVERT: A 1114 PHE cc_start: 0.9350 (t80) cc_final: 0.8843 (t80) REVERT: A 1140 ASN cc_start: 0.9039 (t0) cc_final: 0.8396 (p0) REVERT: A 1161 TYR cc_start: 0.8337 (t80) cc_final: 0.7905 (t80) REVERT: A 1162 THR cc_start: 0.9549 (OUTLIER) cc_final: 0.9288 (m) REVERT: A 1283 GLU cc_start: 0.7721 (tp30) cc_final: 0.7474 (tp30) REVERT: A 1301 TYR cc_start: 0.8799 (m-80) cc_final: 0.8584 (m-10) REVERT: A 1310 LYS cc_start: 0.9309 (mmmt) cc_final: 0.8786 (mtmm) REVERT: A 1346 PHE cc_start: 0.9614 (OUTLIER) cc_final: 0.8022 (m-80) REVERT: A 1461 TYR cc_start: 0.8119 (t80) cc_final: 0.7913 (t80) REVERT: A 1558 GLU cc_start: 0.9166 (tp30) cc_final: 0.8879 (tp30) REVERT: A 1586 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7770 (pm20) REVERT: A 1603 ASN cc_start: 0.9010 (OUTLIER) cc_final: 0.8311 (p0) REVERT: A 1802 MET cc_start: 0.9125 (mmm) cc_final: 0.8282 (mmm) REVERT: A 1803 ARG cc_start: 0.9342 (OUTLIER) cc_final: 0.8676 (ttp-110) REVERT: A 1806 MET cc_start: 0.9227 (mpp) cc_final: 0.8058 (mmm) REVERT: A 1880 PHE cc_start: 0.9122 (t80) cc_final: 0.7861 (t80) REVERT: A 1907 GLN cc_start: 0.9042 (tt0) cc_final: 0.8794 (mm-40) REVERT: A 2048 TRP cc_start: 0.6549 (m100) cc_final: 0.6148 (m100) REVERT: A 2063 TYR cc_start: 0.5441 (t80) cc_final: 0.4924 (t80) REVERT: D 16 ASN cc_start: 0.8584 (m-40) cc_final: 0.8179 (t0) REVERT: D 19 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8661 (mm-30) REVERT: D 53 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8293 (tm-30) REVERT: D 73 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8595 (mp0) REVERT: D 85 THR cc_start: 0.8619 (m) cc_final: 0.8133 (p) REVERT: D 90 ARG cc_start: 0.8799 (ttm-80) cc_final: 0.7822 (ttt180) REVERT: C 185 ILE cc_start: 0.9563 (OUTLIER) cc_final: 0.9323 (tt) REVERT: C 222 MET cc_start: 0.8783 (mmm) cc_final: 0.8311 (mmm) REVERT: C 282 MET cc_start: 0.8745 (tpt) cc_final: 0.8387 (tpp) REVERT: C 334 HIS cc_start: 0.8355 (m-70) cc_final: 0.7848 (t-90) REVERT: C 364 PHE cc_start: 0.7897 (t80) cc_final: 0.7488 (t80) REVERT: C 396 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8819 (tt) REVERT: C 540 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8600 (mp0) REVERT: C 658 ASP cc_start: 0.8635 (m-30) cc_final: 0.8405 (m-30) REVERT: C 719 MET cc_start: 0.9186 (tpp) cc_final: 0.8843 (tpp) REVERT: C 760 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6506 (tt) REVERT: C 931 TYR cc_start: 0.9285 (p90) cc_final: 0.8853 (p90) REVERT: C 965 ASP cc_start: 0.9392 (OUTLIER) cc_final: 0.9038 (p0) REVERT: G 45 LYS cc_start: 0.8475 (mmtm) cc_final: 0.8249 (tptt) REVERT: G 49 GLU cc_start: 0.9267 (mm-30) cc_final: 0.9020 (mm-30) REVERT: G 53 GLN cc_start: 0.7776 (pp30) cc_final: 0.7570 (pp30) REVERT: G 54 VAL cc_start: 0.8900 (p) cc_final: 0.8643 (m) REVERT: G 57 GLU cc_start: 0.9544 (tp30) cc_final: 0.9074 (tp30) REVERT: G 88 GLU cc_start: 0.9282 (tp30) cc_final: 0.8868 (tp30) REVERT: H 315 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9245 (mm) REVERT: H 379 ASP cc_start: 0.8926 (m-30) cc_final: 0.8491 (p0) REVERT: H 425 GLN cc_start: 0.9294 (tt0) cc_final: 0.8992 (tt0) REVERT: H 429 ASN cc_start: 0.9409 (m-40) cc_final: 0.9162 (m110) REVERT: H 454 ASP cc_start: 0.7785 (m-30) cc_final: 0.7478 (m-30) REVERT: H 477 MET cc_start: 0.8194 (ptm) cc_final: 0.7824 (ptp) REVERT: J 231 SER cc_start: 0.9055 (t) cc_final: 0.8724 (t) REVERT: J 280 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.7819 (mp10) REVERT: J 332 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8347 (mmt90) REVERT: J 355 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.9041 (t) REVERT: J 377 ASP cc_start: 0.8912 (t0) cc_final: 0.8678 (t0) REVERT: J 404 CYS cc_start: 0.9031 (t) cc_final: 0.8615 (t) REVERT: J 443 ASN cc_start: 0.8931 (m-40) cc_final: 0.8499 (t0) REVERT: K 62 GLU cc_start: 0.9294 (OUTLIER) cc_final: 0.8849 (tm-30) REVERT: K 66 CYS cc_start: 0.9341 (OUTLIER) cc_final: 0.8895 (t) REVERT: K 73 TYR cc_start: 0.9444 (t80) cc_final: 0.9187 (t80) REVERT: K 106 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7673 (mp) REVERT: K 118 GLN cc_start: 0.8577 (mt0) cc_final: 0.8242 (pm20) REVERT: K 199 ASP cc_start: 0.9271 (m-30) cc_final: 0.8868 (t70) REVERT: K 213 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8079 (mtpt) REVERT: L 47 GLU cc_start: 0.9225 (tp30) cc_final: 0.9012 (tp30) REVERT: L 126 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6511 (ttt180) REVERT: L 130 GLU cc_start: 0.9143 (pt0) cc_final: 0.8618 (mm-30) REVERT: L 142 PHE cc_start: 0.9178 (OUTLIER) cc_final: 0.7474 (p90) REVERT: M 38 SER cc_start: 0.9151 (p) cc_final: 0.8910 (p) REVERT: M 44 ASN cc_start: 0.7578 (OUTLIER) cc_final: 0.7366 (p0) REVERT: M 78 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8773 (mttp) REVERT: M 188 TYR cc_start: 0.8778 (m-10) cc_final: 0.8500 (m-10) REVERT: M 214 ASP cc_start: 0.9305 (m-30) cc_final: 0.8725 (t0) REVERT: N 30 GLN cc_start: 0.9068 (mt0) cc_final: 0.8790 (mt0) REVERT: N 43 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8752 (tt) REVERT: N 88 ASP cc_start: 0.8469 (m-30) cc_final: 0.8172 (m-30) REVERT: N 93 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7917 (tt) REVERT: N 105 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7786 (pttm) REVERT: O 35 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.7821 (mttm) REVERT: O 62 PHE cc_start: 0.8701 (t80) cc_final: 0.8408 (m-80) REVERT: O 151 MET cc_start: 0.8363 (ptm) cc_final: 0.8142 (ptt) REVERT: O 154 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8455 (mt-10) REVERT: O 158 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8429 (mmm-85) REVERT: O 184 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8271 (tp30) REVERT: O 189 ARG cc_start: 0.9338 (OUTLIER) cc_final: 0.8943 (mtt-85) REVERT: O 212 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.8149 (p0) REVERT: O 219 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: O 233 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8315 (tm-30) REVERT: P 8 GLN cc_start: 0.8178 (pp30) cc_final: 0.7929 (pp30) REVERT: R 9 LYS cc_start: 0.8656 (ttpp) cc_final: 0.8446 (ptmt) REVERT: S 73 GLN cc_start: 0.8860 (mt0) cc_final: 0.8575 (tm-30) REVERT: S 95 ASP cc_start: 0.8997 (t0) cc_final: 0.8657 (t0) REVERT: S 117 HIS cc_start: 0.9219 (OUTLIER) cc_final: 0.8816 (m170) REVERT: S 126 ILE cc_start: 0.9284 (mm) cc_final: 0.8876 (mm) REVERT: S 156 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.7912 (t80) REVERT: S 163 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8725 (pp20) REVERT: S 189 TYR cc_start: 0.9188 (OUTLIER) cc_final: 0.7672 (t80) REVERT: S 201 THR cc_start: 0.9420 (m) cc_final: 0.9011 (p) REVERT: b 26 ASP cc_start: 0.6136 (m-30) cc_final: 0.5884 (p0) REVERT: b 39 LYS cc_start: 0.8598 (ttpt) cc_final: 0.8031 (mmtt) REVERT: b 41 MET cc_start: 0.9195 (mmm) cc_final: 0.8930 (mmp) REVERT: b 46 ASN cc_start: 0.8831 (t0) cc_final: 0.8618 (t0) REVERT: b 47 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7846 (pm20) REVERT: b 93 LEU cc_start: 0.8276 (mt) cc_final: 0.8007 (mt) REVERT: b 94 SER cc_start: 0.9370 (p) cc_final: 0.9003 (m) REVERT: e 47 ASP cc_start: 0.7111 (t70) cc_final: 0.6579 (m-30) REVERT: e 82 LEU cc_start: 0.6957 (tp) cc_final: 0.6435 (pp) REVERT: g 8 LYS cc_start: 0.8769 (mptt) cc_final: 0.8290 (tppt) REVERT: g 11 MET cc_start: 0.6328 (mmm) cc_final: 0.5927 (mmm) REVERT: g 17 LEU cc_start: 0.7121 (mp) cc_final: 0.6728 (tt) REVERT: g 23 ARG cc_start: 0.6312 (mtm180) cc_final: 0.6061 (mtm-85) REVERT: g 35 PHE cc_start: 0.8718 (m-80) cc_final: 0.8512 (t80) REVERT: g 59 LEU cc_start: 0.6968 (mm) cc_final: 0.6712 (tp) REVERT: g 72 GLU cc_start: 0.5212 (tm-30) cc_final: 0.4897 (tm-30) REVERT: h 1 MET cc_start: 0.6094 (ptp) cc_final: 0.5288 (pmm) REVERT: h 2 LYS cc_start: 0.8062 (mttm) cc_final: 0.7545 (tppt) REVERT: h 42 ASP cc_start: 0.8982 (t0) cc_final: 0.8632 (t0) REVERT: h 44 LYS cc_start: 0.8817 (ttpp) cc_final: 0.8507 (mmtt) REVERT: h 102 ASN cc_start: 0.8198 (m-40) cc_final: 0.7919 (t0) REVERT: j 28 HIS cc_start: 0.7965 (m90) cc_final: 0.7703 (p-80) REVERT: j 70 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7736 (tp30) REVERT: j 89 ARG cc_start: 0.7334 (ttp-170) cc_final: 0.6774 (mpt180) REVERT: j 90 PHE cc_start: 0.8758 (m-80) cc_final: 0.8499 (t80) REVERT: j 92 SER cc_start: 0.9440 (m) cc_final: 0.9029 (p) outliers start: 383 outliers final: 257 residues processed: 996 average time/residue: 0.5578 time to fit residues: 962.5102 Evaluate side-chains 934 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 636 time to evaluate : 4.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 610 ARG Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 749 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 944 TYR Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1317 ARG Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1346 PHE Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain A residue 1387 VAL Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1431 HIS Chi-restraints excluded: chain A residue 1433 ASP Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1452 LEU Chi-restraints excluded: chain A residue 1491 ILE Chi-restraints excluded: chain A residue 1498 ASP Chi-restraints excluded: chain A residue 1586 GLN Chi-restraints excluded: chain A residue 1589 LYS Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1603 ASN Chi-restraints excluded: chain A residue 1614 ILE Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1646 ILE Chi-restraints excluded: chain A residue 1648 ILE Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1789 ASN Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1803 ARG Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 500 ARG Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 681 CYS Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain C residue 965 ASP Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 4 ASN Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 306 ASP Chi-restraints excluded: chain H residue 315 LEU Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 352 THR Chi-restraints excluded: chain H residue 373 ILE Chi-restraints excluded: chain H residue 394 TYR Chi-restraints excluded: chain H residue 457 HIS Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 184 THR Chi-restraints excluded: chain J residue 194 HIS Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 232 ILE Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 248 ILE Chi-restraints excluded: chain J residue 261 THR Chi-restraints excluded: chain J residue 263 VAL Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 280 GLN Chi-restraints excluded: chain J residue 286 THR Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 332 ARG Chi-restraints excluded: chain J residue 334 TRP Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 355 THR Chi-restraints excluded: chain J residue 358 ILE Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 397 GLU Chi-restraints excluded: chain J residue 423 ILE Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 66 CYS Chi-restraints excluded: chain K residue 87 ASN Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 111 HIS Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 162 GLU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 176 ASN Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 196 THR Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain K residue 213 LYS Chi-restraints excluded: chain L residue 3 ARG Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 36 ASP Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 38 SER Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 108 CYS Chi-restraints excluded: chain L residue 126 ARG Chi-restraints excluded: chain L residue 138 THR Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain L residue 142 PHE Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 44 ASN Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 111 CYS Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 147 ASN Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 181 CYS Chi-restraints excluded: chain M residue 189 GLN Chi-restraints excluded: chain M residue 254 ILE Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 94 VAL Chi-restraints excluded: chain N residue 105 LYS Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 158 ARG Chi-restraints excluded: chain O residue 179 SER Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain O residue 189 ARG Chi-restraints excluded: chain O residue 200 ILE Chi-restraints excluded: chain O residue 206 LYS Chi-restraints excluded: chain O residue 212 ASP Chi-restraints excluded: chain O residue 219 TYR Chi-restraints excluded: chain O residue 237 ILE Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 117 HIS Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 143 GLU Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 146 LEU Chi-restraints excluded: chain S residue 156 TYR Chi-restraints excluded: chain S residue 158 LYS Chi-restraints excluded: chain S residue 188 ILE Chi-restraints excluded: chain S residue 189 TYR Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 234 ASN Chi-restraints excluded: chain S residue 263 SER Chi-restraints excluded: chain S residue 266 LEU Chi-restraints excluded: chain b residue 38 ASP Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 95 THR Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain d residue 20 SER Chi-restraints excluded: chain d residue 77 LEU Chi-restraints excluded: chain f residue 31 LEU Chi-restraints excluded: chain f residue 78 VAL Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 34 ILE Chi-restraints excluded: chain g residue 66 ASN Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain h residue 6 PHE Chi-restraints excluded: chain h residue 16 THR Chi-restraints excluded: chain j residue 61 PHE Chi-restraints excluded: chain j residue 94 LEU Chi-restraints excluded: chain j residue 96 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 773 random chunks: chunk 251 optimal weight: 0.6980 chunk 672 optimal weight: 30.0000 chunk 147 optimal weight: 2.9990 chunk 438 optimal weight: 6.9990 chunk 184 optimal weight: 0.5980 chunk 747 optimal weight: 20.0000 chunk 620 optimal weight: 30.0000 chunk 346 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 247 optimal weight: 3.9990 chunk 392 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 GLN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 ASN A 636 HIS ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 380 GLN ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 HIS ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 35 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 65132 Z= 0.208 Angle : 0.614 13.566 90610 Z= 0.307 Chirality : 0.039 0.221 10977 Planarity : 0.004 0.154 9985 Dihedral : 18.626 165.681 15000 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.63 % Favored : 95.22 % Rotamer: Outliers : 6.33 % Allowed : 23.29 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.10), residues: 7089 helix: 2.49 (0.09), residues: 3219 sheet: -1.85 (0.17), residues: 816 loop : -1.77 (0.11), residues: 3054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 221 HIS 0.012 0.001 HIS g 55 PHE 0.024 0.001 PHE D 47 TYR 0.036 0.001 TYR C 862 ARG 0.013 0.001 ARG K 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14178 Ramachandran restraints generated. 7089 Oldfield, 0 Emsley, 7089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14178 Ramachandran restraints generated. 7089 Oldfield, 0 Emsley, 7089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1037 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 739 time to evaluate : 5.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 TYR cc_start: 0.8170 (OUTLIER) cc_final: 0.6821 (t80) REVERT: A 308 MET cc_start: 0.8909 (tpp) cc_final: 0.8477 (mmm) REVERT: A 331 PHE cc_start: 0.9356 (OUTLIER) cc_final: 0.8426 (t80) REVERT: A 392 ASN cc_start: 0.8941 (t0) cc_final: 0.8477 (t0) REVERT: A 412 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.5926 (tm-30) REVERT: A 425 ASP cc_start: 0.6900 (OUTLIER) cc_final: 0.6367 (t0) REVERT: A 477 MET cc_start: 0.9284 (mtm) cc_final: 0.8801 (mtp) REVERT: A 514 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.8219 (m-80) REVERT: A 553 ASN cc_start: 0.9002 (m-40) cc_final: 0.8612 (m-40) REVERT: A 610 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.8640 (ttm-80) REVERT: A 634 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7734 (t70) REVERT: A 701 CYS cc_start: 0.7933 (t) cc_final: 0.7326 (t) REVERT: A 770 MET cc_start: 0.8877 (pmt) cc_final: 0.8474 (pmm) REVERT: A 813 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8323 (tt0) REVERT: A 933 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8097 (mm-30) REVERT: A 952 ASN cc_start: 0.9102 (m-40) cc_final: 0.8901 (m110) REVERT: A 969 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8071 (pt) REVERT: A 971 MET cc_start: 0.8618 (mmt) cc_final: 0.8015 (mmt) REVERT: A 992 ASP cc_start: 0.9166 (m-30) cc_final: 0.8658 (p0) REVERT: A 1004 ASP cc_start: 0.9078 (OUTLIER) cc_final: 0.8593 (t0) REVERT: A 1051 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7649 (pt0) REVERT: A 1056 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8924 (mt-10) REVERT: A 1057 MET cc_start: 0.9115 (tmm) cc_final: 0.8486 (tmm) REVERT: A 1114 PHE cc_start: 0.9275 (t80) cc_final: 0.8783 (t80) REVERT: A 1140 ASN cc_start: 0.9022 (t0) cc_final: 0.8389 (p0) REVERT: A 1161 TYR cc_start: 0.8189 (t80) cc_final: 0.7670 (t80) REVERT: A 1162 THR cc_start: 0.9489 (OUTLIER) cc_final: 0.9274 (m) REVERT: A 1261 SER cc_start: 0.8575 (t) cc_final: 0.8205 (p) REVERT: A 1283 GLU cc_start: 0.7487 (tp30) cc_final: 0.7075 (tp30) REVERT: A 1301 TYR cc_start: 0.8757 (m-80) cc_final: 0.8536 (m-10) REVERT: A 1315 ARG cc_start: 0.8307 (ttm-80) cc_final: 0.7948 (tpp-160) REVERT: A 1461 TYR cc_start: 0.8032 (t80) cc_final: 0.7812 (t80) REVERT: A 1558 GLU cc_start: 0.9165 (tp30) cc_final: 0.8879 (tp30) REVERT: A 1586 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7781 (pm20) REVERT: A 1603 ASN cc_start: 0.9098 (OUTLIER) cc_final: 0.8822 (p0) REVERT: A 1802 MET cc_start: 0.9132 (mmm) cc_final: 0.8543 (mmm) REVERT: A 1803 ARG cc_start: 0.9328 (OUTLIER) cc_final: 0.8659 (ttp-110) REVERT: A 1806 MET cc_start: 0.9177 (mpp) cc_final: 0.8281 (mmm) REVERT: A 1880 PHE cc_start: 0.9191 (t80) cc_final: 0.7926 (t80) REVERT: A 1907 GLN cc_start: 0.9022 (tt0) cc_final: 0.8820 (mm-40) REVERT: A 2048 TRP cc_start: 0.6535 (m100) cc_final: 0.6114 (m100) REVERT: A 2063 TYR cc_start: 0.5428 (t80) cc_final: 0.4926 (t80) REVERT: D 16 ASN cc_start: 0.8559 (m-40) cc_final: 0.8159 (t0) REVERT: D 19 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8671 (mm-30) REVERT: D 47 PHE cc_start: 0.8740 (m-80) cc_final: 0.8486 (m-80) REVERT: D 53 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8220 (tm-30) REVERT: D 73 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8550 (mp0) REVERT: D 85 THR cc_start: 0.8613 (m) cc_final: 0.8172 (p) REVERT: D 90 ARG cc_start: 0.8766 (ttm-80) cc_final: 0.7776 (ttt180) REVERT: C 185 ILE cc_start: 0.9536 (OUTLIER) cc_final: 0.9329 (tt) REVERT: C 222 MET cc_start: 0.8701 (mmm) cc_final: 0.8294 (mmm) REVERT: C 238 VAL cc_start: 0.9608 (t) cc_final: 0.9390 (m) REVERT: C 251 GLN cc_start: 0.9127 (tp-100) cc_final: 0.8767 (tp-100) REVERT: C 334 HIS cc_start: 0.8277 (m-70) cc_final: 0.7761 (t-90) REVERT: C 364 PHE cc_start: 0.7870 (t80) cc_final: 0.7536 (t80) REVERT: C 540 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8607 (mp0) REVERT: C 600 GLU cc_start: 0.9361 (tp30) cc_final: 0.8603 (mt-10) REVERT: C 658 ASP cc_start: 0.8597 (m-30) cc_final: 0.8337 (m-30) REVERT: C 719 MET cc_start: 0.9154 (tpp) cc_final: 0.8795 (tpp) REVERT: C 760 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.6044 (tt) REVERT: C 931 TYR cc_start: 0.9178 (p90) cc_final: 0.8899 (p90) REVERT: C 965 ASP cc_start: 0.9335 (OUTLIER) cc_final: 0.8822 (p0) REVERT: G 33 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8508 (pm20) REVERT: G 53 GLN cc_start: 0.7969 (pp30) cc_final: 0.7761 (pp30) REVERT: G 54 VAL cc_start: 0.8976 (p) cc_final: 0.8679 (m) REVERT: G 57 GLU cc_start: 0.9540 (tp30) cc_final: 0.9057 (tp30) REVERT: G 88 GLU cc_start: 0.9114 (tp30) cc_final: 0.8563 (tp30) REVERT: G 91 ARG cc_start: 0.8705 (mtt180) cc_final: 0.7643 (mmp-170) REVERT: H 315 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9236 (mm) REVERT: H 379 ASP cc_start: 0.8858 (m-30) cc_final: 0.8490 (p0) REVERT: H 402 LEU cc_start: 0.5777 (OUTLIER) cc_final: 0.5528 (mt) REVERT: H 417 ARG cc_start: 0.8362 (ptt90) cc_final: 0.8116 (ptm160) REVERT: H 425 GLN cc_start: 0.9223 (tt0) cc_final: 0.8900 (tt0) REVERT: H 429 ASN cc_start: 0.9322 (m-40) cc_final: 0.9110 (m110) REVERT: H 454 ASP cc_start: 0.7658 (m-30) cc_final: 0.7262 (m-30) REVERT: H 477 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7700 (ptp) REVERT: H 480 ARG cc_start: 0.7458 (ppt170) cc_final: 0.6805 (mmp80) REVERT: J 231 SER cc_start: 0.8866 (t) cc_final: 0.8509 (t) REVERT: J 237 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7347 (p0) REVERT: J 245 ASP cc_start: 0.8863 (m-30) cc_final: 0.8584 (t0) REVERT: J 280 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7993 (mp10) REVERT: J 332 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8385 (mmt90) REVERT: J 404 CYS cc_start: 0.8945 (t) cc_final: 0.8566 (t) REVERT: J 443 ASN cc_start: 0.8828 (m-40) cc_final: 0.8433 (t0) REVERT: K 62 GLU cc_start: 0.9282 (OUTLIER) cc_final: 0.8825 (tm-30) REVERT: K 73 TYR cc_start: 0.9389 (t80) cc_final: 0.9104 (t80) REVERT: K 106 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7777 (mp) REVERT: K 118 GLN cc_start: 0.8529 (mt0) cc_final: 0.8198 (pm20) REVERT: K 149 MET cc_start: 0.8546 (tpp) cc_final: 0.7922 (tpt) REVERT: K 199 ASP cc_start: 0.9172 (m-30) cc_final: 0.8840 (t0) REVERT: K 213 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8080 (mtpt) REVERT: L 10 LYS cc_start: 0.9334 (mmtp) cc_final: 0.8967 (ttpp) REVERT: L 47 GLU cc_start: 0.9170 (tp30) cc_final: 0.8897 (tp30) REVERT: L 50 TRP cc_start: 0.8834 (m-10) cc_final: 0.8536 (m-10) REVERT: L 130 GLU cc_start: 0.9135 (pt0) cc_final: 0.8607 (mm-30) REVERT: L 142 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.7436 (p90) REVERT: M 78 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8667 (mttp) REVERT: M 188 TYR cc_start: 0.8778 (m-10) cc_final: 0.8496 (m-10) REVERT: M 197 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8587 (mm-30) REVERT: M 214 ASP cc_start: 0.9293 (m-30) cc_final: 0.8726 (t0) REVERT: N 30 GLN cc_start: 0.8994 (mt0) cc_final: 0.8716 (mt0) REVERT: N 43 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8878 (tt) REVERT: N 88 ASP cc_start: 0.8347 (m-30) cc_final: 0.8039 (m-30) REVERT: N 93 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8052 (tt) REVERT: N 105 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7654 (pttm) REVERT: N 254 GLN cc_start: 0.6162 (pt0) cc_final: 0.5448 (mm110) REVERT: O 18 ASP cc_start: 0.8809 (t0) cc_final: 0.8315 (t0) REVERT: O 28 TYR cc_start: 0.8671 (m-10) cc_final: 0.8425 (m-10) REVERT: O 35 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8103 (mttm) REVERT: O 62 PHE cc_start: 0.8626 (t80) cc_final: 0.8388 (m-80) REVERT: O 154 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8461 (mt-10) REVERT: O 161 ASN cc_start: 0.7989 (t0) cc_final: 0.7708 (t0) REVERT: O 184 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8222 (tp30) REVERT: O 189 ARG cc_start: 0.9349 (OUTLIER) cc_final: 0.8958 (mtt-85) REVERT: S 95 ASP cc_start: 0.9037 (t0) cc_final: 0.8601 (t0) REVERT: S 117 HIS cc_start: 0.9156 (OUTLIER) cc_final: 0.8655 (m170) REVERT: S 126 ILE cc_start: 0.9284 (mm) cc_final: 0.8865 (mm) REVERT: S 156 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.7816 (t80) REVERT: S 163 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8707 (pp20) REVERT: S 189 TYR cc_start: 0.9184 (OUTLIER) cc_final: 0.7690 (t80) REVERT: S 201 THR cc_start: 0.9467 (m) cc_final: 0.9092 (p) REVERT: S 218 THR cc_start: 0.7898 (OUTLIER) cc_final: 0.7616 (p) REVERT: b 35 MET cc_start: 0.8887 (mtp) cc_final: 0.7978 (mmm) REVERT: b 39 LYS cc_start: 0.8685 (ttpt) cc_final: 0.8202 (mmtt) REVERT: b 41 MET cc_start: 0.9187 (mmm) cc_final: 0.8914 (mmp) REVERT: b 46 ASN cc_start: 0.8831 (t0) cc_final: 0.8463 (t0) REVERT: b 47 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7912 (pm20) REVERT: b 93 LEU cc_start: 0.8429 (mt) cc_final: 0.8105 (mt) REVERT: b 94 SER cc_start: 0.9376 (p) cc_final: 0.9095 (m) REVERT: e 47 ASP cc_start: 0.7092 (t70) cc_final: 0.6553 (m-30) REVERT: g 8 LYS cc_start: 0.8752 (mptt) cc_final: 0.8195 (tppt) REVERT: g 11 MET cc_start: 0.6291 (mmm) cc_final: 0.5212 (mmm) REVERT: g 17 LEU cc_start: 0.7278 (mp) cc_final: 0.6805 (tt) REVERT: g 59 LEU cc_start: 0.6827 (mm) cc_final: 0.6567 (tp) REVERT: g 72 GLU cc_start: 0.4976 (tm-30) cc_final: 0.4620 (tm-30) REVERT: h 1 MET cc_start: 0.6203 (ptp) cc_final: 0.5619 (pmm) REVERT: h 2 LYS cc_start: 0.8058 (mttm) cc_final: 0.7535 (tppt) REVERT: h 42 ASP cc_start: 0.8980 (t0) cc_final: 0.8602 (t0) REVERT: h 44 LYS cc_start: 0.8825 (ttpp) cc_final: 0.8522 (mmtt) REVERT: h 102 ASN cc_start: 0.8196 (m-40) cc_final: 0.7922 (t0) REVERT: j 24 PHE cc_start: 0.7918 (t80) cc_final: 0.7603 (t80) REVERT: j 27 LYS cc_start: 0.7508 (mmtt) cc_final: 0.7108 (ptpt) REVERT: j 28 HIS cc_start: 0.8015 (m90) cc_final: 0.7695 (p-80) REVERT: j 38 MET cc_start: 0.5251 (mmm) cc_final: 0.5018 (mmm) REVERT: j 70 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7741 (tp30) REVERT: j 89 ARG cc_start: 0.7253 (ttp-170) cc_final: 0.6707 (mpt180) REVERT: j 90 PHE cc_start: 0.8688 (m-80) cc_final: 0.8464 (t80) REVERT: j 92 SER cc_start: 0.9505 (m) cc_final: 0.9146 (p) outliers start: 298 outliers final: 198 residues processed: 971 average time/residue: 0.5671 time to fit residues: 953.9497 Evaluate side-chains 896 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 659 time to evaluate : 4.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 610 ARG Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 749 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 944 TYR Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1317 ARG Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain A residue 1420 THR Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1433 ASP Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1498 ASP Chi-restraints excluded: chain A residue 1586 GLN Chi-restraints excluded: chain A residue 1589 LYS Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1603 ASN Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1646 ILE Chi-restraints excluded: chain A residue 1648 ILE Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1803 ARG Chi-restraints excluded: chain A residue 1881 THR Chi-restraints excluded: chain A residue 2031 THR Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 500 ARG Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain C residue 965 ASP Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 33 GLN Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 306 ASP Chi-restraints excluded: chain H residue 315 LEU Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 373 ILE Chi-restraints excluded: chain H residue 394 TYR Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 457 HIS Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 477 MET Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 161 ASP Chi-restraints excluded: chain J residue 184 THR Chi-restraints excluded: chain J residue 194 HIS Chi-restraints excluded: chain J residue 232 ILE Chi-restraints excluded: chain J residue 237 ASP Chi-restraints excluded: chain J residue 248 ILE Chi-restraints excluded: chain J residue 261 THR Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 280 GLN Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 332 ARG Chi-restraints excluded: chain J residue 334 TRP Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 358 ILE Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 423 ILE Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 87 ASN Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 111 HIS Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 196 THR Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain K residue 213 LYS Chi-restraints excluded: chain L residue 3 ARG Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 36 ASP Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 38 SER Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 84 GLU Chi-restraints excluded: chain L residue 108 CYS Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain L residue 142 PHE Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 111 CYS Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 147 ASN Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 189 GLN Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 94 VAL Chi-restraints excluded: chain N residue 105 LYS Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 205 PHE Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 179 SER Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain O residue 189 ARG Chi-restraints excluded: chain O residue 206 LYS Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain S residue 43 LEU Chi-restraints excluded: chain S residue 117 HIS Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 143 GLU Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 146 LEU Chi-restraints excluded: chain S residue 156 TYR Chi-restraints excluded: chain S residue 158 LYS Chi-restraints excluded: chain S residue 188 ILE Chi-restraints excluded: chain S residue 189 TYR Chi-restraints excluded: chain S residue 218 THR Chi-restraints excluded: chain S residue 234 ASN Chi-restraints excluded: chain S residue 263 SER Chi-restraints excluded: chain S residue 266 LEU Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain d residue 74 VAL Chi-restraints excluded: chain d residue 77 LEU Chi-restraints excluded: chain e residue 10 MET Chi-restraints excluded: chain e residue 14 ILE Chi-restraints excluded: chain e residue 53 VAL Chi-restraints excluded: chain f residue 31 LEU Chi-restraints excluded: chain f residue 78 VAL Chi-restraints excluded: chain g residue 34 ILE Chi-restraints excluded: chain g residue 66 ASN Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain j residue 61 PHE Chi-restraints excluded: chain j residue 94 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 773 random chunks: chunk 721 optimal weight: 50.0000 chunk 84 optimal weight: 0.7980 chunk 426 optimal weight: 3.9990 chunk 546 optimal weight: 0.0770 chunk 423 optimal weight: 0.7980 chunk 629 optimal weight: 40.0000 chunk 417 optimal weight: 3.9990 chunk 745 optimal weight: 8.9990 chunk 466 optimal weight: 1.9990 chunk 454 optimal weight: 6.9990 chunk 343 optimal weight: 4.9990 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 367 GLN ** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 380 GLN J 126 HIS ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 ASN ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 65132 Z= 0.228 Angle : 0.618 13.573 90610 Z= 0.308 Chirality : 0.039 0.221 10977 Planarity : 0.004 0.069 9985 Dihedral : 18.517 167.016 14987 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.18 % Favored : 94.64 % Rotamer: Outliers : 6.35 % Allowed : 24.25 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.10), residues: 7089 helix: 2.48 (0.09), residues: 3233 sheet: -1.69 (0.17), residues: 838 loop : -1.67 (0.11), residues: 3018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 823 HIS 0.005 0.001 HIS A 948 PHE 0.015 0.001 PHE J 198 TYR 0.031 0.001 TYR C 862 ARG 0.007 0.000 ARG K 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14178 Ramachandran restraints generated. 7089 Oldfield, 0 Emsley, 7089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14178 Ramachandran restraints generated. 7089 Oldfield, 0 Emsley, 7089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 986 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 299 poor density : 687 time to evaluate : 5.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.6796 (t80) REVERT: A 183 TRP cc_start: 0.9319 (p90) cc_final: 0.8809 (p90) REVERT: A 308 MET cc_start: 0.8942 (tpp) cc_final: 0.8550 (mmm) REVERT: A 331 PHE cc_start: 0.9349 (OUTLIER) cc_final: 0.8336 (t80) REVERT: A 392 ASN cc_start: 0.8950 (t0) cc_final: 0.8521 (t0) REVERT: A 415 GLU cc_start: 0.4929 (OUTLIER) cc_final: 0.4033 (tm-30) REVERT: A 425 ASP cc_start: 0.6899 (OUTLIER) cc_final: 0.6352 (t0) REVERT: A 477 MET cc_start: 0.9324 (mtm) cc_final: 0.8824 (mtp) REVERT: A 514 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.8144 (m-80) REVERT: A 553 ASN cc_start: 0.9002 (m-40) cc_final: 0.8618 (m-40) REVERT: A 595 TYR cc_start: 0.9253 (m-80) cc_final: 0.8925 (m-80) REVERT: A 610 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8597 (ttm-80) REVERT: A 634 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7659 (t70) REVERT: A 701 CYS cc_start: 0.8105 (t) cc_final: 0.7571 (t) REVERT: A 755 ASP cc_start: 0.9040 (t0) cc_final: 0.8676 (t0) REVERT: A 770 MET cc_start: 0.8902 (pmt) cc_final: 0.8602 (pmm) REVERT: A 813 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8323 (tt0) REVERT: A 933 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8069 (mm-30) REVERT: A 952 ASN cc_start: 0.9114 (m-40) cc_final: 0.8905 (m110) REVERT: A 969 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8076 (pt) REVERT: A 971 MET cc_start: 0.8640 (mmt) cc_final: 0.8023 (mmt) REVERT: A 1004 ASP cc_start: 0.9039 (OUTLIER) cc_final: 0.8562 (t0) REVERT: A 1051 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7696 (pt0) REVERT: A 1056 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8921 (mt-10) REVERT: A 1057 MET cc_start: 0.9074 (tmm) cc_final: 0.8480 (tmm) REVERT: A 1114 PHE cc_start: 0.9294 (t80) cc_final: 0.8835 (t80) REVERT: A 1140 ASN cc_start: 0.9021 (t0) cc_final: 0.8391 (p0) REVERT: A 1161 TYR cc_start: 0.8197 (t80) cc_final: 0.7798 (t80) REVERT: A 1261 SER cc_start: 0.8582 (t) cc_final: 0.8240 (p) REVERT: A 1283 GLU cc_start: 0.7478 (tp30) cc_final: 0.7167 (tp30) REVERT: A 1315 ARG cc_start: 0.8319 (ttm-80) cc_final: 0.8042 (tpp-160) REVERT: A 1558 GLU cc_start: 0.9172 (tp30) cc_final: 0.8896 (tp30) REVERT: A 1586 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7862 (pm20) REVERT: A 1603 ASN cc_start: 0.8989 (OUTLIER) cc_final: 0.8756 (p0) REVERT: A 1802 MET cc_start: 0.9140 (mmm) cc_final: 0.8624 (mmm) REVERT: A 1803 ARG cc_start: 0.9333 (OUTLIER) cc_final: 0.8662 (ttp-110) REVERT: A 1806 MET cc_start: 0.9120 (mpp) cc_final: 0.8065 (mmp) REVERT: A 1880 PHE cc_start: 0.9182 (t80) cc_final: 0.7878 (t80) REVERT: A 1907 GLN cc_start: 0.9015 (tt0) cc_final: 0.8792 (mm-40) REVERT: A 2048 TRP cc_start: 0.6527 (m100) cc_final: 0.6151 (m100) REVERT: A 2063 TYR cc_start: 0.5588 (t80) cc_final: 0.5116 (t80) REVERT: D 16 ASN cc_start: 0.8553 (m-40) cc_final: 0.8147 (t0) REVERT: D 19 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8625 (mm-30) REVERT: D 47 PHE cc_start: 0.8688 (m-80) cc_final: 0.8449 (m-80) REVERT: D 53 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8220 (tm-30) REVERT: D 73 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8546 (mp0) REVERT: D 85 THR cc_start: 0.8570 (m) cc_final: 0.8142 (p) REVERT: D 90 ARG cc_start: 0.8764 (ttm-80) cc_final: 0.7781 (ttt180) REVERT: C 116 THR cc_start: 0.9035 (OUTLIER) cc_final: 0.8803 (m) REVERT: C 185 ILE cc_start: 0.9576 (OUTLIER) cc_final: 0.9352 (tt) REVERT: C 222 MET cc_start: 0.8694 (mmm) cc_final: 0.8353 (mmm) REVERT: C 225 THR cc_start: 0.9112 (p) cc_final: 0.8672 (p) REVERT: C 251 GLN cc_start: 0.9101 (tp-100) cc_final: 0.8772 (tp-100) REVERT: C 334 HIS cc_start: 0.8249 (m-70) cc_final: 0.7737 (t-90) REVERT: C 364 PHE cc_start: 0.7890 (t80) cc_final: 0.7571 (t80) REVERT: C 540 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8626 (mp0) REVERT: C 600 GLU cc_start: 0.9305 (tp30) cc_final: 0.8510 (mt-10) REVERT: C 658 ASP cc_start: 0.8492 (m-30) cc_final: 0.8212 (m-30) REVERT: C 719 MET cc_start: 0.9165 (tpp) cc_final: 0.8814 (tpp) REVERT: C 760 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6534 (tt) REVERT: C 931 TYR cc_start: 0.9194 (p90) cc_final: 0.8901 (p90) REVERT: C 965 ASP cc_start: 0.9344 (OUTLIER) cc_final: 0.8835 (p0) REVERT: G 17 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8757 (mt-10) REVERT: G 33 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8490 (pm20) REVERT: G 57 GLU cc_start: 0.9550 (tp30) cc_final: 0.9092 (tp30) REVERT: G 88 GLU cc_start: 0.9113 (tp30) cc_final: 0.8564 (tp30) REVERT: G 91 ARG cc_start: 0.8634 (mtt180) cc_final: 0.7554 (mmp-170) REVERT: H 315 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9245 (mm) REVERT: H 379 ASP cc_start: 0.8832 (m-30) cc_final: 0.8484 (p0) REVERT: H 402 LEU cc_start: 0.5413 (OUTLIER) cc_final: 0.5169 (mt) REVERT: H 417 ARG cc_start: 0.8303 (ptt90) cc_final: 0.8037 (ttp80) REVERT: H 425 GLN cc_start: 0.9227 (tt0) cc_final: 0.8889 (tt0) REVERT: H 429 ASN cc_start: 0.9309 (m-40) cc_final: 0.9092 (m110) REVERT: H 454 ASP cc_start: 0.7688 (m-30) cc_final: 0.7293 (m-30) REVERT: H 477 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7599 (ptp) REVERT: H 480 ARG cc_start: 0.7308 (ppt170) cc_final: 0.6599 (mmp80) REVERT: J 231 SER cc_start: 0.8854 (t) cc_final: 0.8518 (t) REVERT: J 237 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7531 (p0) REVERT: J 253 MET cc_start: 0.8934 (mmm) cc_final: 0.8608 (mmt) REVERT: J 280 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7970 (mp10) REVERT: J 332 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8390 (mmt90) REVERT: J 404 CYS cc_start: 0.8824 (t) cc_final: 0.8154 (t) REVERT: J 443 ASN cc_start: 0.8810 (m-40) cc_final: 0.8341 (t0) REVERT: K 62 GLU cc_start: 0.9305 (tm-30) cc_final: 0.8843 (tm-30) REVERT: K 75 GLN cc_start: 0.8697 (tt0) cc_final: 0.8449 (tm-30) REVERT: K 106 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7810 (mp) REVERT: K 118 GLN cc_start: 0.8530 (mt0) cc_final: 0.8198 (pm20) REVERT: K 149 MET cc_start: 0.8572 (tpp) cc_final: 0.7968 (tpt) REVERT: K 199 ASP cc_start: 0.9209 (m-30) cc_final: 0.8836 (t70) REVERT: K 213 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7958 (mtpt) REVERT: L 10 LYS cc_start: 0.9317 (mmtp) cc_final: 0.8927 (ttpp) REVERT: L 47 GLU cc_start: 0.9159 (tp30) cc_final: 0.8887 (tp30) REVERT: L 50 TRP cc_start: 0.8856 (m-10) cc_final: 0.8524 (m-10) REVERT: L 130 GLU cc_start: 0.9222 (pt0) cc_final: 0.8653 (mm-30) REVERT: L 142 PHE cc_start: 0.9155 (OUTLIER) cc_final: 0.7394 (p90) REVERT: M 78 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8762 (mttp) REVERT: M 114 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7706 (ptt-90) REVERT: M 188 TYR cc_start: 0.8816 (m-10) cc_final: 0.8532 (m-10) REVERT: M 214 ASP cc_start: 0.9294 (m-30) cc_final: 0.8731 (t0) REVERT: N 30 GLN cc_start: 0.8978 (mt0) cc_final: 0.8751 (mt0) REVERT: N 43 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8801 (tt) REVERT: N 72 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8434 (mm-40) REVERT: N 88 ASP cc_start: 0.8342 (m-30) cc_final: 0.8036 (m-30) REVERT: N 105 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7672 (pttm) REVERT: N 254 GLN cc_start: 0.6302 (pt0) cc_final: 0.5534 (mm110) REVERT: O 28 TYR cc_start: 0.8637 (m-10) cc_final: 0.8323 (m-10) REVERT: O 35 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.7931 (mttm) REVERT: O 154 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8486 (mt-10) REVERT: O 158 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8357 (mmm-85) REVERT: O 161 ASN cc_start: 0.7985 (t0) cc_final: 0.7690 (t0) REVERT: O 173 GLU cc_start: 0.9417 (tp30) cc_final: 0.9032 (mt-10) REVERT: O 184 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8508 (tp30) REVERT: O 189 ARG cc_start: 0.9321 (OUTLIER) cc_final: 0.8931 (mtt-85) REVERT: O 219 TYR cc_start: 0.8244 (OUTLIER) cc_final: 0.7505 (m-80) REVERT: O 234 ASP cc_start: 0.8548 (m-30) cc_final: 0.8132 (m-30) REVERT: S 95 ASP cc_start: 0.9032 (t0) cc_final: 0.8622 (t0) REVERT: S 117 HIS cc_start: 0.9121 (OUTLIER) cc_final: 0.8748 (m170) REVERT: S 156 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.7870 (t80) REVERT: S 163 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8653 (tm-30) REVERT: S 189 TYR cc_start: 0.9203 (OUTLIER) cc_final: 0.7717 (t80) REVERT: S 201 THR cc_start: 0.9465 (m) cc_final: 0.9117 (p) REVERT: S 218 THR cc_start: 0.7859 (OUTLIER) cc_final: 0.7577 (p) REVERT: b 35 MET cc_start: 0.8891 (mtp) cc_final: 0.8102 (mmm) REVERT: b 39 LYS cc_start: 0.8789 (ttpt) cc_final: 0.8304 (mmtt) REVERT: b 41 MET cc_start: 0.9230 (mmm) cc_final: 0.8935 (mmp) REVERT: b 43 LEU cc_start: 0.9432 (mm) cc_final: 0.9022 (tp) REVERT: b 46 ASN cc_start: 0.8845 (t0) cc_final: 0.8622 (t0) REVERT: b 47 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7850 (pm20) REVERT: b 94 SER cc_start: 0.9361 (p) cc_final: 0.9040 (m) REVERT: e 47 ASP cc_start: 0.7079 (t70) cc_final: 0.6540 (m-30) REVERT: e 82 LEU cc_start: 0.7053 (tp) cc_final: 0.6584 (pp) REVERT: g 8 LYS cc_start: 0.8752 (mptt) cc_final: 0.8194 (tppt) REVERT: g 11 MET cc_start: 0.6295 (mmm) cc_final: 0.5217 (mmm) REVERT: g 14 LYS cc_start: 0.9072 (tttp) cc_final: 0.8870 (tptp) REVERT: g 17 LEU cc_start: 0.7371 (mp) cc_final: 0.6915 (tt) REVERT: g 59 LEU cc_start: 0.6825 (mm) cc_final: 0.6565 (tp) REVERT: h 1 MET cc_start: 0.6224 (ptp) cc_final: 0.5682 (pmm) REVERT: h 2 LYS cc_start: 0.7909 (mttm) cc_final: 0.7436 (tppt) REVERT: h 42 ASP cc_start: 0.8959 (t0) cc_final: 0.8563 (t0) REVERT: h 44 LYS cc_start: 0.8816 (ttpp) cc_final: 0.8519 (mmtt) REVERT: h 87 ILE cc_start: 0.8989 (mp) cc_final: 0.8787 (mp) REVERT: h 102 ASN cc_start: 0.8207 (m-40) cc_final: 0.7926 (t0) REVERT: j 24 PHE cc_start: 0.7975 (t80) cc_final: 0.7668 (t80) REVERT: j 28 HIS cc_start: 0.8149 (m90) cc_final: 0.7847 (p-80) REVERT: j 70 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7761 (tp30) REVERT: j 92 SER cc_start: 0.9453 (m) cc_final: 0.9055 (p) outliers start: 299 outliers final: 220 residues processed: 920 average time/residue: 0.5780 time to fit residues: 920.5432 Evaluate side-chains 916 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 654 time to evaluate : 4.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 610 ARG Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 749 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 944 TYR Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1317 ARG Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain A residue 1420 THR Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1433 ASP Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1498 ASP Chi-restraints excluded: chain A residue 1586 GLN Chi-restraints excluded: chain A residue 1589 LYS Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1603 ASN Chi-restraints excluded: chain A residue 1615 ASN Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1646 ILE Chi-restraints excluded: chain A residue 1648 ILE Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1789 ASN Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1803 ARG Chi-restraints excluded: chain A residue 1881 THR Chi-restraints excluded: chain A residue 1920 LEU Chi-restraints excluded: chain A residue 2031 THR Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 500 ARG Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain C residue 965 ASP Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 33 GLN Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 306 ASP Chi-restraints excluded: chain H residue 315 LEU Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 352 THR Chi-restraints excluded: chain H residue 373 ILE Chi-restraints excluded: chain H residue 394 TYR Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 457 HIS Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 477 MET Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 161 ASP Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 184 THR Chi-restraints excluded: chain J residue 194 HIS Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 232 ILE Chi-restraints excluded: chain J residue 237 ASP Chi-restraints excluded: chain J residue 248 ILE Chi-restraints excluded: chain J residue 261 THR Chi-restraints excluded: chain J residue 263 VAL Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 280 GLN Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 332 ARG Chi-restraints excluded: chain J residue 334 TRP Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 358 ILE Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain J residue 379 LYS Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 423 ILE Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 87 ASN Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 111 HIS Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 162 GLU Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 196 THR Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain K residue 213 LYS Chi-restraints excluded: chain L residue 3 ARG Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 38 SER Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 84 GLU Chi-restraints excluded: chain L residue 108 CYS Chi-restraints excluded: chain L residue 138 THR Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain L residue 142 PHE Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 44 ASN Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 111 CYS Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain M residue 124 MET Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 147 ASN Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 189 GLN Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 72 GLN Chi-restraints excluded: chain N residue 94 VAL Chi-restraints excluded: chain N residue 105 LYS Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 205 PHE Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 158 ARG Chi-restraints excluded: chain O residue 179 SER Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain O residue 189 ARG Chi-restraints excluded: chain O residue 206 LYS Chi-restraints excluded: chain O residue 219 TYR Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain S residue 117 HIS Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 143 GLU Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 146 LEU Chi-restraints excluded: chain S residue 156 TYR Chi-restraints excluded: chain S residue 158 LYS Chi-restraints excluded: chain S residue 188 ILE Chi-restraints excluded: chain S residue 189 TYR Chi-restraints excluded: chain S residue 218 THR Chi-restraints excluded: chain S residue 234 ASN Chi-restraints excluded: chain S residue 263 SER Chi-restraints excluded: chain S residue 266 LEU Chi-restraints excluded: chain b residue 37 PHE Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 95 THR Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain d residue 20 SER Chi-restraints excluded: chain d residue 74 VAL Chi-restraints excluded: chain e residue 10 MET Chi-restraints excluded: chain e residue 14 ILE Chi-restraints excluded: chain e residue 53 VAL Chi-restraints excluded: chain e residue 54 ILE Chi-restraints excluded: chain f residue 31 LEU Chi-restraints excluded: chain f residue 78 VAL Chi-restraints excluded: chain g residue 34 ILE Chi-restraints excluded: chain g residue 66 ASN Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 61 PHE Chi-restraints excluded: chain j residue 94 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 773 random chunks: chunk 460 optimal weight: 0.9980 chunk 297 optimal weight: 6.9990 chunk 444 optimal weight: 0.9980 chunk 224 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 144 optimal weight: 0.6980 chunk 473 optimal weight: 2.9990 chunk 507 optimal weight: 2.9990 chunk 368 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 585 optimal weight: 50.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 ASN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 905 GLN ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 148 HIS ** K 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 65132 Z= 0.240 Angle : 0.625 14.620 90610 Z= 0.309 Chirality : 0.039 0.230 10977 Planarity : 0.004 0.068 9985 Dihedral : 18.427 169.428 14977 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.29 % Favored : 94.53 % Rotamer: Outliers : 6.35 % Allowed : 24.52 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.10), residues: 7089 helix: 2.44 (0.09), residues: 3232 sheet: -1.63 (0.18), residues: 812 loop : -1.57 (0.11), residues: 3045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 823 HIS 0.007 0.001 HIS A 138 PHE 0.027 0.001 PHE j 24 TYR 0.030 0.001 TYR C 862 ARG 0.007 0.000 ARG K 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14178 Ramachandran restraints generated. 7089 Oldfield, 0 Emsley, 7089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14178 Ramachandran restraints generated. 7089 Oldfield, 0 Emsley, 7089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 973 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 299 poor density : 674 time to evaluate : 4.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.6769 (t80) REVERT: A 308 MET cc_start: 0.8926 (tpp) cc_final: 0.8578 (mmm) REVERT: A 331 PHE cc_start: 0.9335 (OUTLIER) cc_final: 0.8352 (t80) REVERT: A 392 ASN cc_start: 0.8976 (t0) cc_final: 0.8585 (t0) REVERT: A 415 GLU cc_start: 0.5037 (OUTLIER) cc_final: 0.4006 (tp30) REVERT: A 425 ASP cc_start: 0.6857 (OUTLIER) cc_final: 0.6380 (t0) REVERT: A 477 MET cc_start: 0.9338 (mtm) cc_final: 0.8823 (mtp) REVERT: A 479 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8796 (mt) REVERT: A 514 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.8052 (m-80) REVERT: A 553 ASN cc_start: 0.9001 (m-40) cc_final: 0.8620 (m-40) REVERT: A 595 TYR cc_start: 0.9229 (m-80) cc_final: 0.8891 (m-80) REVERT: A 610 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8602 (ttm-80) REVERT: A 634 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7646 (t70) REVERT: A 682 ASP cc_start: 0.8244 (m-30) cc_final: 0.7840 (m-30) REVERT: A 701 CYS cc_start: 0.8061 (t) cc_final: 0.7404 (t) REVERT: A 755 ASP cc_start: 0.9057 (t0) cc_final: 0.8634 (t0) REVERT: A 813 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8331 (tt0) REVERT: A 917 GLU cc_start: 0.9083 (pt0) cc_final: 0.8872 (mm-30) REVERT: A 933 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8061 (mm-30) REVERT: A 952 ASN cc_start: 0.9059 (m-40) cc_final: 0.8823 (m110) REVERT: A 969 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.7972 (pt) REVERT: A 971 MET cc_start: 0.8649 (mmt) cc_final: 0.8059 (mmt) REVERT: A 992 ASP cc_start: 0.9152 (m-30) cc_final: 0.8611 (p0) REVERT: A 1004 ASP cc_start: 0.8998 (OUTLIER) cc_final: 0.8321 (t0) REVERT: A 1051 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7689 (pt0) REVERT: A 1056 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8927 (mt-10) REVERT: A 1057 MET cc_start: 0.9043 (tmm) cc_final: 0.8475 (tmm) REVERT: A 1114 PHE cc_start: 0.9294 (t80) cc_final: 0.8837 (t80) REVERT: A 1161 TYR cc_start: 0.8152 (t80) cc_final: 0.7883 (t80) REVERT: A 1261 SER cc_start: 0.8575 (t) cc_final: 0.8356 (p) REVERT: A 1283 GLU cc_start: 0.7447 (tp30) cc_final: 0.7192 (tp30) REVERT: A 1315 ARG cc_start: 0.8348 (ttm-80) cc_final: 0.8065 (tpp-160) REVERT: A 1378 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8837 (ttpp) REVERT: A 1558 GLU cc_start: 0.9165 (tp30) cc_final: 0.8945 (tp30) REVERT: A 1586 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7987 (pm20) REVERT: A 1603 ASN cc_start: 0.9022 (OUTLIER) cc_final: 0.8772 (p0) REVERT: A 1703 MET cc_start: 0.8593 (ptt) cc_final: 0.7823 (ptp) REVERT: A 1781 TYR cc_start: 0.8986 (m-80) cc_final: 0.8595 (m-80) REVERT: A 1802 MET cc_start: 0.9150 (mmm) cc_final: 0.8947 (mmm) REVERT: A 1803 ARG cc_start: 0.9368 (OUTLIER) cc_final: 0.8699 (ttp-110) REVERT: A 1806 MET cc_start: 0.9103 (mpp) cc_final: 0.8048 (ttt) REVERT: A 1880 PHE cc_start: 0.9225 (t80) cc_final: 0.7885 (t80) REVERT: A 2048 TRP cc_start: 0.6547 (m100) cc_final: 0.6176 (m100) REVERT: D 16 ASN cc_start: 0.8560 (m-40) cc_final: 0.8112 (t0) REVERT: D 19 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8622 (mm-30) REVERT: D 47 PHE cc_start: 0.8709 (m-80) cc_final: 0.8474 (m-80) REVERT: D 53 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8151 (tm-30) REVERT: D 73 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8598 (mp0) REVERT: D 85 THR cc_start: 0.8532 (m) cc_final: 0.8113 (p) REVERT: D 90 ARG cc_start: 0.8752 (ttm-80) cc_final: 0.7770 (ttt180) REVERT: C 116 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8821 (m) REVERT: C 185 ILE cc_start: 0.9589 (OUTLIER) cc_final: 0.9387 (tt) REVERT: C 222 MET cc_start: 0.8732 (mmm) cc_final: 0.8513 (mmm) REVERT: C 225 THR cc_start: 0.9138 (p) cc_final: 0.8709 (p) REVERT: C 251 GLN cc_start: 0.9052 (tp-100) cc_final: 0.8761 (tp-100) REVERT: C 334 HIS cc_start: 0.8222 (m-70) cc_final: 0.7712 (t-90) REVERT: C 364 PHE cc_start: 0.7904 (t80) cc_final: 0.7591 (t80) REVERT: C 540 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8580 (mp0) REVERT: C 600 GLU cc_start: 0.9337 (tp30) cc_final: 0.8631 (mt-10) REVERT: C 658 ASP cc_start: 0.8510 (m-30) cc_final: 0.8215 (m-30) REVERT: C 719 MET cc_start: 0.9125 (tpp) cc_final: 0.8779 (tpp) REVERT: C 760 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6509 (tt) REVERT: C 799 PHE cc_start: 0.8627 (t80) cc_final: 0.8410 (t80) REVERT: C 842 MET cc_start: 0.8702 (ppp) cc_final: 0.8425 (ppp) REVERT: C 931 TYR cc_start: 0.9165 (p90) cc_final: 0.8932 (p90) REVERT: C 965 ASP cc_start: 0.9369 (OUTLIER) cc_final: 0.8881 (p0) REVERT: G 57 GLU cc_start: 0.9546 (tp30) cc_final: 0.9117 (tp30) REVERT: G 88 GLU cc_start: 0.9091 (tp30) cc_final: 0.8547 (tp30) REVERT: G 91 ARG cc_start: 0.8627 (mtt180) cc_final: 0.7557 (mmp-170) REVERT: H 315 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9215 (mm) REVERT: H 379 ASP cc_start: 0.8661 (m-30) cc_final: 0.8379 (p0) REVERT: H 402 LEU cc_start: 0.5459 (OUTLIER) cc_final: 0.5208 (mt) REVERT: H 417 ARG cc_start: 0.8246 (ptt90) cc_final: 0.7959 (ttp80) REVERT: H 425 GLN cc_start: 0.9224 (tt0) cc_final: 0.8866 (tt0) REVERT: H 429 ASN cc_start: 0.9293 (m-40) cc_final: 0.9089 (m110) REVERT: H 454 ASP cc_start: 0.7718 (m-30) cc_final: 0.7349 (m-30) REVERT: H 477 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7934 (ptp) REVERT: H 478 ARG cc_start: 0.7958 (mmm160) cc_final: 0.7731 (mmm160) REVERT: J 169 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8249 (mm) REVERT: J 231 SER cc_start: 0.8855 (t) cc_final: 0.8519 (t) REVERT: J 237 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7522 (p0) REVERT: J 253 MET cc_start: 0.8924 (mmm) cc_final: 0.8603 (mmt) REVERT: J 280 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8064 (mp10) REVERT: J 332 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8406 (mmt90) REVERT: J 392 MET cc_start: 0.8271 (mmm) cc_final: 0.7938 (mmm) REVERT: J 404 CYS cc_start: 0.8817 (t) cc_final: 0.8152 (t) REVERT: J 443 ASN cc_start: 0.8779 (m-40) cc_final: 0.8313 (t0) REVERT: K 62 GLU cc_start: 0.9328 (tm-30) cc_final: 0.8883 (tm-30) REVERT: K 66 CYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8897 (t) REVERT: K 75 GLN cc_start: 0.8646 (tt0) cc_final: 0.8413 (tm-30) REVERT: K 76 ARG cc_start: 0.8562 (ttp-110) cc_final: 0.8346 (ttm110) REVERT: K 106 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7874 (mp) REVERT: K 118 GLN cc_start: 0.8491 (mt0) cc_final: 0.8180 (pm20) REVERT: K 199 ASP cc_start: 0.9231 (m-30) cc_final: 0.8803 (t70) REVERT: K 213 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7882 (mtpt) REVERT: L 10 LYS cc_start: 0.9322 (mmtp) cc_final: 0.8947 (ttpp) REVERT: L 47 GLU cc_start: 0.9146 (tp30) cc_final: 0.8890 (tp30) REVERT: L 50 TRP cc_start: 0.8859 (m-10) cc_final: 0.8498 (m-10) REVERT: L 130 GLU cc_start: 0.9188 (pt0) cc_final: 0.8602 (mm-30) REVERT: L 142 PHE cc_start: 0.9138 (OUTLIER) cc_final: 0.7398 (p90) REVERT: M 114 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7702 (ptt-90) REVERT: M 188 TYR cc_start: 0.8812 (m-10) cc_final: 0.8533 (m-10) REVERT: M 214 ASP cc_start: 0.9291 (m-30) cc_final: 0.8723 (t0) REVERT: N 30 GLN cc_start: 0.8980 (mt0) cc_final: 0.8765 (mt0) REVERT: N 43 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8848 (tt) REVERT: N 72 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8369 (mm-40) REVERT: N 88 ASP cc_start: 0.8381 (m-30) cc_final: 0.8078 (m-30) REVERT: N 105 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7712 (pttm) REVERT: N 254 GLN cc_start: 0.6451 (pt0) cc_final: 0.5772 (mm110) REVERT: O 28 TYR cc_start: 0.8641 (m-10) cc_final: 0.8326 (m-10) REVERT: O 35 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8037 (mttm) REVERT: O 90 MET cc_start: 0.8692 (mmm) cc_final: 0.8347 (tmm) REVERT: O 158 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8454 (mmm-85) REVERT: O 161 ASN cc_start: 0.7969 (t0) cc_final: 0.7698 (t0) REVERT: O 184 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8546 (tp30) REVERT: O 189 ARG cc_start: 0.9295 (OUTLIER) cc_final: 0.8924 (mtt-85) REVERT: O 219 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.7499 (m-80) REVERT: O 234 ASP cc_start: 0.8522 (m-30) cc_final: 0.8093 (m-30) REVERT: S 95 ASP cc_start: 0.9064 (t0) cc_final: 0.8651 (t0) REVERT: S 117 HIS cc_start: 0.8974 (OUTLIER) cc_final: 0.8666 (m170) REVERT: S 156 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.7894 (t80) REVERT: S 163 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8567 (tm-30) REVERT: S 189 TYR cc_start: 0.9208 (OUTLIER) cc_final: 0.7817 (t80) REVERT: S 201 THR cc_start: 0.9467 (m) cc_final: 0.9102 (p) REVERT: S 218 THR cc_start: 0.7831 (OUTLIER) cc_final: 0.7549 (p) REVERT: b 35 MET cc_start: 0.8885 (mtp) cc_final: 0.8134 (mmm) REVERT: b 39 LYS cc_start: 0.8779 (ttpt) cc_final: 0.8303 (mmtt) REVERT: b 41 MET cc_start: 0.9275 (mmm) cc_final: 0.9014 (mmp) REVERT: b 46 ASN cc_start: 0.8812 (t0) cc_final: 0.8427 (t0) REVERT: b 47 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7827 (pm20) REVERT: b 93 LEU cc_start: 0.8377 (mt) cc_final: 0.8130 (mt) REVERT: b 94 SER cc_start: 0.9357 (p) cc_final: 0.8866 (m) REVERT: d 35 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7923 (tm-30) REVERT: e 47 ASP cc_start: 0.7112 (t70) cc_final: 0.6584 (m-30) REVERT: e 82 LEU cc_start: 0.7048 (tp) cc_final: 0.6602 (pp) REVERT: g 8 LYS cc_start: 0.8764 (mptt) cc_final: 0.8189 (tppt) REVERT: g 11 MET cc_start: 0.6308 (mmm) cc_final: 0.5134 (mmm) REVERT: g 14 LYS cc_start: 0.9101 (tttp) cc_final: 0.8898 (tptp) REVERT: g 17 LEU cc_start: 0.7331 (mp) cc_final: 0.6890 (tt) REVERT: g 44 MET cc_start: 0.6860 (mmm) cc_final: 0.6192 (tmm) REVERT: g 59 LEU cc_start: 0.6498 (mm) cc_final: 0.6201 (tp) REVERT: h 1 MET cc_start: 0.6208 (ptp) cc_final: 0.5626 (pmm) REVERT: h 2 LYS cc_start: 0.7866 (mttm) cc_final: 0.7364 (tppt) REVERT: h 42 ASP cc_start: 0.8657 (t0) cc_final: 0.8335 (t0) REVERT: h 44 LYS cc_start: 0.8815 (ttpp) cc_final: 0.8510 (mmtt) REVERT: h 102 ASN cc_start: 0.8229 (m-40) cc_final: 0.7957 (t0) REVERT: j 28 HIS cc_start: 0.8194 (m90) cc_final: 0.7728 (t70) REVERT: j 38 MET cc_start: 0.5414 (mmm) cc_final: 0.5191 (mmm) REVERT: j 70 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7791 (tp30) REVERT: j 92 SER cc_start: 0.9475 (m) cc_final: 0.9119 (p) REVERT: j 96 LEU cc_start: 0.8456 (tp) cc_final: 0.8085 (pp) outliers start: 299 outliers final: 225 residues processed: 909 average time/residue: 0.5594 time to fit residues: 882.9754 Evaluate side-chains 909 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 641 time to evaluate : 4.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 610 ARG Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 944 TYR Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1317 ARG Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1378 LYS Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain A residue 1420 THR Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1433 ASP Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1491 ILE Chi-restraints excluded: chain A residue 1498 ASP Chi-restraints excluded: chain A residue 1586 GLN Chi-restraints excluded: chain A residue 1589 LYS Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1603 ASN Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1646 ILE Chi-restraints excluded: chain A residue 1648 ILE Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1789 ASN Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1803 ARG Chi-restraints excluded: chain A residue 1881 THR Chi-restraints excluded: chain A residue 1954 ILE Chi-restraints excluded: chain A residue 2031 THR Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 500 ARG Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain C residue 965 ASP Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 4 ASN Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 306 ASP Chi-restraints excluded: chain H residue 315 LEU Chi-restraints excluded: chain H residue 352 THR Chi-restraints excluded: chain H residue 373 ILE Chi-restraints excluded: chain H residue 394 TYR Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 433 LEU Chi-restraints excluded: chain H residue 457 HIS Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 477 MET Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 161 ASP Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 194 HIS Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 232 ILE Chi-restraints excluded: chain J residue 237 ASP Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 248 ILE Chi-restraints excluded: chain J residue 261 THR Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 280 GLN Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 332 ARG Chi-restraints excluded: chain J residue 334 TRP Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 358 ILE Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain J residue 379 LYS Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 423 ILE Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 66 CYS Chi-restraints excluded: chain K residue 87 ASN Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 111 HIS Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 162 GLU Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 196 THR Chi-restraints excluded: chain K residue 213 LYS Chi-restraints excluded: chain L residue 3 ARG Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 38 SER Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 84 GLU Chi-restraints excluded: chain L residue 108 CYS Chi-restraints excluded: chain L residue 138 THR Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain L residue 142 PHE Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 44 ASN Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 111 CYS Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain M residue 124 MET Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 147 ASN Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 189 GLN Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 72 GLN Chi-restraints excluded: chain N residue 94 VAL Chi-restraints excluded: chain N residue 105 LYS Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 158 ARG Chi-restraints excluded: chain O residue 179 SER Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain O residue 189 ARG Chi-restraints excluded: chain O residue 206 LYS Chi-restraints excluded: chain O residue 211 ILE Chi-restraints excluded: chain O residue 219 TYR Chi-restraints excluded: chain O residue 237 ILE Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain S residue 117 HIS Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 143 GLU Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 146 LEU Chi-restraints excluded: chain S residue 156 TYR Chi-restraints excluded: chain S residue 188 ILE Chi-restraints excluded: chain S residue 189 TYR Chi-restraints excluded: chain S residue 218 THR Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 234 ASN Chi-restraints excluded: chain S residue 263 SER Chi-restraints excluded: chain S residue 266 LEU Chi-restraints excluded: chain b residue 37 PHE Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 95 THR Chi-restraints excluded: chain d residue 20 SER Chi-restraints excluded: chain d residue 74 VAL Chi-restraints excluded: chain e residue 10 MET Chi-restraints excluded: chain e residue 14 ILE Chi-restraints excluded: chain e residue 53 VAL Chi-restraints excluded: chain f residue 78 VAL Chi-restraints excluded: chain g residue 34 ILE Chi-restraints excluded: chain g residue 66 ASN Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 61 PHE Chi-restraints excluded: chain j residue 94 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 773 random chunks: chunk 677 optimal weight: 2.9990 chunk 713 optimal weight: 20.0000 chunk 651 optimal weight: 5.9990 chunk 694 optimal weight: 50.0000 chunk 417 optimal weight: 2.9990 chunk 302 optimal weight: 4.9990 chunk 545 optimal weight: 0.3980 chunk 213 optimal weight: 5.9990 chunk 627 optimal weight: 50.0000 chunk 656 optimal weight: 4.9990 chunk 691 optimal weight: 50.0000 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 HIS A 748 GLN ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1907 GLN ** A2038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN C 560 GLN ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 126 HIS ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 25 GLN M 35 ASN ** N 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 17 HIS ** e 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 65132 Z= 0.383 Angle : 0.710 13.567 90610 Z= 0.355 Chirality : 0.042 0.275 10977 Planarity : 0.005 0.071 9985 Dihedral : 18.518 172.132 14967 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.40 % Favored : 93.43 % Rotamer: Outliers : 6.52 % Allowed : 24.44 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.10), residues: 7089 helix: 2.17 (0.09), residues: 3238 sheet: -1.71 (0.17), residues: 830 loop : -1.67 (0.11), residues: 3021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 357 HIS 0.009 0.002 HIS C 557 PHE 0.021 0.002 PHE A 639 TYR 0.029 0.002 TYR C 862 ARG 0.007 0.001 ARG G 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14178 Ramachandran restraints generated. 7089 Oldfield, 0 Emsley, 7089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14178 Ramachandran restraints generated. 7089 Oldfield, 0 Emsley, 7089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 624 time to evaluate : 5.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 TYR cc_start: 0.7742 (OUTLIER) cc_final: 0.6585 (t80) REVERT: A 308 MET cc_start: 0.9028 (tpp) cc_final: 0.8638 (mmm) REVERT: A 331 PHE cc_start: 0.9323 (OUTLIER) cc_final: 0.8394 (t80) REVERT: A 392 ASN cc_start: 0.8885 (t0) cc_final: 0.8398 (t0) REVERT: A 425 ASP cc_start: 0.6838 (OUTLIER) cc_final: 0.6523 (t0) REVERT: A 477 MET cc_start: 0.9391 (mtm) cc_final: 0.8901 (mtp) REVERT: A 479 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8868 (mt) REVERT: A 514 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.8200 (m-80) REVERT: A 553 ASN cc_start: 0.9076 (m-40) cc_final: 0.8836 (m-40) REVERT: A 595 TYR cc_start: 0.9288 (m-80) cc_final: 0.8941 (m-80) REVERT: A 610 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8571 (ttm-80) REVERT: A 634 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7763 (t70) REVERT: A 770 MET cc_start: 0.8532 (pmm) cc_final: 0.8144 (pmm) REVERT: A 813 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8422 (tt0) REVERT: A 952 ASN cc_start: 0.9091 (m-40) cc_final: 0.8850 (m110) REVERT: A 969 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8121 (pt) REVERT: A 971 MET cc_start: 0.8715 (mmt) cc_final: 0.8073 (mmt) REVERT: A 992 ASP cc_start: 0.9182 (m-30) cc_final: 0.8650 (p0) REVERT: A 1056 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8891 (mt-10) REVERT: A 1057 MET cc_start: 0.9015 (tmm) cc_final: 0.8471 (tmm) REVERT: A 1114 PHE cc_start: 0.9330 (t80) cc_final: 0.8839 (t80) REVERT: A 1161 TYR cc_start: 0.8243 (t80) cc_final: 0.7956 (t80) REVERT: A 1237 SER cc_start: 0.9114 (OUTLIER) cc_final: 0.8811 (m) REVERT: A 1433 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6991 (m-30) REVERT: A 1520 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6834 (tm-30) REVERT: A 1558 GLU cc_start: 0.9168 (tp30) cc_final: 0.8934 (tp30) REVERT: A 1586 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8143 (pm20) REVERT: A 1603 ASN cc_start: 0.9062 (OUTLIER) cc_final: 0.8384 (p0) REVERT: A 1703 MET cc_start: 0.8534 (ptt) cc_final: 0.8322 (ptm) REVERT: A 1781 TYR cc_start: 0.9054 (m-80) cc_final: 0.8702 (m-80) REVERT: A 1802 MET cc_start: 0.9129 (mmm) cc_final: 0.8593 (mmm) REVERT: A 1803 ARG cc_start: 0.9377 (OUTLIER) cc_final: 0.8709 (ttp-110) REVERT: A 1880 PHE cc_start: 0.9073 (t80) cc_final: 0.7726 (t80) REVERT: A 2048 TRP cc_start: 0.6623 (m100) cc_final: 0.6272 (m100) REVERT: A 2063 TYR cc_start: 0.5525 (t80) cc_final: 0.5032 (t80) REVERT: D 16 ASN cc_start: 0.8504 (m-40) cc_final: 0.7991 (t0) REVERT: D 19 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8644 (mm-30) REVERT: D 47 PHE cc_start: 0.8864 (m-80) cc_final: 0.8581 (m-80) REVERT: D 53 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8238 (tm-30) REVERT: D 85 THR cc_start: 0.8566 (m) cc_final: 0.8168 (p) REVERT: D 90 ARG cc_start: 0.8766 (ttm-80) cc_final: 0.7783 (ttt180) REVERT: C 222 MET cc_start: 0.8653 (mmm) cc_final: 0.8320 (mmm) REVERT: C 334 HIS cc_start: 0.8294 (m-70) cc_final: 0.7842 (t-90) REVERT: C 364 PHE cc_start: 0.7938 (t80) cc_final: 0.7567 (t80) REVERT: C 600 GLU cc_start: 0.9394 (tp30) cc_final: 0.8498 (mt-10) REVERT: C 658 ASP cc_start: 0.8661 (m-30) cc_final: 0.8440 (m-30) REVERT: C 719 MET cc_start: 0.9182 (tpp) cc_final: 0.8870 (tpp) REVERT: C 760 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6402 (tt) REVERT: C 842 MET cc_start: 0.8578 (ppp) cc_final: 0.8312 (ppp) REVERT: C 931 TYR cc_start: 0.9221 (p90) cc_final: 0.8896 (p90) REVERT: C 965 ASP cc_start: 0.9380 (OUTLIER) cc_final: 0.8981 (p0) REVERT: C 982 MET cc_start: 0.6528 (tmm) cc_final: 0.6315 (tmm) REVERT: G 57 GLU cc_start: 0.9546 (tp30) cc_final: 0.9117 (tp30) REVERT: G 88 GLU cc_start: 0.9253 (tp30) cc_final: 0.8823 (tp30) REVERT: G 91 ARG cc_start: 0.8875 (mtt180) cc_final: 0.7776 (mmp-170) REVERT: H 315 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9230 (mm) REVERT: H 379 ASP cc_start: 0.8755 (m-30) cc_final: 0.8393 (p0) REVERT: H 417 ARG cc_start: 0.8201 (ptt90) cc_final: 0.7441 (ptm-80) REVERT: H 425 GLN cc_start: 0.9299 (tt0) cc_final: 0.8973 (tt0) REVERT: H 429 ASN cc_start: 0.9341 (m-40) cc_final: 0.9129 (m110) REVERT: H 454 ASP cc_start: 0.7756 (m-30) cc_final: 0.7486 (m-30) REVERT: H 477 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7718 (ptp) REVERT: H 480 ARG cc_start: 0.7294 (ppt170) cc_final: 0.6563 (mmp80) REVERT: J 231 SER cc_start: 0.8920 (t) cc_final: 0.8593 (t) REVERT: J 237 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7478 (p0) REVERT: J 253 MET cc_start: 0.9133 (mmm) cc_final: 0.8657 (mmt) REVERT: J 280 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7851 (mp10) REVERT: J 332 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8493 (mmt90) REVERT: J 404 CYS cc_start: 0.8882 (t) cc_final: 0.8271 (t) REVERT: J 443 ASN cc_start: 0.8819 (m-40) cc_final: 0.8454 (t0) REVERT: K 62 GLU cc_start: 0.9359 (tm-30) cc_final: 0.8876 (tm-30) REVERT: K 66 CYS cc_start: 0.9318 (OUTLIER) cc_final: 0.8884 (t) REVERT: K 73 TYR cc_start: 0.9494 (t80) cc_final: 0.9278 (t80) REVERT: K 106 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7754 (mp) REVERT: K 118 GLN cc_start: 0.8496 (mt0) cc_final: 0.8211 (pm20) REVERT: K 149 MET cc_start: 0.8431 (tpp) cc_final: 0.7637 (tpt) REVERT: K 213 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7886 (mtpt) REVERT: L 47 GLU cc_start: 0.9171 (tp30) cc_final: 0.8916 (tp30) REVERT: L 50 TRP cc_start: 0.8994 (m-10) cc_final: 0.8629 (m-10) REVERT: L 126 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6707 (ttt180) REVERT: L 142 PHE cc_start: 0.9190 (OUTLIER) cc_final: 0.7378 (p90) REVERT: M 188 TYR cc_start: 0.8796 (m-10) cc_final: 0.8477 (m-10) REVERT: M 214 ASP cc_start: 0.9295 (m-30) cc_final: 0.8601 (t0) REVERT: M 217 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8315 (tm-30) REVERT: N 30 GLN cc_start: 0.9114 (mt0) cc_final: 0.8882 (mt0) REVERT: N 72 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8208 (mm-40) REVERT: N 88 ASP cc_start: 0.8504 (m-30) cc_final: 0.8208 (m-30) REVERT: N 105 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7878 (pttm) REVERT: N 254 GLN cc_start: 0.6471 (pt0) cc_final: 0.5961 (mm110) REVERT: O 35 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.7852 (mttm) REVERT: O 90 MET cc_start: 0.8664 (mmm) cc_final: 0.8293 (tmm) REVERT: O 158 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8464 (mmm-85) REVERT: O 161 ASN cc_start: 0.7874 (t0) cc_final: 0.7525 (t0) REVERT: O 184 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8591 (tp30) REVERT: O 189 ARG cc_start: 0.9367 (OUTLIER) cc_final: 0.8977 (mtt-85) REVERT: O 219 TYR cc_start: 0.8328 (OUTLIER) cc_final: 0.7635 (m-80) REVERT: S 95 ASP cc_start: 0.9105 (t0) cc_final: 0.8676 (t0) REVERT: S 117 HIS cc_start: 0.9111 (OUTLIER) cc_final: 0.8682 (m170) REVERT: S 156 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.8046 (t80) REVERT: S 163 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8592 (tm-30) REVERT: S 189 TYR cc_start: 0.9219 (OUTLIER) cc_final: 0.7794 (t80) REVERT: S 201 THR cc_start: 0.9432 (m) cc_final: 0.9058 (p) REVERT: b 39 LYS cc_start: 0.8783 (ttpt) cc_final: 0.8321 (mmtt) REVERT: b 41 MET cc_start: 0.9227 (mmm) cc_final: 0.8996 (mmp) REVERT: b 47 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7848 (pm20) REVERT: b 93 LEU cc_start: 0.8376 (mt) cc_final: 0.7973 (mt) REVERT: b 94 SER cc_start: 0.9333 (p) cc_final: 0.9118 (t) REVERT: d 35 GLU cc_start: 0.8260 (tm-30) cc_final: 0.8053 (tm-30) REVERT: e 47 ASP cc_start: 0.7221 (t70) cc_final: 0.6585 (m-30) REVERT: e 82 LEU cc_start: 0.6770 (tp) cc_final: 0.6374 (pp) REVERT: g 11 MET cc_start: 0.6332 (mmm) cc_final: 0.5556 (mmm) REVERT: g 14 LYS cc_start: 0.9118 (tttp) cc_final: 0.8916 (tptp) REVERT: g 17 LEU cc_start: 0.7487 (mp) cc_final: 0.7156 (tt) REVERT: g 59 LEU cc_start: 0.6490 (mm) cc_final: 0.6155 (tp) REVERT: h 1 MET cc_start: 0.6066 (ptp) cc_final: 0.5366 (pmm) REVERT: h 2 LYS cc_start: 0.7906 (mttm) cc_final: 0.7390 (tppt) REVERT: h 42 ASP cc_start: 0.8599 (t0) cc_final: 0.8314 (t0) REVERT: h 44 LYS cc_start: 0.8870 (ttpp) cc_final: 0.8613 (mmtt) REVERT: h 102 ASN cc_start: 0.8227 (m-40) cc_final: 0.7963 (t0) REVERT: j 24 PHE cc_start: 0.8022 (t80) cc_final: 0.7715 (t80) REVERT: j 28 HIS cc_start: 0.8057 (m90) cc_final: 0.7615 (t70) REVERT: j 38 MET cc_start: 0.5580 (mmm) cc_final: 0.5313 (mmm) REVERT: j 70 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7637 (tp30) REVERT: j 71 ASN cc_start: 0.7509 (m110) cc_final: 0.7079 (m110) REVERT: j 92 SER cc_start: 0.9464 (m) cc_final: 0.9124 (p) REVERT: j 96 LEU cc_start: 0.8475 (tp) cc_final: 0.8203 (pp) outliers start: 307 outliers final: 237 residues processed: 871 average time/residue: 0.5664 time to fit residues: 860.4140 Evaluate side-chains 868 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 595 time to evaluate : 6.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 610 ARG Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1237 SER Chi-restraints excluded: chain A residue 1317 ARG Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain A residue 1387 VAL Chi-restraints excluded: chain A residue 1420 THR Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1433 ASP Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1491 ILE Chi-restraints excluded: chain A residue 1498 ASP Chi-restraints excluded: chain A residue 1520 GLU Chi-restraints excluded: chain A residue 1586 GLN Chi-restraints excluded: chain A residue 1589 LYS Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1603 ASN Chi-restraints excluded: chain A residue 1614 ILE Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1646 ILE Chi-restraints excluded: chain A residue 1648 ILE Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1789 ASN Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1803 ARG Chi-restraints excluded: chain A residue 1881 THR Chi-restraints excluded: chain A residue 1920 LEU Chi-restraints excluded: chain A residue 1954 ILE Chi-restraints excluded: chain A residue 2031 THR Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 500 ARG Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain C residue 965 ASP Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 4 ASN Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 306 ASP Chi-restraints excluded: chain H residue 315 LEU Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 352 THR Chi-restraints excluded: chain H residue 372 ASP Chi-restraints excluded: chain H residue 373 ILE Chi-restraints excluded: chain H residue 394 TYR Chi-restraints excluded: chain H residue 433 LEU Chi-restraints excluded: chain H residue 457 HIS Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 477 MET Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 161 ASP Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 194 HIS Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 232 ILE Chi-restraints excluded: chain J residue 237 ASP Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 248 ILE Chi-restraints excluded: chain J residue 261 THR Chi-restraints excluded: chain J residue 263 VAL Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 280 GLN Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 332 ARG Chi-restraints excluded: chain J residue 334 TRP Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 358 ILE Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain J residue 379 LYS Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 423 ILE Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 66 CYS Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 87 ASN Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 111 HIS Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 176 ASN Chi-restraints excluded: chain K residue 196 THR Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain K residue 213 LYS Chi-restraints excluded: chain L residue 3 ARG Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 38 SER Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 84 GLU Chi-restraints excluded: chain L residue 108 CYS Chi-restraints excluded: chain L residue 126 ARG Chi-restraints excluded: chain L residue 138 THR Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain L residue 142 PHE Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 44 ASN Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 111 CYS Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain M residue 124 MET Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 147 ASN Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 189 GLN Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 254 ILE Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 72 GLN Chi-restraints excluded: chain N residue 105 LYS Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 158 ARG Chi-restraints excluded: chain O residue 179 SER Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain O residue 189 ARG Chi-restraints excluded: chain O residue 200 ILE Chi-restraints excluded: chain O residue 205 LYS Chi-restraints excluded: chain O residue 206 LYS Chi-restraints excluded: chain O residue 211 ILE Chi-restraints excluded: chain O residue 219 TYR Chi-restraints excluded: chain O residue 237 ILE Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain S residue 117 HIS Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 143 GLU Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 146 LEU Chi-restraints excluded: chain S residue 156 TYR Chi-restraints excluded: chain S residue 188 ILE Chi-restraints excluded: chain S residue 189 TYR Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 234 ASN Chi-restraints excluded: chain S residue 263 SER Chi-restraints excluded: chain S residue 266 LEU Chi-restraints excluded: chain b residue 37 PHE Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 86 ILE Chi-restraints excluded: chain d residue 20 SER Chi-restraints excluded: chain e residue 10 MET Chi-restraints excluded: chain e residue 14 ILE Chi-restraints excluded: chain e residue 53 VAL Chi-restraints excluded: chain f residue 31 LEU Chi-restraints excluded: chain f residue 51 LEU Chi-restraints excluded: chain f residue 78 VAL Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 34 ILE Chi-restraints excluded: chain g residue 66 ASN Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 61 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 773 random chunks: chunk 455 optimal weight: 0.9990 chunk 734 optimal weight: 40.0000 chunk 448 optimal weight: 10.0000 chunk 348 optimal weight: 8.9990 chunk 510 optimal weight: 10.0000 chunk 770 optimal weight: 10.0000 chunk 708 optimal weight: 20.0000 chunk 613 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 473 optimal weight: 0.9990 chunk 376 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 GLN ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 34 GLN e 86 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 65132 Z= 0.417 Angle : 0.724 13.570 90610 Z= 0.363 Chirality : 0.042 0.263 10977 Planarity : 0.005 0.071 9985 Dihedral : 18.637 172.473 14955 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.26 % Favored : 93.60 % Rotamer: Outliers : 6.14 % Allowed : 25.14 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.10), residues: 7089 helix: 1.98 (0.09), residues: 3234 sheet: -1.71 (0.18), residues: 803 loop : -1.73 (0.11), residues: 3052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 357 HIS 0.010 0.002 HIS A 138 PHE 0.025 0.002 PHE j 90 TYR 0.030 0.002 TYR C 862 ARG 0.008 0.001 ARG D 50 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14178 Ramachandran restraints generated. 7089 Oldfield, 0 Emsley, 7089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14178 Ramachandran restraints generated. 7089 Oldfield, 0 Emsley, 7089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 904 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 615 time to evaluate : 4.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 TYR cc_start: 0.7810 (OUTLIER) cc_final: 0.6879 (t80) REVERT: A 308 MET cc_start: 0.9038 (tpp) cc_final: 0.8631 (mmm) REVERT: A 331 PHE cc_start: 0.9322 (OUTLIER) cc_final: 0.8345 (t80) REVERT: A 392 ASN cc_start: 0.8899 (t0) cc_final: 0.8413 (t0) REVERT: A 425 ASP cc_start: 0.6827 (OUTLIER) cc_final: 0.6509 (t0) REVERT: A 477 MET cc_start: 0.9399 (mtm) cc_final: 0.8916 (mtp) REVERT: A 479 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8881 (mt) REVERT: A 514 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.8288 (m-80) REVERT: A 553 ASN cc_start: 0.9095 (m-40) cc_final: 0.8860 (m-40) REVERT: A 595 TYR cc_start: 0.9296 (m-80) cc_final: 0.8938 (m-80) REVERT: A 610 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8608 (ttm-80) REVERT: A 634 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8041 (t70) REVERT: A 701 CYS cc_start: 0.8256 (t) cc_final: 0.7853 (t) REVERT: A 743 LYS cc_start: 0.9500 (OUTLIER) cc_final: 0.9092 (tptm) REVERT: A 755 ASP cc_start: 0.9137 (t0) cc_final: 0.8919 (t0) REVERT: A 759 ARG cc_start: 0.8340 (mtp-110) cc_final: 0.7868 (mtt90) REVERT: A 770 MET cc_start: 0.8779 (pmm) cc_final: 0.8358 (pmm) REVERT: A 813 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8416 (tt0) REVERT: A 952 ASN cc_start: 0.9102 (m-40) cc_final: 0.8867 (m110) REVERT: A 969 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8083 (pt) REVERT: A 971 MET cc_start: 0.8739 (mmt) cc_final: 0.8206 (mmt) REVERT: A 1056 GLU cc_start: 0.9191 (mt-10) cc_final: 0.8957 (mt-10) REVERT: A 1057 MET cc_start: 0.9021 (tmm) cc_final: 0.8490 (tmm) REVERT: A 1114 PHE cc_start: 0.9315 (t80) cc_final: 0.8820 (t80) REVERT: A 1161 TYR cc_start: 0.8237 (t80) cc_final: 0.8019 (t80) REVERT: A 1237 SER cc_start: 0.9122 (OUTLIER) cc_final: 0.8816 (m) REVERT: A 1433 ASP cc_start: 0.7303 (OUTLIER) cc_final: 0.7090 (m-30) REVERT: A 1467 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8182 (pp20) REVERT: A 1520 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6770 (tm-30) REVERT: A 1558 GLU cc_start: 0.9164 (tp30) cc_final: 0.8895 (tp30) REVERT: A 1586 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8161 (pm20) REVERT: A 1640 THR cc_start: 0.9276 (OUTLIER) cc_final: 0.8932 (t) REVERT: A 1802 MET cc_start: 0.9129 (mmm) cc_final: 0.8864 (mmm) REVERT: A 1803 ARG cc_start: 0.9422 (OUTLIER) cc_final: 0.8790 (ttp-110) REVERT: A 1806 MET cc_start: 0.9097 (mpp) cc_final: 0.8089 (ttt) REVERT: A 2048 TRP cc_start: 0.6783 (m100) cc_final: 0.6450 (m100) REVERT: D 16 ASN cc_start: 0.8510 (m-40) cc_final: 0.7983 (t0) REVERT: D 19 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8652 (mm-30) REVERT: D 45 THR cc_start: 0.9471 (OUTLIER) cc_final: 0.9206 (p) REVERT: D 85 THR cc_start: 0.8620 (m) cc_final: 0.8200 (p) REVERT: D 90 ARG cc_start: 0.8788 (ttm-80) cc_final: 0.7751 (ttt180) REVERT: F 21 LYS cc_start: 0.8514 (tptt) cc_final: 0.7894 (tttp) REVERT: C 334 HIS cc_start: 0.8326 (m-70) cc_final: 0.7902 (t-90) REVERT: C 540 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8470 (mp0) REVERT: C 600 GLU cc_start: 0.9395 (tp30) cc_final: 0.8520 (mt-10) REVERT: C 658 ASP cc_start: 0.8712 (m-30) cc_final: 0.8488 (m-30) REVERT: C 719 MET cc_start: 0.9164 (tpp) cc_final: 0.8954 (tpp) REVERT: C 760 LEU cc_start: 0.6620 (OUTLIER) cc_final: 0.6167 (tt) REVERT: C 842 MET cc_start: 0.8716 (ppp) cc_final: 0.8405 (ppp) REVERT: C 931 TYR cc_start: 0.9174 (p90) cc_final: 0.8913 (p90) REVERT: C 965 ASP cc_start: 0.9363 (OUTLIER) cc_final: 0.8921 (p0) REVERT: G 57 GLU cc_start: 0.9557 (tp30) cc_final: 0.8923 (tp30) REVERT: G 61 LYS cc_start: 0.8963 (mmtt) cc_final: 0.8710 (mmtp) REVERT: G 88 GLU cc_start: 0.9244 (tp30) cc_final: 0.8818 (tp30) REVERT: G 91 ARG cc_start: 0.8852 (mtt180) cc_final: 0.7807 (mmp-170) REVERT: H 315 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9235 (mm) REVERT: H 379 ASP cc_start: 0.8751 (m-30) cc_final: 0.8416 (p0) REVERT: H 417 ARG cc_start: 0.8189 (ptt90) cc_final: 0.7394 (ptm-80) REVERT: H 425 GLN cc_start: 0.9291 (tt0) cc_final: 0.8992 (tt0) REVERT: H 429 ASN cc_start: 0.9342 (m-40) cc_final: 0.9133 (m110) REVERT: H 454 ASP cc_start: 0.7942 (m-30) cc_final: 0.7681 (m-30) REVERT: H 477 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7672 (ptp) REVERT: J 231 SER cc_start: 0.8901 (t) cc_final: 0.8584 (t) REVERT: J 237 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7491 (p0) REVERT: J 253 MET cc_start: 0.9182 (mmm) cc_final: 0.8681 (mmt) REVERT: J 280 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.7862 (mp10) REVERT: J 332 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8545 (mmt90) REVERT: J 369 ASP cc_start: 0.8354 (m-30) cc_final: 0.8118 (p0) REVERT: J 404 CYS cc_start: 0.8866 (t) cc_final: 0.8267 (t) REVERT: J 443 ASN cc_start: 0.9008 (m-40) cc_final: 0.8546 (t0) REVERT: K 62 GLU cc_start: 0.9371 (tm-30) cc_final: 0.8862 (tm-30) REVERT: K 66 CYS cc_start: 0.9274 (OUTLIER) cc_final: 0.8785 (t) REVERT: K 73 TYR cc_start: 0.9446 (t80) cc_final: 0.9209 (t80) REVERT: K 75 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8315 (tt0) REVERT: K 106 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7924 (mp) REVERT: K 118 GLN cc_start: 0.8491 (mt0) cc_final: 0.8208 (pm20) REVERT: K 149 MET cc_start: 0.8351 (tpp) cc_final: 0.7772 (tpt) REVERT: K 213 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7929 (mtpt) REVERT: L 47 GLU cc_start: 0.9181 (tp30) cc_final: 0.8934 (tp30) REVERT: L 50 TRP cc_start: 0.9002 (m-10) cc_final: 0.8622 (m-10) REVERT: L 126 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6767 (ttt180) REVERT: L 132 GLU cc_start: 0.9289 (tp30) cc_final: 0.9004 (tm-30) REVERT: L 142 PHE cc_start: 0.9173 (OUTLIER) cc_final: 0.7391 (p90) REVERT: M 188 TYR cc_start: 0.8813 (m-10) cc_final: 0.8490 (m-10) REVERT: M 214 ASP cc_start: 0.9301 (m-30) cc_final: 0.8612 (t0) REVERT: M 217 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8280 (tm-30) REVERT: N 30 GLN cc_start: 0.9156 (mt0) cc_final: 0.8923 (mt0) REVERT: N 72 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8181 (mm-40) REVERT: N 88 ASP cc_start: 0.8533 (m-30) cc_final: 0.8240 (m-30) REVERT: N 105 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7999 (pttm) REVERT: N 254 GLN cc_start: 0.6471 (pt0) cc_final: 0.6061 (mm110) REVERT: O 35 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.7792 (mttm) REVERT: O 90 MET cc_start: 0.8681 (mmm) cc_final: 0.8327 (tmm) REVERT: O 158 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8591 (mmm-85) REVERT: O 161 ASN cc_start: 0.7794 (t0) cc_final: 0.7465 (t0) REVERT: O 184 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8583 (tp30) REVERT: O 189 ARG cc_start: 0.9388 (OUTLIER) cc_final: 0.8983 (mtt-85) REVERT: O 219 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.7657 (m-80) REVERT: S 83 ARG cc_start: 0.8281 (mmt-90) cc_final: 0.7787 (mmt90) REVERT: S 95 ASP cc_start: 0.9126 (t0) cc_final: 0.8688 (t0) REVERT: S 117 HIS cc_start: 0.9146 (OUTLIER) cc_final: 0.8738 (m170) REVERT: S 156 TYR cc_start: 0.8707 (OUTLIER) cc_final: 0.8011 (t80) REVERT: S 163 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8542 (tm-30) REVERT: S 189 TYR cc_start: 0.9215 (OUTLIER) cc_final: 0.7823 (t80) REVERT: S 201 THR cc_start: 0.9377 (m) cc_final: 0.8966 (p) REVERT: b 39 LYS cc_start: 0.8825 (ttpt) cc_final: 0.8400 (mmtt) REVERT: b 47 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7900 (pm20) REVERT: b 94 SER cc_start: 0.9327 (p) cc_final: 0.8849 (t) REVERT: d 35 GLU cc_start: 0.8230 (tm-30) cc_final: 0.8011 (tm-30) REVERT: e 47 ASP cc_start: 0.7251 (t70) cc_final: 0.6671 (m-30) REVERT: e 82 LEU cc_start: 0.6724 (tp) cc_final: 0.6396 (pp) REVERT: g 11 MET cc_start: 0.6467 (mmm) cc_final: 0.5694 (mmm) REVERT: g 14 LYS cc_start: 0.9123 (tttp) cc_final: 0.8917 (tptp) REVERT: g 17 LEU cc_start: 0.7411 (mp) cc_final: 0.7079 (tt) REVERT: g 59 LEU cc_start: 0.6276 (mm) cc_final: 0.5876 (tp) REVERT: h 1 MET cc_start: 0.6155 (ptp) cc_final: 0.5688 (ptt) REVERT: h 2 LYS cc_start: 0.7956 (mttm) cc_final: 0.7547 (tppt) REVERT: h 42 ASP cc_start: 0.8561 (t0) cc_final: 0.8344 (t0) REVERT: h 44 LYS cc_start: 0.8855 (ttpp) cc_final: 0.8633 (mmtt) REVERT: h 102 ASN cc_start: 0.8236 (m-40) cc_final: 0.7970 (t0) REVERT: j 28 HIS cc_start: 0.7938 (m90) cc_final: 0.7503 (t70) REVERT: j 70 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7599 (tp30) REVERT: j 71 ASN cc_start: 0.7567 (m110) cc_final: 0.7142 (m110) REVERT: j 90 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7933 (t80) REVERT: j 92 SER cc_start: 0.9337 (m) cc_final: 0.8778 (p) REVERT: j 96 LEU cc_start: 0.8490 (tp) cc_final: 0.8173 (pp) outliers start: 289 outliers final: 233 residues processed: 848 average time/residue: 0.5869 time to fit residues: 870.5779 Evaluate side-chains 864 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 592 time to evaluate : 4.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 610 ARG Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 859 ASN Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1237 SER Chi-restraints excluded: chain A residue 1317 ARG Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain A residue 1387 VAL Chi-restraints excluded: chain A residue 1401 SER Chi-restraints excluded: chain A residue 1420 THR Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1433 ASP Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1491 ILE Chi-restraints excluded: chain A residue 1498 ASP Chi-restraints excluded: chain A residue 1520 GLU Chi-restraints excluded: chain A residue 1586 GLN Chi-restraints excluded: chain A residue 1589 LYS Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1614 ILE Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1640 THR Chi-restraints excluded: chain A residue 1646 ILE Chi-restraints excluded: chain A residue 1648 ILE Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1789 ASN Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1803 ARG Chi-restraints excluded: chain A residue 1881 THR Chi-restraints excluded: chain A residue 1920 LEU Chi-restraints excluded: chain A residue 1954 ILE Chi-restraints excluded: chain A residue 2031 THR Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 500 ARG Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain C residue 965 ASP Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 4 ASN Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 306 ASP Chi-restraints excluded: chain H residue 315 LEU Chi-restraints excluded: chain H residue 352 THR Chi-restraints excluded: chain H residue 373 ILE Chi-restraints excluded: chain H residue 394 TYR Chi-restraints excluded: chain H residue 433 LEU Chi-restraints excluded: chain H residue 457 HIS Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 477 MET Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 161 ASP Chi-restraints excluded: chain J residue 194 HIS Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 232 ILE Chi-restraints excluded: chain J residue 237 ASP Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 248 ILE Chi-restraints excluded: chain J residue 261 THR Chi-restraints excluded: chain J residue 263 VAL Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 280 GLN Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 332 ARG Chi-restraints excluded: chain J residue 334 TRP Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 358 ILE Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 423 ILE Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 66 CYS Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 87 ASN Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 111 HIS Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 176 ASN Chi-restraints excluded: chain K residue 196 THR Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain K residue 213 LYS Chi-restraints excluded: chain L residue 3 ARG Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 108 CYS Chi-restraints excluded: chain L residue 126 ARG Chi-restraints excluded: chain L residue 138 THR Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain L residue 142 PHE Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 111 CYS Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain M residue 124 MET Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 147 ASN Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 189 GLN Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 254 ILE Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 72 GLN Chi-restraints excluded: chain N residue 105 LYS Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 309 ASN Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 158 ARG Chi-restraints excluded: chain O residue 171 ILE Chi-restraints excluded: chain O residue 179 SER Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain O residue 189 ARG Chi-restraints excluded: chain O residue 200 ILE Chi-restraints excluded: chain O residue 205 LYS Chi-restraints excluded: chain O residue 206 LYS Chi-restraints excluded: chain O residue 211 ILE Chi-restraints excluded: chain O residue 219 TYR Chi-restraints excluded: chain O residue 237 ILE Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 117 HIS Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 143 GLU Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 146 LEU Chi-restraints excluded: chain S residue 156 TYR Chi-restraints excluded: chain S residue 188 ILE Chi-restraints excluded: chain S residue 189 TYR Chi-restraints excluded: chain S residue 234 ASN Chi-restraints excluded: chain S residue 263 SER Chi-restraints excluded: chain S residue 266 LEU Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 86 ILE Chi-restraints excluded: chain d residue 20 SER Chi-restraints excluded: chain e residue 10 MET Chi-restraints excluded: chain e residue 14 ILE Chi-restraints excluded: chain e residue 53 VAL Chi-restraints excluded: chain f residue 31 LEU Chi-restraints excluded: chain f residue 78 VAL Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 34 ILE Chi-restraints excluded: chain g residue 66 ASN Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain j residue 48 LEU Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 61 PHE Chi-restraints excluded: chain j residue 90 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 773 random chunks: chunk 487 optimal weight: 7.9990 chunk 653 optimal weight: 9.9990 chunk 187 optimal weight: 3.9990 chunk 565 optimal weight: 40.0000 chunk 90 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 614 optimal weight: 6.9990 chunk 257 optimal weight: 3.9990 chunk 630 optimal weight: 40.0000 chunk 77 optimal weight: 0.0970 chunk 113 optimal weight: 0.6980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 ASN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 HIS A 748 GLN ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.101455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.077243 restraints weight = 221394.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.077960 restraints weight = 143724.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.077896 restraints weight = 103869.578| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 65132 Z= 0.263 Angle : 0.657 14.070 90610 Z= 0.326 Chirality : 0.040 0.317 10977 Planarity : 0.004 0.070 9985 Dihedral : 18.551 173.420 14953 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.67 % Favored : 94.16 % Rotamer: Outliers : 5.61 % Allowed : 26.07 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.10), residues: 7089 helix: 2.18 (0.09), residues: 3238 sheet: -1.76 (0.18), residues: 809 loop : -1.61 (0.11), residues: 3042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 357 HIS 0.006 0.001 HIS N 45 PHE 0.037 0.002 PHE C 446 TYR 0.033 0.002 TYR C 862 ARG 0.016 0.001 ARG j 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15071.38 seconds wall clock time: 271 minutes 22.85 seconds (16282.85 seconds total)