Starting phenix.real_space_refine on Sat Dec 9 11:35:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lj3_4055/12_2023/5lj3_4055_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lj3_4055/12_2023/5lj3_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_4055/12_2023/5lj3_4055.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lj3_4055/12_2023/5lj3_4055.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lj3_4055/12_2023/5lj3_4055_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lj3_4055/12_2023/5lj3_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-1.21rc1-5172/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: 26.06, per 1000 atoms: 0.41 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: 22.61 Conformation dependent library (CDL) restraints added in 7.7 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: 22.87 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: 36.76 Time building geometry restraints manager: 24.65 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: 37025 34.22 - 68.44: 1954 68.44 - 102.66: 192 102.66 - 136.88: 11 136.88 - 171.10: 5 Dihedral angle restraints: 39187 sinusoidal: 17422 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 39184 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: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 16.570 Check model and map are aligned: 0.720 Set scattering table: 0.450 Process input model: 168.360 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.320 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: 0.010 Load rotamer database and sin/cos tables:2.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 193.590 ------------------------------------------------------------------------------- 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 : 19.063 171.096 24941 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 : 5.085 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 outliers start: 402 outliers final: 110 residues processed: 1650 average time/residue: 0.6947 time to fit residues: 1904.1244 Evaluate side-chains 836 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 726 time to evaluate : 5.062 Switching outliers to nearest non-outliers outliers start: 110 outliers final: 0 residues processed: 110 average time/residue: 0.5644 time to fit residues: 115.3460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 773 random chunks: chunk 652 optimal weight: 8.9990 chunk 585 optimal weight: 30.0000 chunk 325 optimal weight: 1.9990 chunk 200 optimal weight: 0.8980 chunk 395 optimal weight: 2.9990 chunk 313 optimal weight: 7.9990 chunk 605 optimal weight: 5.9990 chunk 234 optimal weight: 8.9990 chunk 368 optimal weight: 5.9990 chunk 450 optimal weight: 0.8980 chunk 701 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS A 216 GLN A 265 ASN A 310 ASN A 326 ASN A 344 ASN A 508 GLN A 509 HIS ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A1417 GLN A1449 ASN A1568 ASN A1687 HIS A1799 GLN A2018 ASN A2068 ASN C 158 HIS 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 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN C 557 HIS C 608 GLN ** C 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 794 GLN ** C 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 869 HIS C 905 GLN G 60 GLN H 260 GLN H 358 GLN H 362 ASN H 368 ASN J 121 GLN ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 233 HIS J 273 GLN J 280 GLN J 443 ASN ** K 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN K 210 ASN ** K 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 GLN L 115 ASN ** M 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 72 GLN N 85 GLN ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 47 GLN S 61 ASN S 78 GLN S 79 HIS S 214 ASN d 4 ASN d 41 ASN e 24 GLN e 86 ASN f 24 ASN g 66 ASN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 65132 Z= 0.341 Angle : 0.751 13.159 90610 Z= 0.388 Chirality : 0.045 0.333 10977 Planarity : 0.006 0.102 9985 Dihedral : 17.585 177.751 14257 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.12 % Favored : 94.67 % Rotamer: Outliers : 4.55 % Allowed : 18.72 % Favored : 76.73 % 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: 0.31 (0.10), residues: 7089 helix: 3.19 (0.09), residues: 3227 sheet: -2.53 (0.16), residues: 777 loop : -2.54 (0.10), residues: 3085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP J 293 HIS 0.008 0.001 HIS N 45 PHE 0.046 0.002 PHE j 26 TYR 0.024 0.002 TYR H 369 ARG 0.011 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 1039 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 825 time to evaluate : 5.190 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 outliers start: 214 outliers final: 109 residues processed: 981 average time/residue: 0.5856 time to fit residues: 985.4214 Evaluate side-chains 735 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 626 time to evaluate : 5.102 Switching outliers to nearest non-outliers outliers start: 109 outliers final: 0 residues processed: 109 average time/residue: 0.4679 time to fit residues: 102.2074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 773 random chunks: chunk 390 optimal weight: 1.9990 chunk 217 optimal weight: 9.9990 chunk 584 optimal weight: 30.0000 chunk 477 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 chunk 703 optimal weight: 0.7980 chunk 759 optimal weight: 0.7980 chunk 626 optimal weight: 30.0000 chunk 697 optimal weight: 4.9990 chunk 239 optimal weight: 6.9990 chunk 564 optimal weight: 30.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 553 ASN A 636 HIS A 997 GLN A1087 ASN ** A1368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 358 ASN C 776 ASN G 9 ASN H 260 GLN H 368 ASN ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 GLN K 64 GLN ** K 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 144 GLN ** M 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 239 GLN ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 214 ASN ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 71 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 65132 Z= 0.236 Angle : 0.657 13.381 90610 Z= 0.335 Chirality : 0.042 0.530 10977 Planarity : 0.005 0.100 9985 Dihedral : 17.353 172.452 14257 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.92 % Favored : 94.87 % Rotamer: Outliers : 3.02 % Allowed : 20.36 % Favored : 76.63 % 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: 0.55 (0.11), residues: 7089 helix: 3.17 (0.09), residues: 3224 sheet: -2.17 (0.17), residues: 727 loop : -2.21 (0.10), residues: 3138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 183 HIS 0.015 0.001 HIS S 117 PHE 0.027 0.002 PHE A1851 TYR 0.026 0.002 TYR A1116 ARG 0.016 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 900 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 758 time to evaluate : 5.085 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 outliers start: 142 outliers final: 61 residues processed: 866 average time/residue: 0.5929 time to fit residues: 885.4766 Evaluate side-chains 687 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 626 time to evaluate : 5.077 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.4813 time to fit residues: 61.1821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 773 random chunks: chunk 694 optimal weight: 50.0000 chunk 528 optimal weight: 5.9990 chunk 364 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 335 optimal weight: 0.0170 chunk 472 optimal weight: 5.9990 chunk 705 optimal weight: 50.0000 chunk 747 optimal weight: 30.0000 chunk 368 optimal weight: 9.9990 chunk 668 optimal weight: 6.9990 chunk 201 optimal weight: 2.9990 overall best weight: 3.4026 ------------------------------------------------------------------------------- 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 638 GLN A 748 GLN ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 ASN A 848 ASN ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN A1190 ASN ** A1368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1548 GLN ** A1618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1895 HIS A1929 GLN C 87 GLN ** C 194 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 511 GLN H 368 ASN ** H 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 ASN ** K 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 128 GLN ** M 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 201 ASN N 81 HIS N 85 GLN N 321 GLN ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 212 HIS e 15 ASN j 35 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 65132 Z= 0.402 Angle : 0.716 13.713 90610 Z= 0.364 Chirality : 0.043 0.311 10977 Planarity : 0.005 0.107 9985 Dihedral : 17.388 167.717 14257 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.59 % Favored : 94.20 % Rotamer: Outliers : 3.72 % Allowed : 21.99 % Favored : 74.29 % 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: 0.11 (0.10), residues: 7089 helix: 2.43 (0.09), residues: 3231 sheet: -2.06 (0.17), residues: 785 loop : -2.06 (0.10), residues: 3073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 183 HIS 0.010 0.002 HIS S 117 PHE 0.023 0.002 PHE j 24 TYR 0.031 0.002 TYR S 156 ARG 0.017 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 848 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 673 time to evaluate : 5.221 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 outliers start: 175 outliers final: 95 residues processed: 789 average time/residue: 0.5900 time to fit residues: 813.3192 Evaluate side-chains 674 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 579 time to evaluate : 5.166 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 0 residues processed: 95 average time/residue: 0.4555 time to fit residues: 89.5820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 773 random chunks: chunk 622 optimal weight: 6.9990 chunk 424 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 556 optimal weight: 40.0000 chunk 308 optimal weight: 0.8980 chunk 637 optimal weight: 10.0000 chunk 516 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 381 optimal weight: 0.0030 chunk 670 optimal weight: 20.0000 chunk 188 optimal weight: 1.9990 overall best weight: 2.1796 ------------------------------------------------------------------------------- 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 570 GLN A1368 GLN ** A1618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 280 GLN J 360 GLN ** K 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 HIS ** M 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 155 GLN M 235 GLN ** N 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 8 HIS h 30 GLN j 35 ASN j 52 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 65132 Z= 0.276 Angle : 0.642 13.529 90610 Z= 0.325 Chirality : 0.041 0.259 10977 Planarity : 0.005 0.074 9985 Dihedral : 17.286 166.217 14257 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.94 % Favored : 94.89 % Rotamer: Outliers : 2.44 % Allowed : 23.67 % Favored : 73.88 % 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: 0.20 (0.10), residues: 7089 helix: 2.42 (0.09), residues: 3230 sheet: -1.99 (0.17), residues: 808 loop : -1.89 (0.11), residues: 3051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A2048 HIS 0.009 0.001 HIS J 194 PHE 0.030 0.002 PHE C 364 TYR 0.030 0.002 TYR S 156 ARG 0.011 0.001 ARG j 87 *********************** 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 792 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 677 time to evaluate : 5.154 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 outliers start: 115 outliers final: 58 residues processed: 759 average time/residue: 0.5876 time to fit residues: 779.0523 Evaluate side-chains 649 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 591 time to evaluate : 5.134 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.4825 time to fit residues: 59.4272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 438 optimal weight: 0.9990 chunk 184 optimal weight: 0.9990 chunk 747 optimal weight: 30.0000 chunk 620 optimal weight: 30.0000 chunk 346 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 247 optimal weight: 0.9980 chunk 392 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 A 343 ASN A 497 GLN A 553 ASN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 GLN ** A1618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 GLN ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** H 368 ASN ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4477 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= 0.186 Angle : 0.612 13.872 90610 Z= 0.306 Chirality : 0.039 0.241 10977 Planarity : 0.004 0.093 9985 Dihedral : 17.126 164.372 14257 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.63 % Favored : 95.22 % Rotamer: Outliers : 1.89 % Allowed : 24.67 % Favored : 73.44 % 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: 0.38 (0.10), residues: 7089 helix: 2.50 (0.09), residues: 3224 sheet: -1.81 (0.17), residues: 795 loop : -1.74 (0.11), residues: 3070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A 183 HIS 0.015 0.001 HIS g 55 PHE 0.027 0.001 PHE C 364 TYR 0.035 0.002 TYR A2063 ARG 0.017 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 806 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 717 time to evaluate : 5.256 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 outliers start: 89 outliers final: 31 residues processed: 778 average time/residue: 0.5939 time to fit residues: 806.8216 Evaluate side-chains 638 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 607 time to evaluate : 5.050 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.5165 time to fit residues: 35.6923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 426 optimal weight: 0.9990 chunk 546 optimal weight: 0.0970 chunk 423 optimal weight: 0.9990 chunk 629 optimal weight: 6.9990 chunk 417 optimal weight: 0.4980 chunk 745 optimal weight: 0.0050 chunk 466 optimal weight: 0.0980 chunk 454 optimal weight: 0.5980 chunk 343 optimal weight: 9.9990 overall best weight: 0.2592 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 HIS C 194 ASN ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 ASN H 368 ASN ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 GLN ** K 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 ASN ** N 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 65132 Z= 0.162 Angle : 0.610 13.523 90610 Z= 0.304 Chirality : 0.039 0.336 10977 Planarity : 0.004 0.131 9985 Dihedral : 16.990 168.498 14257 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.43 % Favored : 95.40 % Rotamer: Outliers : 1.23 % Allowed : 25.46 % Favored : 73.31 % 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: 0.45 (0.10), residues: 7089 helix: 2.52 (0.09), residues: 3225 sheet: -1.66 (0.18), residues: 803 loop : -1.68 (0.11), residues: 3061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 183 HIS 0.005 0.001 HIS N 45 PHE 0.024 0.001 PHE C 364 TYR 0.037 0.001 TYR A2063 ARG 0.011 0.000 ARG K 47 *********************** 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 764 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 706 time to evaluate : 5.143 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 outliers start: 58 outliers final: 20 residues processed: 744 average time/residue: 0.6014 time to fit residues: 779.6544 Evaluate side-chains 623 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 603 time to evaluate : 5.165 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.5861 time to fit residues: 27.7902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 773 random chunks: chunk 460 optimal weight: 9.9990 chunk 297 optimal weight: 3.9990 chunk 444 optimal weight: 0.7980 chunk 224 optimal weight: 9.9990 chunk 146 optimal weight: 0.5980 chunk 144 optimal weight: 0.0170 chunk 473 optimal weight: 2.9990 chunk 507 optimal weight: 3.9990 chunk 368 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 585 optimal weight: 50.0000 overall best weight: 1.4822 ------------------------------------------------------------------------------- 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 ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 ASN H 368 ASN J 126 HIS ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 280 GLN ** K 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 115 ASN ** N 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 117 HIS f 34 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 65132 Z= 0.225 Angle : 0.623 14.487 90610 Z= 0.310 Chirality : 0.040 0.337 10977 Planarity : 0.004 0.105 9985 Dihedral : 16.943 170.951 14257 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.84 % Favored : 94.99 % Rotamer: Outliers : 1.40 % Allowed : 26.01 % Favored : 72.59 % 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: 0.52 (0.10), residues: 7089 helix: 2.53 (0.09), residues: 3223 sheet: -1.59 (0.18), residues: 804 loop : -1.61 (0.11), residues: 3062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 183 HIS 0.006 0.001 HIS N 45 PHE 0.020 0.001 PHE C 364 TYR 0.064 0.002 TYR S 105 ARG 0.011 0.000 ARG K 47 *********************** 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 689 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 623 time to evaluate : 5.287 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 outliers start: 66 outliers final: 39 residues processed: 665 average time/residue: 0.5868 time to fit residues: 683.6092 Evaluate side-chains 620 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 581 time to evaluate : 5.157 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.4927 time to fit residues: 42.9666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 773 random chunks: chunk 677 optimal weight: 9.9990 chunk 713 optimal weight: 0.0470 chunk 651 optimal weight: 6.9990 chunk 694 optimal weight: 50.0000 chunk 417 optimal weight: 0.9980 chunk 302 optimal weight: 4.9990 chunk 545 optimal weight: 1.9990 chunk 213 optimal weight: 8.9990 chunk 627 optimal weight: 50.0000 chunk 656 optimal weight: 8.9990 chunk 691 optimal weight: 50.0000 overall best weight: 3.0084 ------------------------------------------------------------------------------- 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 692 ASN ** A2038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN C 514 GLN ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 ASN ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 GLN ** K 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 HIS ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.5116 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= 0.359 Angle : 0.705 13.945 90610 Z= 0.355 Chirality : 0.042 0.325 10977 Planarity : 0.005 0.093 9985 Dihedral : 17.093 173.247 14257 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.92 % Favored : 93.91 % Rotamer: Outliers : 1.08 % Allowed : 26.03 % Favored : 72.89 % 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: 0.27 (0.10), residues: 7089 helix: 2.28 (0.09), residues: 3219 sheet: -1.72 (0.17), residues: 836 loop : -1.65 (0.11), residues: 3034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP A 183 HIS 0.007 0.002 HIS A1559 PHE 0.030 0.002 PHE j 90 TYR 0.043 0.002 TYR S 105 ARG 0.011 0.001 ARG j 87 *********************** 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 644 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 593 time to evaluate : 5.144 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 outliers start: 51 outliers final: 22 residues processed: 619 average time/residue: 0.5966 time to fit residues: 645.7538 Evaluate side-chains 582 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 560 time to evaluate : 5.083 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.4884 time to fit residues: 26.6402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 773 random chunks: chunk 455 optimal weight: 2.9990 chunk 734 optimal weight: 50.0000 chunk 448 optimal weight: 6.9990 chunk 348 optimal weight: 5.9990 chunk 510 optimal weight: 5.9990 chunk 770 optimal weight: 10.0000 chunk 708 optimal weight: 50.0000 chunk 613 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 473 optimal weight: 8.9990 chunk 376 optimal weight: 0.8980 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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** ** A2038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 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** ** K 217 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** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.5335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 65132 Z= 0.385 Angle : 0.720 16.554 90610 Z= 0.362 Chirality : 0.042 0.292 10977 Planarity : 0.005 0.163 9985 Dihedral : 17.180 173.579 14257 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.74 % Favored : 94.09 % Rotamer: Outliers : 0.59 % Allowed : 26.90 % Favored : 72.50 % 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: 0.10 (0.10), residues: 7089 helix: 2.07 (0.09), residues: 3232 sheet: -1.65 (0.17), residues: 833 loop : -1.73 (0.11), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.097 0.002 TRP A 183 HIS 0.008 0.001 HIS D 38 PHE 0.035 0.002 PHE j 61 TYR 0.051 0.002 TYR S 105 ARG 0.023 0.001 ARG K 47 ********************** 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 609 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 581 time to evaluate : 5.477 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 outliers start: 28 outliers final: 16 residues processed: 595 average time/residue: 0.6364 time to fit residues: 668.1413 Evaluate side-chains 569 residues out of total 6627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 553 time to evaluate : 5.157 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.5136 time to fit residues: 22.1704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 773 random chunks: chunk 487 optimal weight: 9.9990 chunk 653 optimal weight: 0.9980 chunk 187 optimal weight: 8.9990 chunk 565 optimal weight: 40.0000 chunk 90 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 614 optimal weight: 5.9990 chunk 257 optimal weight: 0.9980 chunk 630 optimal weight: 30.0000 chunk 77 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 194 HIS A 497 GLN A 541 ASN ** A2038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 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 265 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** ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.103497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.079507 restraints weight = 221927.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.079874 restraints weight = 146797.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.080033 restraints weight = 100881.533| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.5445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 65132 Z= 0.202 Angle : 0.653 13.665 90610 Z= 0.324 Chirality : 0.040 0.264 10977 Planarity : 0.004 0.085 9985 Dihedral : 17.069 174.844 14257 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.66 % Favored : 95.19 % Rotamer: Outliers : 0.40 % Allowed : 27.31 % Favored : 72.29 % 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: 0.36 (0.10), residues: 7089 helix: 2.32 (0.09), residues: 3215 sheet: -1.59 (0.17), residues: 843 loop : -1.58 (0.11), residues: 3031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.002 TRP A 183 HIS 0.010 0.001 HIS A 948 PHE 0.031 0.001 PHE j 61 TYR 0.052 0.002 TYR S 105 ARG 0.011 0.000 ARG b 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14143.33 seconds wall clock time: 249 minutes 38.06 seconds (14978.06 seconds total)