Starting phenix.real_space_refine on Wed Feb 14 06:30:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mps_3539/02_2024/5mps_3539_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mps_3539/02_2024/5mps_3539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mps_3539/02_2024/5mps_3539.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mps_3539/02_2024/5mps_3539.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mps_3539/02_2024/5mps_3539_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mps_3539/02_2024/5mps_3539_updated.pdb" } resolution = 3.85 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: 8 Type Number sf(0) Gaussians K 2 8.98 5 Zn 6 6.06 5 P 348 5.49 5 Mg 3 5.21 5 S 192 5.16 5 C 36219 2.51 5 N 10406 2.21 5 O 11753 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 284": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A GLU 624": "OE1" <-> "OE2" Residue "A ARG 668": "NH1" <-> "NH2" Residue "A ARG 749": "NH1" <-> "NH2" Residue "A ARG 775": "NH1" <-> "NH2" Residue "A ARG 780": "NH1" <-> "NH2" Residue "A ARG 1163": "NH1" <-> "NH2" Residue "A ARG 1442": "NH1" <-> "NH2" Residue "A PHE 1606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1650": "NH1" <-> "NH2" Residue "A ARG 1962": "NH1" <-> "NH2" Residue "C ARG 120": "NH1" <-> "NH2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 401": "NH1" <-> "NH2" Residue "C ARG 430": "NH1" <-> "NH2" Residue "C ARG 500": "NH1" <-> "NH2" Residue "C TYR 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 938": "NH1" <-> "NH2" Residue "H PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 349": "NH1" <-> "NH2" Residue "H ARG 382": "NH1" <-> "NH2" Residue "H ARG 439": "NH1" <-> "NH2" Residue "J ARG 143": "NH1" <-> "NH2" Residue "J ARG 186": "NH1" <-> "NH2" Residue "J TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 47": "NH1" <-> "NH2" Residue "K ARG 88": "NH1" <-> "NH2" Residue "K ARG 184": "NH1" <-> "NH2" Residue "K ARG 185": "NH1" <-> "NH2" Residue "K ARG 220": "NH1" <-> "NH2" Residue "L ARG 3": "NH1" <-> "NH2" Residue "L ARG 7": "NH1" <-> "NH2" Residue "L ARG 61": "NH1" <-> "NH2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 63": "NH1" <-> "NH2" Residue "M ARG 121": "NH1" <-> "NH2" Residue "M ARG 131": "NH1" <-> "NH2" Residue "M ARG 161": "NH1" <-> "NH2" Residue "M ARG 166": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 79": "NH1" <-> "NH2" Residue "N ARG 111": "NH1" <-> "NH2" Residue "N ARG 252": "NH1" <-> "NH2" Residue "N ARG 261": "NH1" <-> "NH2" Residue "O ARG 104": "NH1" <-> "NH2" Residue "O ARG 158": "NH1" <-> "NH2" Residue "O ARG 169": "NH1" <-> "NH2" Residue "O ARG 189": "NH1" <-> "NH2" Residue "P ARG 6": "NH1" <-> "NH2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "R ARG 22": "NH1" <-> "NH2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "S ARG 82": "NH1" <-> "NH2" Residue "S ARG 219": "NH1" <-> "NH2" Residue "a ARG 80": "NH1" <-> "NH2" Residue "c ARG 170": "NH1" <-> "NH2" Residue "o ARG 60": "NH1" <-> "NH2" Residue "o ARG 63": "NH1" <-> "NH2" Residue "o ARG 278": "NH1" <-> "NH2" Residue "o TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 396": "NH1" <-> "NH2" Residue "y ARG 110": "NH1" <-> "NH2" Residue "b ARG 11": "NH1" <-> "NH2" 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 ARG 97": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 58929 Number of models: 1 Model: "" Number of chains: 36 Chain: "I" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 714 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 13, 'rna3p_pyr': 18} Link IDs: {'rna2p': 3, 'rna3p': 30} Chain breaks: 1 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: "2" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1025 Classifications: {'RNA': 49} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 15, 'rna3p_pyr': 26} Link IDs: {'rna2p': 8, 'rna3p': 40} Chain: "6" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 2108 Classifications: {'RNA': 99} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 12, 'rna3p_pur': 45, 'rna3p_pyr': 34} Link IDs: {'rna2p': 20, 'rna3p': 78} Chain breaks: 1 Chain: "5" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2999 Classifications: {'RNA': 141} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 7, 'rna3p_pur': 59, 'rna3p_pyr': 61} Link IDs: {'rna2p': 20, 'rna3p': 120} Chain breaks: 2 Chain: "A" Number of atoms: 15199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1914, 15199 Classifications: {'peptide': 1914} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 162} Link IDs: {'PCIS': 2, 'PTRANS': 98, 'TRANS': 1813} Chain breaks: 3 Unresolved non-hydrogen bonds: 604 Unresolved non-hydrogen angles: 747 Unresolved non-hydrogen dihedrals: 469 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 28, 'PHE:plan': 1, 'GLU:plan': 69, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 459 Chain: "C" Number of atoms: 6562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 874, 6562 Classifications: {'peptide': 874} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PTRANS': 49, 'TRANS': 824} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 438 Unresolved non-hydrogen angles: 528 Unresolved non-hydrogen dihedrals: 368 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 16, 'PHE:plan': 1, 'GLU:plan': 37, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 280 Chain: "H" Number of atoms: 3261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3261 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 394} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "J" Number of atoms: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2690 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 12, 'TRANS': 329} Chain: "K" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1458 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "L" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1162 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 4, 'TRANS': 150} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ARG:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 76 Chain: "M" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2016 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 241} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "N" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1798 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "O" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1755 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 6, 'TRANS': 204} Chain breaks: 1 Chain: "P" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 565 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain breaks: 2 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: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 614 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 1, 'TRANS': 106} Chain breaks: 1 Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 320 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 14, 'ARG:plan': 9, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 13, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 173 Chain: "S" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3229 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 201} Link IDs: {'PTRANS': 8, 'TRANS': 459} Chain breaks: 14 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 853 Unresolved non-hydrogen angles: 1096 Unresolved non-hydrogen dihedrals: 742 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 17, 'ASN:plan1': 5, 'TRP:plan': 8, 'ASP:plan': 12, 'PHE:plan': 11, 'GLU:plan': 25, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 513 Chain: "T" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 1684 Classifications: {'peptide': 338} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 307} Link IDs: {'PTRANS': 11, 'TRANS': 326} Chain breaks: 13 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1155 Unresolved non-hydrogen angles: 1495 Unresolved non-hydrogen dihedrals: 976 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 4, 'UNK:plan-1': 18, 'TYR:plan': 16, 'ASN:plan1': 11, 'TRP:plan': 9, 'ASP:plan': 11, 'PHE:plan': 16, 'GLU:plan': 35, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 655 Chain: "a" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1119 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "c" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 786 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain breaks: 2 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 75 Planarities with less than four sites: {'GLU:plan': 8, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 60 Chain: "o" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2425 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 296} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "X" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 338 Classifications: {'peptide': 68} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 66} Link IDs: {'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 68} Unresolved non-hydrogen planarities: 68 Chain: "y" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 679 Classifications: {'peptide': 83} Link IDs: {'TRANS': 82} Chain breaks: 2 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: "6" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 2, ' MG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 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 37170 SG CYS L 104 119.572 159.622 55.145 1.00 75.41 S ATOM 37176 SG CYS L 105 116.218 159.636 57.619 1.00 94.62 S ATOM 37201 SG CYS L 108 119.316 156.956 57.042 1.00 75.02 S ATOM 37481 SG CYS L 148 117.163 157.670 54.259 1.00 84.39 S ATOM 37170 SG CYS L 104 119.572 159.622 55.145 1.00 75.41 S ATOM 37300 SG CYS L 122 122.565 156.429 55.032 1.00 79.14 S ATOM 37491 SG CYS L 150 120.985 158.015 52.098 1.00 83.92 S ATOM 37506 SG CYS L 153 122.563 160.191 54.033 1.00108.43 S ATOM 37201 SG CYS L 108 119.316 156.956 57.042 1.00 75.02 S ATOM 37286 SG CYS L 120 121.751 154.131 56.547 1.00 81.56 S ATOM 37300 SG CYS L 122 122.565 156.429 55.032 1.00 79.14 S ATOM 37458 SG CYS L 145 118.892 154.002 54.771 1.00 99.48 S ATOM 38091 SG CYS M 73 111.787 135.605 43.452 1.00 81.57 S ATOM 38153 SG CYS M 81 110.505 138.634 41.803 1.00 83.60 S ATOM 38193 SG CYS M 87 113.773 138.819 44.049 1.00106.84 S ATOM 39775 SG CYS N 34 114.684 121.535 69.008 1.00 79.22 S ATOM 39798 SG CYS N 37 114.780 119.622 71.558 1.00 94.61 S ATOM 39997 SG CYS N 61 117.804 121.307 71.827 1.00 90.51 S ATOM 40021 SG CYS N 64 117.609 118.493 70.140 1.00101.83 S ATOM 39617 SG CYS N 13 130.577 123.842 61.112 1.00136.95 S ATOM 39641 SG CYS N 16 127.770 126.378 59.960 1.00150.78 S ATOM 40075 SG CYS N 71 126.934 123.725 62.872 1.00119.28 S ATOM 40096 SG CYS N 74 127.840 123.931 59.418 1.00120.09 S Time building chain proxies: 23.71, per 1000 atoms: 0.40 Number of scatterers: 58929 At special positions: 0 Unit cell: (190.19, 260.26, 201.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 6 29.99 K 2 19.00 S 192 16.00 P 348 15.00 Mg 3 11.99 O 11753 8.00 N 10406 7.00 C 36219 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: 20.20 Conformation dependent library (CDL) restraints added in 7.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L1000 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 104 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 148 " 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 150 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 122 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 153 " pdb=" ZN L1002 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 108 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 122 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 120 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 145 " pdb=" ZN M1000 " pdb="ZN ZN M1000 " - pdb=" NE2 HIS M 91 " pdb="ZN ZN M1000 " - pdb=" SG CYS M 73 " pdb="ZN ZN M1000 " - pdb=" SG CYS M 87 " pdb="ZN ZN M1000 " - pdb=" SG CYS M 81 " pdb=" ZN N 401 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 34 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 64 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 37 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 61 " pdb=" ZN N 402 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 71 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 16 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 74 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 13 " Number of angles added : 33 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13020 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 258 helices and 55 sheets defined 45.4% alpha, 8.2% beta 99 base pairs and 168 stacking pairs defined. Time for finding SS restraints: 25.01 Creating SS restraints... Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 156 through 177 removed outlier: 4.397A pdb=" N LYS A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 4.415A 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 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 305 through 317 Proline residue: A 317 - end of helix Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 333 through 342 Processing helix 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 removed outlier: 3.883A pdb=" N SER A 478 " --> pdb=" O LYS A 474 " (cutoff:3.500A) 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 613 Processing helix chain 'A' and resid 619 through 640 Processing helix chain 'A' and resid 646 through 658 Processing helix chain 'A' and resid 660 through 663 No H-bonds generated for 'chain 'A' and resid 660 through 663' Processing helix chain 'A' and resid 666 through 669 No H-bonds generated for 'chain 'A' and resid 666 through 669' Processing helix chain 'A' and resid 671 through 691 removed outlier: 4.011A pdb=" N TYR A 688 " --> pdb=" O HIS A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 734 Proline residue: A 720 - end of helix Processing helix chain 'A' and resid 750 through 769 Processing helix chain 'A' and resid 776 through 795 removed outlier: 3.705A pdb=" N THR A 781 " --> pdb=" O LYS A 777 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 782 " --> pdb=" O LYS A 778 " (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 925 removed outlier: 3.717A pdb=" N VAL A 922 " --> pdb=" O ASP A 918 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N SER A 925 " --> pdb=" O ASP A 921 " (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: 3.714A 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 Processing helix chain 'A' and resid 1076 through 1086 Processing helix chain 'A' and resid 1109 through 1135 removed outlier: 3.940A pdb=" N GLY A1127 " --> pdb=" O LEU A1124 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N GLN A1128 " --> pdb=" O LEU A1125 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU A1129 " --> pdb=" O LEU A1126 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG A1130 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA A1131 " --> pdb=" O GLN A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1155 Processing helix chain 'A' and resid 1176 through 1189 Processing helix chain 'A' and resid 1217 through 1233 Processing helix chain 'A' and resid 1243 through 1245 No H-bonds generated for 'chain 'A' and resid 1243 through 1245' 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 1386 through 1389 No H-bonds generated for 'chain 'A' and resid 1386 through 1389' 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 1441 through 1443 No H-bonds generated for 'chain 'A' and resid 1441 through 1443' Processing helix chain 'A' and resid 1447 through 1471 Processing helix chain 'A' and resid 1483 through 1485 No H-bonds generated for 'chain 'A' and resid 1483 through 1485' Processing helix chain 'A' and resid 1491 through 1494 Processing helix chain 'A' and resid 1499 through 1504 removed outlier: 5.396A pdb=" N TYR A1504 " --> pdb=" O HIS A1500 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1515 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 Processing helix chain 'A' and resid 1552 through 1559 removed outlier: 4.180A pdb=" N GLU A1558 " --> pdb=" O GLU A1554 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N HIS A1559 " --> pdb=" O THR A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1562 through 1565 No H-bonds generated for 'chain 'A' and resid 1562 through 1565' Processing helix chain 'A' and resid 1571 through 1573 No H-bonds generated for 'chain 'A' and resid 1571 through 1573' Processing helix chain 'A' and resid 1602 through 1609 removed outlier: 3.857A pdb=" N PHE A1606 " --> pdb=" O PRO A1602 " (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 Processing helix chain 'A' and resid 1653 through 1671 Processing helix chain 'A' and resid 1688 through 1691 Processing helix chain 'A' and resid 1749 through 1759 Processing helix chain 'A' and resid 1795 through 1808 Processing helix chain 'A' and resid 1810 through 1822 Processing helix chain 'A' and resid 1841 through 1843 No H-bonds generated for 'chain 'A' and resid 1841 through 1843' Processing helix chain 'A' and resid 1896 through 1900 Processing helix chain 'A' and resid 1905 through 1923 removed outlier: 3.668A pdb=" N LYS A1910 " --> pdb=" O SER A1906 " (cutoff:3.500A) Processing helix chain 'A' and resid 1941 through 1950 removed outlier: 3.807A pdb=" N VAL A1946 " --> pdb=" O ASP A1942 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASP A1950 " --> pdb=" O VAL A1946 " (cutoff:3.500A) Processing helix chain 'A' and resid 1967 through 1970 Processing helix chain 'A' and resid 1972 through 1980 Processing helix chain 'A' and resid 1994 through 1998 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 2066 Processing helix chain 'A' and resid 2075 through 2083 Processing helix chain 'A' and resid 2091 through 2099 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 221 through 231 Processing helix chain 'C' and resid 247 through 259 Processing helix chain 'C' and resid 270 through 275 Processing helix chain 'C' and resid 281 through 298 Processing helix chain 'C' and resid 324 through 331 Processing helix chain 'C' and resid 339 through 348 removed outlier: 3.878A pdb=" N ASP C 342 " --> pdb=" O SER C 339 " (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 414 removed outlier: 3.860A pdb=" N GLN C 414 " --> pdb=" O GLN C 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 410 through 414' Processing helix chain 'C' and resid 417 through 428 Processing helix chain 'C' and resid 434 through 444 Processing helix chain 'C' and resid 447 through 456 removed outlier: 3.548A pdb=" N ASP C 450 " --> pdb=" O GLU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 465 No H-bonds generated for 'chain 'C' and resid 463 through 465' Processing helix chain 'C' and resid 508 through 514 Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' 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 662 Processing helix chain 'C' and resid 717 through 724 removed outlier: 3.600A pdb=" N GLN C 721 " --> pdb=" O SER C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 755 Processing helix chain 'C' and resid 760 through 764 Processing helix chain 'C' and resid 782 through 785 No H-bonds generated for 'chain 'C' and resid 782 through 785' Processing helix chain 'C' and resid 793 through 804 Processing helix chain 'C' and resid 831 through 852 Proline residue: C 840 - end of helix Processing helix chain 'C' and resid 870 through 882 Proline residue: C 874 - end of helix Processing helix chain 'C' and resid 914 through 921 Processing helix chain 'C' and resid 962 through 974 Processing helix chain 'C' and resid 991 through 996 Processing helix chain 'H' and resid 12 through 31 Proline residue: H 27 - end of helix removed outlier: 3.826A pdb=" N SER H 30 " --> pdb=" O SER H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 removed outlier: 4.092A pdb=" N LEU H 37 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLN H 38 " --> pdb=" O ASP H 35 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLU H 39 " --> pdb=" O ASN H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 65 Processing helix chain 'H' and resid 72 through 86 Processing helix chain 'H' and resid 88 through 107 Processing helix chain 'H' and resid 111 through 126 Processing helix chain 'H' and resid 134 through 144 Processing helix chain 'H' and resid 152 through 164 removed outlier: 5.808A pdb=" N TRP H 160 " --> pdb=" O LYS H 156 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LYS H 161 " --> pdb=" O ILE H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 182 Processing helix chain 'H' and resid 188 through 203 removed outlier: 3.681A pdb=" N LYS H 203 " --> pdb=" O GLU H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 261 removed outlier: 3.810A pdb=" N THR H 252 " --> pdb=" O PHE H 248 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA H 254 " --> pdb=" O GLU H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 290 through 301 Processing helix chain 'H' and resid 305 through 314 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 370 Processing helix chain 'H' and resid 372 through 375 Processing helix chain 'H' and resid 378 through 392 Processing helix chain 'H' and resid 416 through 430 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 111 through 120 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 88 through 91 Processing helix chain 'K' and resid 154 through 163 Proline residue: K 160 - end of helix Processing helix chain 'K' and resid 182 through 185 No H-bonds generated for 'chain 'K' and resid 182 through 185' Processing helix chain 'K' and resid 201 through 224 Processing helix chain 'L' and resid 14 through 33 removed outlier: 3.715A pdb=" N GLU L 17 " --> pdb=" O ASP L 14 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS L 18 " --> pdb=" O GLY L 15 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS L 20 " --> pdb=" O GLU L 17 " (cutoff:3.500A) Proline residue: L 21 - end of helix removed outlier: 3.691A pdb=" N THR L 24 " --> pdb=" O PRO L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 67 Processing helix chain 'L' and resid 75 through 84 Processing helix chain 'L' and resid 89 through 96 Processing helix chain 'L' and resid 106 through 109 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 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 102 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: 3.655A pdb=" N ARG M 166 " --> pdb=" O PHE M 162 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU M 167 " --> pdb=" O VAL M 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 198 Processing helix chain 'M' and resid 232 through 253 removed outlier: 4.182A pdb=" N ARG M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 68 Processing helix chain 'N' and resid 84 through 93 Processing helix chain 'N' and resid 107 through 115 removed outlier: 4.013A pdb=" N ARG N 111 " --> pdb=" O ASP N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 127 removed outlier: 4.287A pdb=" N ILE N 125 " --> pdb=" O GLY N 121 " (cutoff:3.500A) Processing helix chain 'N' and resid 129 through 143 Processing helix chain 'N' and resid 216 through 225 Processing helix chain 'N' and resid 256 through 265 Processing helix chain 'N' and resid 307 through 323 Processing helix chain 'O' and resid 15 through 28 Processing helix chain 'O' and resid 33 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 106 Processing helix chain 'O' and resid 145 through 159 Processing helix chain 'O' and resid 165 through 194 Processing helix chain 'O' and resid 231 through 250 Processing helix chain 'P' and resid 15 through 19 Processing helix chain 'P' and resid 164 through 172 Processing helix chain 'R' and resid 11 through 14 No H-bonds generated for 'chain 'R' and resid 11 through 14' Processing helix chain 'R' and resid 26 through 30 Processing helix chain 'R' and resid 37 through 46 removed outlier: 3.589A pdb=" N GLN R 43 " --> pdb=" O ARG R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 86 Processing helix chain 'R' and resid 92 through 115 Processing helix chain 'S' and resid 40 through 60 Processing helix chain 'S' and resid 65 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 133 through 146 Processing helix chain 'S' and resid 149 through 162 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 260 through 273 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 removed outlier: 3.562A pdb=" N LYS S 425 " --> pdb=" O PRO S 421 " (cutoff:3.500A) 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 408 through 419 removed outlier: 3.877A pdb=" N LYS T 419 " --> pdb=" O VAL T 415 " (cutoff:3.500A) Processing helix chain 'T' and resid 425 through 434 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 450 through 460 Processing helix chain 'T' and resid 463 through 474 Processing helix chain 'T' and resid 484 through 496 removed outlier: 3.517A pdb=" N ARG T 494 " --> pdb=" O ASN T 490 " (cutoff:3.500A) Processing helix chain 'T' and resid 503 through 522 Proline residue: T 515 - end of helix 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 596 Processing helix chain 'T' and resid 602 through 613 Proline residue: T 613 - end of helix Processing helix chain 'T' and resid 619 through 633 Processing helix chain 'T' and resid 642 through 654 Processing helix chain 'T' and resid 662 through 676 Processing helix chain 'T' and resid 681 through 692 Processing helix chain 'T' and resid 703 through 718 Processing helix chain 'T' and resid 724 through 734 Processing helix chain 'T' and resid 740 through 754 Processing helix chain 'T' and resid 759 through 770 Processing helix chain 'T' and resid 778 through 789 Processing helix chain 'T' and resid 1001 through 1016 Processing helix chain 'a' and resid 77 through 88 Processing helix chain 'a' and resid 107 through 126 Processing helix chain 'a' and resid 134 through 152 removed outlier: 4.052A pdb=" N ASP a 138 " --> pdb=" O GLU a 134 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS a 141 " --> pdb=" O LEU a 137 " (cutoff:3.500A) Proline residue: a 145 - end of helix removed outlier: 3.746A pdb=" N ARG a 152 " --> pdb=" O LEU a 148 " (cutoff:3.500A) Processing helix chain 'a' and resid 157 through 171 removed outlier: 3.558A pdb=" N SER a 162 " --> pdb=" O ASP a 158 " (cutoff:3.500A) Processing helix chain 'a' and resid 176 through 187 Processing helix chain 'a' and resid 226 through 245 Processing helix chain 'c' and resid 167 through 171 Processing helix chain 'c' and resid 180 through 195 removed outlier: 3.588A pdb=" N ASP c 192 " --> pdb=" O LYS c 188 " (cutoff:3.500A) Processing helix chain 'c' and resid 218 through 223 Processing helix chain 'c' and resid 295 through 312 Processing helix chain 'c' and resid 325 through 328 No H-bonds generated for 'chain 'c' and resid 325 through 328' Processing helix chain 'c' and resid 334 through 347 removed outlier: 3.711A pdb=" N LEU c 339 " --> pdb=" O TYR c 336 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS c 342 " --> pdb=" O LEU c 339 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN c 345 " --> pdb=" O LYS c 342 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU c 346 " --> pdb=" O ARG c 343 " (cutoff:3.500A) Processing helix chain 'o' and resid 53 through 59 Processing helix chain 'o' and resid 277 through 282 Processing helix chain 'X' and resid 7 through 14 Processing helix chain 'X' and resid 17 through 25 Processing helix chain 'X' and resid 93 through 128 removed outlier: 4.649A pdb=" N UNK X 107 " --> pdb=" O UNK X 103 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N UNK X 108 " --> pdb=" O UNK X 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N UNK X 117 " --> pdb=" O UNK X 113 " (cutoff:3.500A) Processing helix chain 'y' and resid 97 through 113 Processing helix chain 'y' and resid 158 through 183 Processing helix chain 'y' and resid 198 through 208 removed outlier: 3.509A pdb=" N GLN y 202 " --> pdb=" O ASP y 198 " (cutoff:3.500A) 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 13 Processing helix chain 'd' and resid 66 through 68 No H-bonds generated for 'chain 'd' and resid 66 through 68' 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 22 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 30 through 40 removed outlier: 3.994A pdb=" N ILE j 34 " --> pdb=" O MET j 31 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA j 37 " --> pdb=" O ILE j 34 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR j 40 " --> pdb=" O ALA j 37 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 188 through 194 Processing sheet with id= B, first strand: chain 'A' and resid 591 through 593 Processing sheet with id= C, first strand: chain 'A' and resid 968 through 972 Processing sheet with id= D, first strand: chain 'A' and resid 1167 through 1174 Processing sheet with id= E, first strand: chain 'A' and resid 1257 through 1262 removed outlier: 6.935A pdb=" N LEU A1288 " --> pdb=" O THR A1297 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS A1299 " --> pdb=" O TRP A1286 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TRP A1286 " --> pdb=" O LYS A1299 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1406 through 1408 Processing sheet with id= G, first strand: chain 'A' and resid 1624 through 1626 Processing sheet with id= H, first strand: chain 'A' and resid 1731 through 1734 Processing sheet with id= I, first strand: chain 'A' and resid 1773 through 1778 Processing sheet with id= J, first strand: chain 'A' and resid 1880 through 1882 removed outlier: 6.166A pdb=" N GLN A1932 " --> pdb=" O LEU A1850 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL A1852 " --> pdb=" O GLN A1932 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE A1934 " --> pdb=" O VAL A1852 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA A1955 " --> pdb=" O ILE A1933 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N VAL A1935 " --> pdb=" O ALA A1955 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ARG A1957 " --> pdb=" O VAL A1935 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1859 through 1864 removed outlier: 4.560A pdb=" N ARG A1859 " --> pdb=" O ILE A1875 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 133 through 135 removed outlier: 8.931A pdb=" N ILE C 134 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET C 209 " --> pdb=" O ILE C 134 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 238 through 240 removed outlier: 6.327A pdb=" N VAL C 266 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ILE C 312 " --> pdb=" O ILE C 267 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 500 through 503 removed outlier: 4.357A pdb=" N LEU C 468 " --> pdb=" O SER C 579 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP C 469 " --> pdb=" O SER C 490 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER C 490 " --> pdb=" O TRP C 469 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N HIS C 471 " --> pdb=" O ILE C 488 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ILE C 488 " --> pdb=" O HIS C 471 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 474 through 476 Processing sheet with id= P, first strand: chain 'C' and resid 492 through 494 Processing sheet with id= Q, first strand: chain 'C' and resid 543 through 545 Processing sheet with id= R, first strand: chain 'C' and resid 642 through 646 Processing sheet with id= S, first strand: chain 'C' and resid 678 through 681 Processing sheet with id= T, first strand: chain 'C' and resid 775 through 777 removed outlier: 6.395A pdb=" N SER C 709 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 928 through 931 removed outlier: 4.035A pdb=" N LYS C 890 " --> pdb=" O ARG C 903 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLN C 905 " --> pdb=" O ILE C 888 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ILE C 888 " --> pdb=" O GLN C 905 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 144 through 147 removed outlier: 6.462A pdb=" N ASP J 168 " --> pdb=" O LEU J 174 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU J 174 " --> pdb=" O ASP J 168 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 185 through 190 removed outlier: 6.953A pdb=" N VAL J 200 " --> pdb=" O ARG J 186 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL J 188 " --> pdb=" O PHE J 198 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE J 198 " --> pdb=" O VAL J 188 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL J 190 " --> pdb=" O TYR J 196 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TYR J 196 " --> pdb=" O VAL J 190 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ASP J 210 " --> pdb=" O ILE J 216 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ILE J 216 " --> pdb=" O ASP J 210 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 227 through 232 removed outlier: 6.902A pdb=" N ALA J 242 " --> pdb=" O ARG J 228 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL J 230 " --> pdb=" O ALA J 240 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA J 240 " --> pdb=" O VAL J 230 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE J 232 " --> pdb=" O LEU J 238 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU J 238 " --> pdb=" O ILE J 232 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY J 243 " --> pdb=" O VAL J 247 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL J 247 " --> pdb=" O GLY J 243 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE J 248 " --> pdb=" O LEU J 262 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASP J 252 " --> pdb=" O PRO J 258 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'J' and resid 271 through 274 removed outlier: 4.668A pdb=" N VAL J 281 " --> pdb=" O TRP J 293 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ASP J 294 " --> pdb=" O THR J 300 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N THR J 300 " --> pdb=" O ASP J 294 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'J' and resid 314 through 316 Processing sheet with id= AA, first strand: chain 'J' and resid 363 through 367 removed outlier: 3.958A pdb=" N ALA J 366 " --> pdb=" O SER J 374 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASP J 377 " --> pdb=" O LYS J 383 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LYS J 383 " --> pdb=" O ASP J 377 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 129 through 133 removed outlier: 6.641A pdb=" N ILE J 425 " --> pdb=" O SER J 132 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'J' and resid 333 through 335 removed outlier: 4.791A pdb=" N GLY J 335 " --> pdb=" O LEU J 341 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LEU J 341 " --> pdb=" O GLY J 335 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'M' and resid 222 through 225 removed outlier: 3.778A pdb=" N LEU M 137 " --> pdb=" O VAL M 184 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'N' and resid 26 through 28 Processing sheet with id= AF, first strand: chain 'N' and resid 206 through 208 removed outlier: 4.138A pdb=" N PHE N 206 " --> pdb=" O PRO N 292 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE N 290 " --> pdb=" O TYR N 208 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'o' and resid 156 through 158 removed outlier: 4.241A pdb=" N LYS o 450 " --> pdb=" O GLY o 446 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'o' and resid 177 through 179 Processing sheet with id= AI, first strand: chain 'o' and resid 230 through 234 removed outlier: 3.692A pdb=" N ALA o 211 " --> pdb=" O SER o 224 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'o' and resid 252 through 255 removed outlier: 3.637A pdb=" N ASP o 252 " --> pdb=" O GLY o 266 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'o' and resid 339 through 342 removed outlier: 3.503A pdb=" N MET o 339 " --> pdb=" O GLN o 354 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'o' and resid 385 through 388 removed outlier: 4.341A pdb=" N TYR o 385 " --> pdb=" O GLY o 401 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'y' and resid 144 through 146 Processing sheet with id= AN, first strand: chain 'b' and resid 80 through 83 removed outlier: 6.183A pdb=" N CYS b 48 " --> pdb=" O LEU b 82 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ARG b 21 " --> pdb=" O VAL b 97 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N VAL b 97 " --> pdb=" O ARG b 21 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU b 23 " --> pdb=" O THR b 95 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N THR b 95 " --> pdb=" O LEU b 23 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'b' and resid 43 through 45 Processing sheet with id= AP, first strand: chain 'd' and resid 69 through 73 removed outlier: 7.059A pdb=" N GLU d 22 " --> pdb=" O LYS d 70 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE d 72 " --> pdb=" O SER d 20 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N SER d 20 " --> pdb=" O ILE d 72 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN d 43 " --> pdb=" O VAL d 34 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'd' and resid 48 through 50 Processing sheet with id= AR, first strand: chain 'e' and resid 26 through 30 Processing sheet with id= AS, first strand: chain 'e' and resid 52 through 54 removed outlier: 4.090A pdb=" N VAL e 52 " --> pdb=" O LEU e 82 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU e 82 " --> pdb=" O VAL e 52 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'f' and resid 71 through 73 removed outlier: 3.865A pdb=" N GLN f 52 " --> pdb=" O SER f 44 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER f 44 " --> pdb=" O GLN f 52 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ASN f 54 " --> pdb=" O LEU f 42 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU f 42 " --> pdb=" O ASN f 54 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'f' and resid 28 through 31 Processing sheet with id= AV, first strand: chain 'g' and resid 23 through 25 Processing sheet with id= AW, first strand: chain 'g' and resid 38 through 41 Processing sheet with id= AX, first strand: chain 'h' and resid 24 through 26 Processing sheet with id= AY, first strand: chain 'h' and resid 84 through 87 removed outlier: 6.637A pdb=" N THR h 41 " --> pdb=" O LEU h 29 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LEU h 29 " --> pdb=" O THR h 41 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'h' and resid 16 through 19 Processing sheet with id= BA, first strand: chain 'j' and resid 67 through 70 Processing sheet with id= BB, first strand: chain 'j' and resid 72 through 77 Processing sheet with id= BC, first strand: chain 'j' and resid 44 through 48 removed outlier: 3.907A pdb=" N VAL j 103 " --> pdb=" O SER j 47 " (cutoff:3.500A) 2288 hydrogen bonds defined for protein. 6375 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 236 hydrogen bonds 416 hydrogen bond angles 0 basepair planarities 99 basepair parallelities 168 stacking parallelities Total time for adding SS restraints: 30.36 Time building geometry restraints manager: 22.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 8927 1.31 - 1.44: 17815 1.44 - 1.57: 33015 1.57 - 1.70: 683 1.70 - 1.82: 315 Bond restraints: 60755 Sorted by residual: bond pdb=" C SER c 230 " pdb=" O SER c 230 " ideal model delta sigma weight residual 1.231 1.345 -0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" C HIS A1658 " pdb=" O HIS A1658 " ideal model delta sigma weight residual 1.236 1.302 -0.065 1.15e-02 7.56e+03 3.23e+01 bond pdb=" CA PRO e 12 " pdb=" C PRO e 12 " ideal model delta sigma weight residual 1.514 1.546 -0.031 5.50e-03 3.31e+04 3.22e+01 bond pdb=" CD GLN C 251 " pdb=" OE1 GLN C 251 " ideal model delta sigma weight residual 1.231 1.332 -0.101 1.90e-02 2.77e+03 2.84e+01 bond pdb=" ND1 HIS A 194 " pdb=" CE1 HIS A 194 " ideal model delta sigma weight residual 1.321 1.374 -0.053 1.00e-02 1.00e+04 2.79e+01 ... (remaining 60750 not shown) Histogram of bond angle deviations from ideal: 95.93 - 104.08: 1989 104.08 - 112.22: 29026 112.22 - 120.37: 28218 120.37 - 128.52: 23888 128.52 - 136.66: 908 Bond angle restraints: 84029 Sorted by residual: angle pdb=" C ILE T 612 " pdb=" N PRO T 613 " pdb=" CA PRO T 613 " ideal model delta sigma weight residual 119.19 132.68 -13.49 1.06e+00 8.90e-01 1.62e+02 angle pdb=" CA VAL T 514 " pdb=" C VAL T 514 " pdb=" N PRO T 515 " ideal model delta sigma weight residual 120.83 114.65 6.18 6.10e-01 2.69e+00 1.03e+02 angle pdb=" C PHE T 615 " pdb=" N PRO T 616 " pdb=" CA PRO T 616 " ideal model delta sigma weight residual 120.38 130.57 -10.19 1.03e+00 9.43e-01 9.79e+01 angle pdb=" C4' G 5 27 " pdb=" C3' G 5 27 " pdb=" O3' G 5 27 " ideal model delta sigma weight residual 109.40 121.53 -12.13 1.50e+00 4.44e-01 6.54e+01 angle pdb=" C ASP T 436 " pdb=" N PRO T 437 " pdb=" CA PRO T 437 " ideal model delta sigma weight residual 119.28 128.15 -8.87 1.10e+00 8.26e-01 6.50e+01 ... (remaining 84024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 35443 35.47 - 70.93: 1385 70.93 - 106.40: 123 106.40 - 141.86: 13 141.86 - 177.33: 7 Dihedral angle restraints: 36971 sinusoidal: 17019 harmonic: 19952 Sorted by residual: dihedral pdb=" O4' C 5 79 " pdb=" C1' C 5 79 " pdb=" N1 C 5 79 " pdb=" C2 C 5 79 " ideal model delta sinusoidal sigma weight residual 200.00 68.37 131.63 1 1.50e+01 4.44e-03 7.10e+01 dihedral pdb=" O4' U E -9 " pdb=" C1' U E -9 " pdb=" N1 U E -9 " pdb=" C2 U E -9 " ideal model delta sinusoidal sigma weight residual 232.00 83.87 148.13 1 1.70e+01 3.46e-03 6.14e+01 dihedral pdb=" CA ILE C 105 " pdb=" C ILE C 105 " pdb=" N PHE C 106 " pdb=" CA PHE C 106 " ideal model delta harmonic sigma weight residual -180.00 -144.34 -35.66 0 5.00e+00 4.00e-02 5.09e+01 ... (remaining 36968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.990: 9965 0.990 - 1.980: 0 1.980 - 2.970: 0 2.970 - 3.961: 0 3.961 - 4.951: 2 Chirality restraints: 9967 Sorted by residual: chirality pdb=" C2 IHP A3001 " pdb=" C1 IHP A3001 " pdb=" C3 IHP A3001 " pdb=" O12 IHP A3001 " both_signs ideal model delta sigma weight residual False -2.52 2.43 -4.95 2.00e-01 2.50e+01 6.13e+02 chirality pdb=" C3 IHP A3001 " pdb=" C2 IHP A3001 " pdb=" C4 IHP A3001 " pdb=" O13 IHP A3001 " both_signs ideal model delta sigma weight residual False -2.34 2.45 -4.79 2.00e-01 2.50e+01 5.74e+02 chirality pdb=" C3' C 6 92 " pdb=" C4' C 6 92 " pdb=" O3' C 6 92 " pdb=" C2' C 6 92 " both_signs ideal model delta sigma weight residual False -2.74 -2.01 -0.73 2.00e-01 2.50e+01 1.35e+01 ... (remaining 9964 not shown) Planarity restraints: 9414 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE H 73 " 0.071 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO H 74 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO H 74 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO H 74 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 379 " -0.062 5.00e-02 4.00e+02 9.37e-02 1.41e+01 pdb=" N PRO C 380 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO C 380 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 380 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G 5 32 " -0.022 2.00e-02 2.50e+03 2.13e-02 1.36e+01 pdb=" N9 G 5 32 " 0.001 2.00e-02 2.50e+03 pdb=" C8 G 5 32 " 0.008 2.00e-02 2.50e+03 pdb=" N7 G 5 32 " 0.009 2.00e-02 2.50e+03 pdb=" C5 G 5 32 " 0.010 2.00e-02 2.50e+03 pdb=" C6 G 5 32 " 0.011 2.00e-02 2.50e+03 pdb=" O6 G 5 32 " -0.012 2.00e-02 2.50e+03 pdb=" N1 G 5 32 " -0.048 2.00e-02 2.50e+03 pdb=" C2 G 5 32 " 0.046 2.00e-02 2.50e+03 pdb=" N2 G 5 32 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G 5 32 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G 5 32 " -0.003 2.00e-02 2.50e+03 ... (remaining 9411 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.21: 11 2.21 - 2.94: 24243 2.94 - 3.68: 112692 3.68 - 4.41: 178517 4.41 - 5.14: 275286 Nonbonded interactions: 590749 Sorted by model distance: nonbonded pdb=" N1 A 5 45 " pdb=" O4 U 5 74 " model vdw 1.479 2.496 nonbonded pdb=" P G I 1 " pdb=" O2' A I 70 " model vdw 1.619 3.400 nonbonded pdb=" O LYS H 311 " pdb=" CD2 LEU H 315 " model vdw 1.854 3.460 nonbonded pdb=" OP1 G 6 78 " pdb="MG MG 61001 " model vdw 2.100 2.170 nonbonded pdb=" OP2 U 6 80 " pdb="MG MG 61001 " model vdw 2.100 2.170 ... (remaining 590744 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 16.440 Check model and map are aligned: 0.700 Set scattering table: 0.410 Process input model: 158.330 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.170 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 183.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 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 : 0.008 0.114 60755 Z= 0.551 Angle : 1.406 13.862 84029 Z= 0.986 Chirality : 0.110 4.951 9967 Planarity : 0.006 0.108 9414 Dihedral : 17.763 177.326 23951 Min Nonbonded Distance : 1.479 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.88 % Allowed : 8.54 % Favored : 90.57 % Rotamer: Outliers : 2.50 % Allowed : 7.84 % Favored : 89.66 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.05 % 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: -2.11 (0.09), residues: 6554 helix: 0.22 (0.08), residues: 3058 sheet: -3.25 (0.16), residues: 682 loop : -2.81 (0.10), residues: 2814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 711 HIS 0.013 0.002 HIS A 138 PHE 0.039 0.003 PHE J 198 TYR 0.030 0.003 TYR J 378 ARG 0.010 0.001 ARG C 973 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1497 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1369 time to evaluate : 4.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9377 (mmm) cc_final: 0.9089 (mmm) REVERT: A 168 LEU cc_start: 0.9717 (tp) cc_final: 0.9438 (tt) REVERT: A 177 GLU cc_start: 0.9015 (tt0) cc_final: 0.8752 (tt0) REVERT: A 224 MET cc_start: 0.8943 (mtt) cc_final: 0.8622 (mtm) REVERT: A 326 ASN cc_start: 0.9628 (OUTLIER) cc_final: 0.9243 (t0) REVERT: A 375 PHE cc_start: 0.8301 (m-80) cc_final: 0.7919 (m-10) REVERT: A 407 VAL cc_start: 0.9246 (t) cc_final: 0.8907 (m) REVERT: A 423 PHE cc_start: 0.9186 (p90) cc_final: 0.8843 (p90) REVERT: A 493 MET cc_start: 0.8901 (mmt) cc_final: 0.8567 (mmm) REVERT: A 498 ASP cc_start: 0.8879 (m-30) cc_final: 0.8661 (m-30) REVERT: A 527 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8831 (tttp) REVERT: A 588 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.8929 (pp) REVERT: A 610 ARG cc_start: 0.8988 (ttt180) cc_final: 0.8738 (ttp-110) REVERT: A 618 SER cc_start: 0.9428 (t) cc_final: 0.9020 (p) REVERT: A 693 LYS cc_start: 0.8339 (mtmt) cc_final: 0.8008 (pttt) REVERT: A 714 PHE cc_start: 0.9090 (t80) cc_final: 0.8753 (t80) REVERT: A 726 ILE cc_start: 0.9579 (OUTLIER) cc_final: 0.9370 (mm) REVERT: A 754 TYR cc_start: 0.9363 (t80) cc_final: 0.9151 (t80) REVERT: A 780 ARG cc_start: 0.9258 (mmp80) cc_final: 0.8384 (mtt-85) REVERT: A 928 ARG cc_start: 0.8362 (ttp80) cc_final: 0.7996 (tpt170) REVERT: A 933 GLU cc_start: 0.9578 (mt-10) cc_final: 0.9012 (mt-10) REVERT: A 971 MET cc_start: 0.8985 (mmt) cc_final: 0.8748 (mmm) REVERT: A 1004 ASP cc_start: 0.8825 (m-30) cc_final: 0.8492 (t0) REVERT: A 1059 GLU cc_start: 0.8403 (mp0) cc_final: 0.8089 (mp0) REVERT: A 1095 MET cc_start: 0.8832 (ptp) cc_final: 0.8623 (ptp) REVERT: A 1163 ARG cc_start: 0.9180 (ttp80) cc_final: 0.8836 (tmm-80) REVERT: A 1263 CYS cc_start: 0.8926 (m) cc_final: 0.8709 (m) REVERT: A 1288 LEU cc_start: 0.9493 (mp) cc_final: 0.9211 (mt) REVERT: A 1335 TRP cc_start: 0.8820 (t60) cc_final: 0.8394 (t60) REVERT: A 1414 TRP cc_start: 0.9101 (m-90) cc_final: 0.8582 (m-10) REVERT: A 1467 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8801 (tm-30) REVERT: A 1485 ASP cc_start: 0.8850 (m-30) cc_final: 0.8581 (p0) REVERT: A 1516 GLN cc_start: 0.8958 (tt0) cc_final: 0.8512 (mt0) REVERT: A 1539 LEU cc_start: 0.9325 (mt) cc_final: 0.9087 (mt) REVERT: A 1545 ASP cc_start: 0.8952 (m-30) cc_final: 0.8570 (m-30) REVERT: A 1757 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8365 (pp) REVERT: A 1778 ASP cc_start: 0.9358 (t0) cc_final: 0.9117 (t0) REVERT: A 1783 MET cc_start: 0.8780 (mtt) cc_final: 0.8493 (mmm) REVERT: A 1807 LYS cc_start: 0.9312 (tptt) cc_final: 0.8804 (mptt) REVERT: A 1880 PHE cc_start: 0.8042 (t80) cc_final: 0.7740 (t80) REVERT: A 1899 TRP cc_start: 0.9006 (m100) cc_final: 0.8630 (m100) REVERT: A 1903 LYS cc_start: 0.9274 (tppp) cc_final: 0.8961 (tptp) REVERT: A 1908 LEU cc_start: 0.9275 (tp) cc_final: 0.8896 (tp) REVERT: A 1940 MET cc_start: 0.9495 (OUTLIER) cc_final: 0.8909 (tmt) REVERT: A 1979 MET cc_start: 0.9044 (mmp) cc_final: 0.8755 (mmp) REVERT: C 126 MET cc_start: 0.8747 (tpp) cc_final: 0.8396 (tpp) REVERT: C 164 MET cc_start: 0.8865 (ptm) cc_final: 0.8607 (tmm) REVERT: C 221 PHE cc_start: 0.9300 (m-80) cc_final: 0.9058 (m-80) REVERT: C 222 MET cc_start: 0.9519 (mmm) cc_final: 0.9061 (mmp) REVERT: C 264 CYS cc_start: 0.8848 (t) cc_final: 0.8605 (t) REVERT: C 282 MET cc_start: 0.9363 (tpt) cc_final: 0.8893 (tpp) REVERT: C 478 TYR cc_start: 0.8596 (t80) cc_final: 0.8294 (t80) REVERT: C 538 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8548 (tm-30) REVERT: C 540 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8856 (mt-10) REVERT: C 545 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9054 (pp) REVERT: C 603 PHE cc_start: 0.9252 (t80) cc_final: 0.9022 (t80) REVERT: C 614 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8719 (mm-30) REVERT: C 834 MET cc_start: 0.5269 (tpp) cc_final: 0.4931 (tmm) REVERT: C 862 TYR cc_start: 0.9235 (m-80) cc_final: 0.8908 (m-80) REVERT: C 880 MET cc_start: 0.9205 (mmm) cc_final: 0.8823 (mmm) REVERT: C 931 TYR cc_start: 0.9130 (p90) cc_final: 0.8638 (p90) REVERT: C 933 TRP cc_start: 0.7632 (p90) cc_final: 0.7405 (p90) REVERT: C 937 TRP cc_start: 0.8950 (m100) cc_final: 0.8196 (m100) REVERT: H 158 CYS cc_start: 0.9204 (p) cc_final: 0.8655 (p) REVERT: H 170 HIS cc_start: 0.8646 (t-170) cc_final: 0.8298 (t-170) REVERT: H 180 ILE cc_start: 0.8755 (mt) cc_final: 0.8504 (mt) REVERT: H 186 LEU cc_start: 0.7137 (OUTLIER) cc_final: 0.6727 (mt) REVERT: H 195 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7977 (tm-30) REVERT: H 350 MET cc_start: 0.8743 (mtt) cc_final: 0.8318 (mtt) REVERT: H 357 TRP cc_start: 0.9089 (OUTLIER) cc_final: 0.8340 (m-10) REVERT: H 386 LYS cc_start: 0.9549 (mmtp) cc_final: 0.9280 (ttmm) REVERT: H 396 PHE cc_start: 0.8616 (m-10) cc_final: 0.8378 (m-10) REVERT: H 430 GLU cc_start: 0.9060 (tp30) cc_final: 0.8821 (tm-30) REVERT: J 124 GLU cc_start: 0.8852 (pm20) cc_final: 0.8401 (pm20) REVERT: J 131 LEU cc_start: 0.9373 (tp) cc_final: 0.9168 (tt) REVERT: J 187 ASP cc_start: 0.9190 (t70) cc_final: 0.8448 (t0) REVERT: J 203 ASP cc_start: 0.8737 (p0) cc_final: 0.8492 (p0) REVERT: J 245 ASP cc_start: 0.9420 (p0) cc_final: 0.9173 (p0) REVERT: J 273 GLN cc_start: 0.9079 (mm-40) cc_final: 0.8746 (mm-40) REVERT: J 346 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8500 (mp0) REVERT: J 360 GLN cc_start: 0.9284 (tt0) cc_final: 0.9009 (tp40) REVERT: J 382 HIS cc_start: 0.9004 (t70) cc_final: 0.8711 (t70) REVERT: J 443 ASN cc_start: 0.9086 (OUTLIER) cc_final: 0.8878 (t0) REVERT: K 37 ASN cc_start: 0.9195 (OUTLIER) cc_final: 0.8936 (m-40) REVERT: K 42 ASP cc_start: 0.9052 (m-30) cc_final: 0.8739 (m-30) REVERT: K 48 GLN cc_start: 0.8120 (pp30) cc_final: 0.7534 (pp30) REVERT: K 64 GLN cc_start: 0.8759 (mt0) cc_final: 0.8467 (mt0) REVERT: K 112 ILE cc_start: 0.8682 (tt) cc_final: 0.8465 (mm) REVERT: K 120 ASP cc_start: 0.8799 (p0) cc_final: 0.8511 (p0) REVERT: K 123 LEU cc_start: 0.9725 (mp) cc_final: 0.9484 (mt) REVERT: K 141 ASP cc_start: 0.8811 (m-30) cc_final: 0.8443 (m-30) REVERT: K 142 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8675 (tp30) REVERT: L 53 MET cc_start: 0.9084 (tpp) cc_final: 0.8867 (tpp) REVERT: L 55 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9025 (tt) REVERT: L 88 ASP cc_start: 0.9296 (t0) cc_final: 0.8950 (t0) REVERT: M 31 ASN cc_start: 0.8852 (OUTLIER) cc_final: 0.8610 (t0) REVERT: M 32 ILE cc_start: 0.9742 (mm) cc_final: 0.9504 (mm) REVERT: M 34 TYR cc_start: 0.9309 (m-80) cc_final: 0.7893 (m-80) REVERT: M 96 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8797 (pm20) REVERT: M 98 ASP cc_start: 0.9122 (m-30) cc_final: 0.8839 (m-30) REVERT: M 102 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8870 (pt) REVERT: M 136 THR cc_start: 0.9593 (m) cc_final: 0.9169 (p) REVERT: M 171 ASP cc_start: 0.9098 (t70) cc_final: 0.8040 (m-30) REVERT: M 193 GLU cc_start: 0.8528 (mt-10) cc_final: 0.7562 (mt-10) REVERT: M 199 MET cc_start: 0.9156 (mmm) cc_final: 0.8637 (mmm) REVERT: M 235 GLN cc_start: 0.9615 (tp-100) cc_final: 0.8967 (mm110) REVERT: M 238 LEU cc_start: 0.9644 (tt) cc_final: 0.9287 (tp) REVERT: N 6 ASN cc_start: 0.8586 (p0) cc_final: 0.8018 (t0) REVERT: N 68 ARG cc_start: 0.9278 (mpt90) cc_final: 0.8534 (mpt180) REVERT: N 73 CYS cc_start: 0.8530 (m) cc_final: 0.8184 (m) REVERT: N 81 HIS cc_start: 0.8807 (m90) cc_final: 0.7838 (t70) REVERT: N 118 VAL cc_start: 0.8960 (m) cc_final: 0.7512 (m) REVERT: N 134 ASN cc_start: 0.9440 (m-40) cc_final: 0.9230 (m-40) REVERT: N 137 ASP cc_start: 0.9264 (t70) cc_final: 0.8689 (p0) REVERT: O 49 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8804 (tp30) REVERT: O 50 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9189 (tp) REVERT: O 76 LEU cc_start: 0.9293 (mt) cc_final: 0.8997 (mm) REVERT: O 156 ARG cc_start: 0.2227 (tpp-160) cc_final: 0.1550 (tpt170) REVERT: O 173 GLU cc_start: 0.9352 (mt-10) cc_final: 0.9030 (mm-30) REVERT: O 198 VAL cc_start: 0.7744 (t) cc_final: 0.7521 (p) REVERT: O 201 LYS cc_start: 0.8348 (mttm) cc_final: 0.8136 (ttpt) REVERT: O 212 ASP cc_start: 0.8898 (t0) cc_final: 0.8230 (t0) REVERT: O 219 TYR cc_start: 0.8656 (m-80) cc_final: 0.7835 (m-80) REVERT: O 237 ILE cc_start: 0.9483 (tp) cc_final: 0.9272 (pt) REVERT: O 238 LYS cc_start: 0.9395 (ttmt) cc_final: 0.9193 (tptp) REVERT: P 6 ARG cc_start: 0.9063 (mtt180) cc_final: 0.8707 (ttt-90) REVERT: P 35 THR cc_start: 0.9137 (p) cc_final: 0.8901 (p) REVERT: P 157 ILE cc_start: 0.9233 (mt) cc_final: 0.8877 (tp) REVERT: P 160 MET cc_start: 0.9246 (mmm) cc_final: 0.8845 (tpp) REVERT: P 164 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8436 (tp30) REVERT: P 174 VAL cc_start: 0.9104 (t) cc_final: 0.8865 (m) REVERT: R 8 LEU cc_start: 0.8515 (tt) cc_final: 0.8073 (tt) REVERT: R 17 SER cc_start: 0.9570 (OUTLIER) cc_final: 0.9272 (t) REVERT: S 75 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8761 (mm-30) REVERT: S 89 GLU cc_start: 0.9341 (mm-30) cc_final: 0.9123 (mm-30) REVERT: S 95 ASP cc_start: 0.9293 (t0) cc_final: 0.8969 (t0) REVERT: S 122 MET cc_start: 0.8749 (mtm) cc_final: 0.8379 (mtp) REVERT: S 146 LEU cc_start: 0.9269 (mm) cc_final: 0.8937 (mt) REVERT: S 156 TYR cc_start: 0.9064 (OUTLIER) cc_final: 0.8722 (t80) REVERT: S 171 SER cc_start: 0.9366 (m) cc_final: 0.8874 (m) REVERT: S 233 GLN cc_start: 0.8298 (tp40) cc_final: 0.7832 (tp-100) REVERT: S 272 GLU cc_start: 0.9327 (tt0) cc_final: 0.8924 (tm-30) REVERT: a 99 GLN cc_start: 0.8824 (mm110) cc_final: 0.8454 (pt0) REVERT: a 138 ASP cc_start: 0.9331 (m-30) cc_final: 0.8809 (t0) REVERT: a 152 ARG cc_start: 0.8968 (mmm160) cc_final: 0.8708 (tpp80) REVERT: a 154 GLN cc_start: 0.7145 (mt0) cc_final: 0.6532 (mt0) REVERT: a 185 LYS cc_start: 0.9321 (ptmm) cc_final: 0.8420 (tppt) REVERT: a 226 THR cc_start: 0.8960 (m) cc_final: 0.8688 (p) REVERT: c 219 MET cc_start: 0.4183 (ttm) cc_final: 0.3927 (ttm) REVERT: c 297 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8526 (tp) REVERT: c 300 ASN cc_start: 0.9445 (t0) cc_final: 0.9039 (t0) REVERT: c 301 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8698 (mm-30) REVERT: c 326 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8728 (tp-100) REVERT: c 347 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7382 (mt-10) REVERT: o 320 TRP cc_start: 0.8020 (m-10) cc_final: 0.6730 (m-10) REVERT: o 431 GLN cc_start: 0.8577 (mt0) cc_final: 0.8180 (tm-30) REVERT: o 434 TRP cc_start: 0.7004 (m100) cc_final: 0.6401 (m100) REVERT: y 99 GLN cc_start: 0.9277 (mm-40) cc_final: 0.8995 (mt0) REVERT: y 103 LEU cc_start: 0.9246 (mt) cc_final: 0.9043 (mp) REVERT: y 105 TYR cc_start: 0.9298 (t80) cc_final: 0.9026 (t80) REVERT: y 157 ASP cc_start: 0.8739 (m-30) cc_final: 0.8325 (t0) REVERT: y 162 ASN cc_start: 0.9401 (OUTLIER) cc_final: 0.9073 (m-40) REVERT: y 169 GLN cc_start: 0.9581 (mt0) cc_final: 0.9299 (tt0) REVERT: y 182 GLN cc_start: 0.9448 (mt0) cc_final: 0.9091 (mt0) REVERT: y 204 ASN cc_start: 0.9174 (m-40) cc_final: 0.8721 (m110) REVERT: b 20 LEU cc_start: 0.8822 (mp) cc_final: 0.8544 (tp) REVERT: b 41 MET cc_start: 0.9066 (mmm) cc_final: 0.8449 (mtp) REVERT: b 46 ASN cc_start: 0.8050 (t0) cc_final: 0.7462 (t0) REVERT: b 51 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8807 (mp0) REVERT: b 90 GLU cc_start: 0.7362 (tt0) cc_final: 0.7126 (tt0) REVERT: b 94 SER cc_start: 0.9588 (p) cc_final: 0.9180 (t) REVERT: b 100 LYS cc_start: 0.8498 (pttt) cc_final: 0.8272 (mmmt) REVERT: d 9 LYS cc_start: 0.8537 (mttt) cc_final: 0.8232 (mtpp) REVERT: d 19 VAL cc_start: 0.8865 (m) cc_final: 0.8590 (p) REVERT: d 35 GLU cc_start: 0.8721 (tt0) cc_final: 0.8033 (tt0) REVERT: d 39 SER cc_start: 0.9241 (p) cc_final: 0.8887 (p) REVERT: d 45 ARG cc_start: 0.9206 (mtt-85) cc_final: 0.8748 (tpp80) REVERT: d 53 GLN cc_start: 0.7671 (mp10) cc_final: 0.7131 (mp10) REVERT: d 60 ASP cc_start: 0.8731 (m-30) cc_final: 0.8091 (p0) REVERT: d 76 ASP cc_start: 0.9094 (m-30) cc_final: 0.8609 (p0) REVERT: e 22 GLN cc_start: 0.8382 (mt0) cc_final: 0.7790 (mt0) REVERT: e 27 VAL cc_start: 0.7971 (t) cc_final: 0.7535 (t) REVERT: e 50 MET cc_start: 0.7124 (mmm) cc_final: 0.6224 (mtp) REVERT: f 26 ARG cc_start: 0.9055 (ttm170) cc_final: 0.8777 (mtp-110) REVERT: f 55 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7932 (tm-30) REVERT: f 67 THR cc_start: 0.7049 (p) cc_final: 0.6808 (t) REVERT: g 11 MET cc_start: 0.8547 (mmm) cc_final: 0.8071 (mmm) REVERT: g 16 LEU cc_start: 0.7015 (mt) cc_final: 0.6487 (mp) REVERT: g 32 TYR cc_start: 0.6293 (p90) cc_final: 0.5095 (p90) REVERT: g 38 VAL cc_start: 0.8843 (t) cc_final: 0.8614 (p) REVERT: g 56 GLN cc_start: 0.6709 (tt0) cc_final: 0.6125 (pm20) REVERT: g 69 ILE cc_start: 0.7368 (mm) cc_final: 0.6813 (mm) REVERT: g 72 GLU cc_start: 0.7439 (tm-30) cc_final: 0.7193 (mp0) REVERT: g 75 ASP cc_start: 0.6426 (t0) cc_final: 0.6027 (m-30) REVERT: h 18 GLU cc_start: 0.8105 (tt0) cc_final: 0.7850 (tp30) REVERT: h 94 GLN cc_start: 0.8786 (mt0) cc_final: 0.8563 (mm110) REVERT: j 89 ARG cc_start: 0.8276 (ptt180) cc_final: 0.8073 (mmm-85) outliers start: 128 outliers final: 39 residues processed: 1464 average time/residue: 0.6283 time to fit residues: 1536.5572 Evaluate side-chains 878 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 820 time to evaluate : 4.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 527 LYS Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 1212 ARG Chi-restraints excluded: chain A residue 1337 THR Chi-restraints excluded: chain A residue 1650 ARG Chi-restraints excluded: chain A residue 1757 LEU Chi-restraints excluded: chain A residue 1940 MET Chi-restraints excluded: chain A residue 1951 PHE Chi-restraints excluded: chain A residue 1997 ASP Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 590 LYS Chi-restraints excluded: chain C residue 658 ASP Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 193 SER Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 315 LEU Chi-restraints excluded: chain H residue 357 TRP Chi-restraints excluded: chain H residue 419 PHE Chi-restraints excluded: chain H residue 421 LYS Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 216 ILE Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 261 THR Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain J residue 443 ASN Chi-restraints excluded: chain K residue 37 ASN Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 153 CYS Chi-restraints excluded: chain L residue 155 SER Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 288 ILE Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 98 CYS Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain R residue 17 SER Chi-restraints excluded: chain S residue 65 MET Chi-restraints excluded: chain S residue 124 ARG Chi-restraints excluded: chain S residue 156 TYR Chi-restraints excluded: chain S residue 232 LEU Chi-restraints excluded: chain S residue 237 ILE Chi-restraints excluded: chain c residue 297 LEU Chi-restraints excluded: chain o residue 331 ILE Chi-restraints excluded: chain y residue 162 ASN Chi-restraints excluded: chain e residue 92 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 591 optimal weight: 6.9990 chunk 530 optimal weight: 20.0000 chunk 294 optimal weight: 6.9990 chunk 181 optimal weight: 3.9990 chunk 357 optimal weight: 3.9990 chunk 283 optimal weight: 6.9990 chunk 548 optimal weight: 7.9990 chunk 212 optimal weight: 0.9990 chunk 333 optimal weight: 7.9990 chunk 408 optimal weight: 3.9990 chunk 635 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 155 ASN A 344 ASN ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 HIS ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 848 ASN A 997 GLN A1091 ASN A1140 ASN A1190 ASN A1369 ASN ** A1508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1782 ASN A1856 ASN A2047 GLN C 143 HIS C 158 HIS ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 HIS C 289 ASN C 290 HIS C 310 ASN ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 ASN C 431 GLN C 511 GLN C 683 ASN C 764 ASN C 776 ASN ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 320 ASN H 367 GLN J 270 ASN J 443 ASN K 50 ASN K 86 ASN K 171 ASN K 192 ASN K 195 ASN ** L 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 116 ASN ** M 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 ASN M 235 GLN N 106 ASN ** N 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 ASN O 26 GLN ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 161 ASN O 197 ASN P 34 HIS P 158 ASN S 47 GLN S 79 HIS S 147 ASN ** S 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 248 ASN c 183 ASN c 304 GLN ** o 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 348 GLN y 99 GLN y 185 ASN ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 8 HIS b 33 GLN b 40 HIS ** e 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 24 ASN f 47 ASN g 66 ASN j 64 HIS Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 60755 Z= 0.419 Angle : 0.796 21.493 84029 Z= 0.402 Chirality : 0.046 0.555 9967 Planarity : 0.006 0.066 9414 Dihedral : 18.614 175.947 12584 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.33 % Favored : 93.61 % Rotamer: Outliers : 4.78 % Allowed : 14.61 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.02 (0.10), residues: 6554 helix: 1.22 (0.09), residues: 3075 sheet: -2.80 (0.16), residues: 774 loop : -2.32 (0.11), residues: 2705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP a 229 HIS 0.018 0.002 HIS j 28 PHE 0.024 0.002 PHE A1114 TYR 0.026 0.002 TYR f 80 ARG 0.009 0.001 ARG a 123 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1122 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 877 time to evaluate : 5.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9406 (mmm) cc_final: 0.8979 (mmm) REVERT: A 168 LEU cc_start: 0.9668 (tp) cc_final: 0.9380 (tt) REVERT: A 224 MET cc_start: 0.8863 (mtt) cc_final: 0.8593 (mtt) REVERT: A 296 THR cc_start: 0.9279 (OUTLIER) cc_final: 0.9053 (p) REVERT: A 326 ASN cc_start: 0.9614 (OUTLIER) cc_final: 0.9135 (t0) REVERT: A 422 LEU cc_start: 0.9365 (mt) cc_final: 0.9086 (tt) REVERT: A 493 MET cc_start: 0.9051 (mmt) cc_final: 0.8711 (mmm) REVERT: A 497 GLN cc_start: 0.9060 (tt0) cc_final: 0.8859 (tt0) REVERT: A 498 ASP cc_start: 0.9006 (m-30) cc_final: 0.8734 (m-30) REVERT: A 578 MET cc_start: 0.8867 (mtp) cc_final: 0.8516 (mtp) REVERT: A 618 SER cc_start: 0.9367 (t) cc_final: 0.8948 (p) REVERT: A 656 ILE cc_start: 0.9513 (mt) cc_final: 0.9206 (mt) REVERT: A 693 LYS cc_start: 0.8024 (mtmt) cc_final: 0.7768 (pttt) REVERT: A 712 LEU cc_start: 0.9596 (mt) cc_final: 0.9027 (tp) REVERT: A 726 ILE cc_start: 0.9559 (tt) cc_final: 0.9345 (mm) REVERT: A 928 ARG cc_start: 0.8347 (ttp80) cc_final: 0.8090 (tpt170) REVERT: A 933 GLU cc_start: 0.9487 (mt-10) cc_final: 0.9148 (mp0) REVERT: A 1059 GLU cc_start: 0.8291 (mp0) cc_final: 0.8054 (mp0) REVERT: A 1085 LYS cc_start: 0.9467 (tptm) cc_final: 0.9124 (tppp) REVERT: A 1288 LEU cc_start: 0.9449 (mp) cc_final: 0.9155 (mt) REVERT: A 1346 PHE cc_start: 0.9491 (OUTLIER) cc_final: 0.7916 (p90) REVERT: A 1485 ASP cc_start: 0.8841 (m-30) cc_final: 0.8615 (p0) REVERT: A 1519 LEU cc_start: 0.9022 (mt) cc_final: 0.8794 (mt) REVERT: A 1545 ASP cc_start: 0.8932 (m-30) cc_final: 0.8583 (m-30) REVERT: A 1632 ILE cc_start: 0.9673 (mm) cc_final: 0.9391 (pt) REVERT: A 1778 ASP cc_start: 0.9264 (t0) cc_final: 0.8931 (t0) REVERT: A 1807 LYS cc_start: 0.9346 (tptt) cc_final: 0.8667 (mmtt) REVERT: A 1817 GLU cc_start: 0.9556 (tt0) cc_final: 0.8996 (tm-30) REVERT: A 1866 PHE cc_start: 0.8903 (m-10) cc_final: 0.8698 (m-10) REVERT: A 1880 PHE cc_start: 0.7917 (t80) cc_final: 0.7621 (t80) REVERT: A 1908 LEU cc_start: 0.9274 (tp) cc_final: 0.9047 (tp) REVERT: A 1940 MET cc_start: 0.9462 (OUTLIER) cc_final: 0.8706 (tmm) REVERT: A 1979 MET cc_start: 0.8866 (mmp) cc_final: 0.8620 (mmp) REVERT: C 126 MET cc_start: 0.8632 (tpp) cc_final: 0.8248 (tpp) REVERT: C 150 MET cc_start: 0.9549 (mmm) cc_final: 0.9133 (mmm) REVERT: C 210 ILE cc_start: 0.9405 (mt) cc_final: 0.9143 (mt) REVERT: C 222 MET cc_start: 0.9347 (mmm) cc_final: 0.8644 (mmp) REVERT: C 225 THR cc_start: 0.9597 (OUTLIER) cc_final: 0.9007 (p) REVERT: C 282 MET cc_start: 0.9338 (tpt) cc_final: 0.9101 (tpp) REVERT: C 538 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8442 (tm-30) REVERT: C 545 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9213 (pt) REVERT: C 603 PHE cc_start: 0.9168 (t80) cc_final: 0.8876 (t80) REVERT: C 614 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8849 (tp30) REVERT: C 880 MET cc_start: 0.9365 (mmm) cc_final: 0.8756 (mmm) REVERT: C 937 TRP cc_start: 0.9001 (m100) cc_final: 0.8092 (m100) REVERT: H 158 CYS cc_start: 0.9025 (p) cc_final: 0.8534 (p) REVERT: H 160 TRP cc_start: 0.7710 (p-90) cc_final: 0.7497 (p-90) REVERT: H 167 LYS cc_start: 0.8318 (pttp) cc_final: 0.7934 (tttt) REVERT: H 180 ILE cc_start: 0.8767 (mt) cc_final: 0.8493 (mt) REVERT: H 195 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8018 (tm-30) REVERT: H 357 TRP cc_start: 0.9096 (OUTLIER) cc_final: 0.8360 (m-10) REVERT: H 373 ILE cc_start: 0.8927 (tp) cc_final: 0.8707 (tp) REVERT: H 386 LYS cc_start: 0.9499 (mmtp) cc_final: 0.9266 (ttmm) REVERT: H 430 GLU cc_start: 0.9183 (tp30) cc_final: 0.8839 (tm-30) REVERT: H 473 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7578 (pp) REVERT: J 124 GLU cc_start: 0.8736 (pm20) cc_final: 0.8274 (pm20) REVERT: J 187 ASP cc_start: 0.9242 (t70) cc_final: 0.8654 (t0) REVERT: J 273 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8788 (mm-40) REVERT: J 346 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8510 (mp0) REVERT: J 360 GLN cc_start: 0.9295 (tt0) cc_final: 0.9066 (tp40) REVERT: K 37 ASN cc_start: 0.9189 (OUTLIER) cc_final: 0.8871 (m-40) REVERT: K 42 ASP cc_start: 0.8910 (m-30) cc_final: 0.8480 (m-30) REVERT: L 55 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9187 (tt) REVERT: M 136 THR cc_start: 0.9485 (m) cc_final: 0.9170 (p) REVERT: M 171 ASP cc_start: 0.9153 (t70) cc_final: 0.8299 (m-30) REVERT: M 188 TYR cc_start: 0.9441 (m-80) cc_final: 0.9129 (m-80) REVERT: M 193 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8425 (mt-10) REVERT: M 199 MET cc_start: 0.9018 (mmm) cc_final: 0.8722 (mmm) REVERT: M 235 GLN cc_start: 0.9585 (tp40) cc_final: 0.9000 (mm110) REVERT: N 88 ASP cc_start: 0.8876 (m-30) cc_final: 0.7482 (t0) REVERT: N 137 ASP cc_start: 0.9060 (t70) cc_final: 0.8655 (p0) REVERT: N 221 ASP cc_start: 0.8940 (m-30) cc_final: 0.8561 (p0) REVERT: O 48 SER cc_start: 0.9743 (t) cc_final: 0.9358 (p) REVERT: O 53 ASN cc_start: 0.9533 (m-40) cc_final: 0.9154 (m-40) REVERT: O 173 GLU cc_start: 0.9441 (mt-10) cc_final: 0.9167 (mm-30) REVERT: O 185 LEU cc_start: 0.9464 (tp) cc_final: 0.9145 (tp) REVERT: O 201 LYS cc_start: 0.8531 (mttm) cc_final: 0.8317 (ttpt) REVERT: O 219 TYR cc_start: 0.8275 (m-80) cc_final: 0.7957 (m-80) REVERT: O 238 LYS cc_start: 0.9434 (ttmt) cc_final: 0.9169 (tptp) REVERT: P 6 ARG cc_start: 0.8882 (mtt180) cc_final: 0.8443 (ttm-80) REVERT: P 8 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8238 (tm-30) REVERT: P 157 ILE cc_start: 0.9197 (mt) cc_final: 0.8867 (tp) REVERT: P 164 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8337 (tp30) REVERT: R 8 LEU cc_start: 0.8301 (tt) cc_final: 0.8072 (tp) REVERT: S 75 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8514 (tp30) REVERT: S 95 ASP cc_start: 0.9352 (t0) cc_final: 0.8943 (t0) REVERT: S 122 MET cc_start: 0.8644 (mtm) cc_final: 0.8389 (mtp) REVERT: S 146 LEU cc_start: 0.9506 (mm) cc_final: 0.9270 (mt) REVERT: S 163 GLU cc_start: 0.9449 (mt-10) cc_final: 0.8591 (tm-30) REVERT: S 272 GLU cc_start: 0.9197 (tt0) cc_final: 0.8734 (tm-30) REVERT: a 79 GLU cc_start: 0.7692 (pt0) cc_final: 0.7457 (pt0) REVERT: a 138 ASP cc_start: 0.9376 (m-30) cc_final: 0.8885 (t0) REVERT: a 152 ARG cc_start: 0.8972 (mmm160) cc_final: 0.8728 (mmm-85) REVERT: a 154 GLN cc_start: 0.6659 (mt0) cc_final: 0.6089 (mt0) REVERT: a 185 LYS cc_start: 0.9344 (ptmm) cc_final: 0.9068 (tmtt) REVERT: c 181 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8253 (tm-30) REVERT: c 297 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8701 (tp) REVERT: c 300 ASN cc_start: 0.9431 (t0) cc_final: 0.9024 (t0) REVERT: c 301 GLU cc_start: 0.9391 (mt-10) cc_final: 0.8657 (mm-30) REVERT: c 326 GLN cc_start: 0.9076 (mm-40) cc_final: 0.8840 (tp-100) REVERT: c 343 ARG cc_start: 0.8333 (ttm-80) cc_final: 0.8099 (ttm-80) REVERT: c 347 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7376 (mm-30) REVERT: o 194 HIS cc_start: 0.8449 (m-70) cc_final: 0.7869 (p90) REVERT: o 262 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8240 (tt0) REVERT: o 320 TRP cc_start: 0.7894 (m-10) cc_final: 0.7090 (m-10) REVERT: o 385 TYR cc_start: 0.8444 (t80) cc_final: 0.8118 (t80) REVERT: o 431 GLN cc_start: 0.8345 (mt0) cc_final: 0.7994 (tm-30) REVERT: y 99 GLN cc_start: 0.9153 (mm110) cc_final: 0.8940 (mt0) REVERT: y 103 LEU cc_start: 0.9208 (mt) cc_final: 0.8980 (mm) REVERT: y 105 TYR cc_start: 0.9341 (t80) cc_final: 0.9117 (t80) REVERT: y 157 ASP cc_start: 0.8788 (m-30) cc_final: 0.8317 (t0) REVERT: y 162 ASN cc_start: 0.9428 (OUTLIER) cc_final: 0.9049 (m-40) REVERT: y 169 GLN cc_start: 0.9577 (mt0) cc_final: 0.9365 (tt0) REVERT: y 182 GLN cc_start: 0.9331 (mt0) cc_final: 0.9105 (mt0) REVERT: b 23 LEU cc_start: 0.9015 (tp) cc_final: 0.8801 (tp) REVERT: b 31 ILE cc_start: 0.8365 (pt) cc_final: 0.8109 (pt) REVERT: b 35 MET cc_start: 0.8581 (mmm) cc_final: 0.8309 (mmm) REVERT: b 41 MET cc_start: 0.9157 (mmm) cc_final: 0.8559 (mtp) REVERT: b 93 LEU cc_start: 0.8711 (mt) cc_final: 0.8315 (mt) REVERT: b 94 SER cc_start: 0.9531 (p) cc_final: 0.8985 (t) REVERT: d 9 LYS cc_start: 0.8753 (mttt) cc_final: 0.8350 (mtpp) REVERT: d 29 TYR cc_start: 0.8392 (m-80) cc_final: 0.8176 (m-80) REVERT: d 45 ARG cc_start: 0.8982 (mtt-85) cc_final: 0.8633 (tpp80) REVERT: d 60 ASP cc_start: 0.8624 (m-30) cc_final: 0.8310 (p0) REVERT: d 76 ASP cc_start: 0.9111 (m-30) cc_final: 0.8763 (p0) REVERT: e 50 MET cc_start: 0.7093 (mmm) cc_final: 0.6198 (mtp) REVERT: g 56 GLN cc_start: 0.6882 (tt0) cc_final: 0.6027 (pm20) REVERT: g 69 ILE cc_start: 0.7011 (mm) cc_final: 0.6720 (mm) REVERT: g 75 ASP cc_start: 0.6701 (t0) cc_final: 0.6198 (m-30) REVERT: h 96 ILE cc_start: 0.9215 (mt) cc_final: 0.9003 (mm) REVERT: j 89 ARG cc_start: 0.8257 (ptt180) cc_final: 0.7951 (mmm-85) outliers start: 245 outliers final: 137 residues processed: 1060 average time/residue: 0.5298 time to fit residues: 973.9155 Evaluate side-chains 858 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 709 time to evaluate : 4.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 694 ASN Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1212 ARG Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1313 ASP Chi-restraints excluded: chain A residue 1319 ILE Chi-restraints excluded: chain A residue 1337 THR Chi-restraints excluded: chain A residue 1346 PHE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1420 THR Chi-restraints excluded: chain A residue 1439 THR Chi-restraints excluded: chain A residue 1440 ILE Chi-restraints excluded: chain A residue 1444 ILE Chi-restraints excluded: chain A residue 1457 VAL Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1553 ILE Chi-restraints excluded: chain A residue 1621 VAL Chi-restraints excluded: chain A residue 1650 ARG Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1757 LEU Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1940 MET Chi-restraints excluded: chain A residue 1951 PHE Chi-restraints excluded: chain A residue 1995 TRP Chi-restraints excluded: chain A residue 1997 ASP Chi-restraints excluded: chain A residue 2017 THR Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 182 GLN Chi-restraints excluded: chain H residue 193 SER Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 357 TRP Chi-restraints excluded: chain H residue 433 LEU Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 211 LEU Chi-restraints excluded: chain J residue 232 ILE Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 261 THR Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 327 CYS Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain J residue 352 ILE Chi-restraints excluded: chain J residue 408 ASP Chi-restraints excluded: chain K residue 37 ASN Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 155 SER Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 163 VAL Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain N residue 288 ILE Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 98 CYS Chi-restraints excluded: chain O residue 211 ILE Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 37 LEU Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 161 THR Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain S residue 58 LEU Chi-restraints excluded: chain S residue 124 ARG Chi-restraints excluded: chain S residue 128 THR Chi-restraints excluded: chain S residue 156 TYR Chi-restraints excluded: chain S residue 157 THR Chi-restraints excluded: chain S residue 232 LEU Chi-restraints excluded: chain S residue 237 ILE Chi-restraints excluded: chain S residue 279 LEU Chi-restraints excluded: chain a residue 132 HIS Chi-restraints excluded: chain a residue 137 LEU Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 171 GLN Chi-restraints excluded: chain a residue 177 ASN Chi-restraints excluded: chain c residue 178 SER Chi-restraints excluded: chain c residue 297 LEU Chi-restraints excluded: chain c residue 332 ASN Chi-restraints excluded: chain o residue 173 LYS Chi-restraints excluded: chain o residue 331 ILE Chi-restraints excluded: chain o residue 381 SER Chi-restraints excluded: chain y residue 96 SER Chi-restraints excluded: chain y residue 112 LEU Chi-restraints excluded: chain y residue 161 VAL Chi-restraints excluded: chain y residue 162 ASN Chi-restraints excluded: chain y residue 164 LEU Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain d residue 22 GLU Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 74 VAL Chi-restraints excluded: chain d residue 85 LYS Chi-restraints excluded: chain e residue 15 ASN Chi-restraints excluded: chain h residue 6 PHE Chi-restraints excluded: chain h residue 42 ASP Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain j residue 91 ILE Chi-restraints excluded: chain j residue 101 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 353 optimal weight: 0.9990 chunk 197 optimal weight: 6.9990 chunk 529 optimal weight: 1.9990 chunk 432 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 636 optimal weight: 10.0000 chunk 687 optimal weight: 0.4980 chunk 567 optimal weight: 10.0000 chunk 631 optimal weight: 7.9990 chunk 217 optimal weight: 4.9990 chunk 510 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 254 HIS A 532 ASN ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN A1030 GLN A1097 HIS ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1508 HIS A2018 ASN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN H 59 ASN H 425 GLN K 37 ASN K 194 ASN L 115 ASN ** M 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 ASN ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 158 ASN P 167 GLN ** S 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 233 GLN ** a 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 14 ASN ** e 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 86 ASN g 66 ASN ** h 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 60755 Z= 0.220 Angle : 0.675 19.182 84029 Z= 0.337 Chirality : 0.042 0.435 9967 Planarity : 0.004 0.064 9414 Dihedral : 18.329 175.035 12543 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.58 % Favored : 94.37 % Rotamer: Outliers : 4.76 % Allowed : 16.38 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.46 (0.11), residues: 6554 helix: 1.64 (0.09), residues: 3088 sheet: -2.50 (0.16), residues: 774 loop : -2.00 (0.12), residues: 2692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP a 229 HIS 0.014 0.001 HIS H 170 PHE 0.028 0.002 PHE S 250 TYR 0.021 0.002 TYR H 369 ARG 0.007 0.000 ARG c 194 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1108 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 864 time to evaluate : 5.151 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: A 199 ILE cc_start: 0.9676 (tp) cc_final: 0.9246 (tt) REVERT: A 224 MET cc_start: 0.8827 (mtt) cc_final: 0.8603 (mtm) REVERT: A 326 ASN cc_start: 0.9317 (OUTLIER) cc_final: 0.8804 (t0) REVERT: A 493 MET cc_start: 0.9032 (mmt) cc_final: 0.8550 (mmm) REVERT: A 551 LEU cc_start: 0.9622 (mt) cc_final: 0.9367 (mp) REVERT: A 578 MET cc_start: 0.8799 (mtp) cc_final: 0.8577 (mtp) REVERT: A 588 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8932 (pp) REVERT: A 618 SER cc_start: 0.9157 (t) cc_final: 0.8832 (p) REVERT: A 626 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9179 (tp) REVERT: A 693 LYS cc_start: 0.8036 (mtmt) cc_final: 0.7833 (pttt) REVERT: A 712 LEU cc_start: 0.9453 (mt) cc_final: 0.9158 (mm) REVERT: A 726 ILE cc_start: 0.9522 (OUTLIER) cc_final: 0.9267 (mm) REVERT: A 780 ARG cc_start: 0.8935 (mmp80) cc_final: 0.8127 (mtt-85) REVERT: A 832 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8754 (mp0) REVERT: A 852 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9043 (tt) REVERT: A 905 TYR cc_start: 0.7409 (m-80) cc_final: 0.6973 (m-80) REVERT: A 933 GLU cc_start: 0.9452 (mt-10) cc_final: 0.9142 (mp0) REVERT: A 1085 LYS cc_start: 0.9476 (tptm) cc_final: 0.9077 (tppp) REVERT: A 1101 TYR cc_start: 0.8217 (t80) cc_final: 0.7946 (t80) REVERT: A 1288 LEU cc_start: 0.9420 (mp) cc_final: 0.9102 (mt) REVERT: A 1346 PHE cc_start: 0.9379 (OUTLIER) cc_final: 0.7763 (p90) REVERT: A 1400 ILE cc_start: 0.9492 (mm) cc_final: 0.9288 (mt) REVERT: A 1443 TYR cc_start: 0.8349 (m-80) cc_final: 0.8141 (m-10) REVERT: A 1450 GLU cc_start: 0.9173 (tp30) cc_final: 0.8576 (tm-30) REVERT: A 1485 ASP cc_start: 0.8790 (m-30) cc_final: 0.8565 (p0) REVERT: A 1519 LEU cc_start: 0.8999 (mt) cc_final: 0.8539 (mt) REVERT: A 1545 ASP cc_start: 0.8960 (m-30) cc_final: 0.8582 (m-30) REVERT: A 1687 HIS cc_start: 0.8967 (m-70) cc_final: 0.8616 (p-80) REVERT: A 1778 ASP cc_start: 0.9206 (t0) cc_final: 0.8910 (t0) REVERT: A 1783 MET cc_start: 0.8955 (mmm) cc_final: 0.8481 (mmm) REVERT: A 1807 LYS cc_start: 0.9324 (tptt) cc_final: 0.8658 (mmtt) REVERT: A 1817 GLU cc_start: 0.9495 (tt0) cc_final: 0.8895 (tm-30) REVERT: A 1880 PHE cc_start: 0.7795 (t80) cc_final: 0.7474 (t80) REVERT: A 1948 MET cc_start: 0.9224 (mmm) cc_final: 0.8693 (ppp) REVERT: A 1979 MET cc_start: 0.8824 (mmp) cc_final: 0.8613 (mmp) REVERT: A 1983 GLU cc_start: 0.8584 (pt0) cc_final: 0.8236 (pm20) REVERT: A 1986 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8636 (tpp) REVERT: C 150 MET cc_start: 0.9500 (mmm) cc_final: 0.9272 (mmm) REVERT: C 222 MET cc_start: 0.9185 (mmm) cc_final: 0.8768 (mmp) REVERT: C 282 MET cc_start: 0.9335 (tpt) cc_final: 0.9093 (tpp) REVERT: C 295 ILE cc_start: 0.9690 (mt) cc_final: 0.9436 (mt) REVERT: C 391 MET cc_start: 0.8772 (ttp) cc_final: 0.8307 (ttm) REVERT: C 538 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8428 (tm-30) REVERT: C 540 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8747 (mm-30) REVERT: C 545 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.8957 (pp) REVERT: C 880 MET cc_start: 0.9409 (mmm) cc_final: 0.8727 (mmm) REVERT: C 937 TRP cc_start: 0.8899 (m100) cc_final: 0.7941 (m100) REVERT: H 158 CYS cc_start: 0.9013 (p) cc_final: 0.8558 (t) REVERT: H 160 TRP cc_start: 0.7751 (p-90) cc_final: 0.7380 (p-90) REVERT: H 161 LYS cc_start: 0.9016 (tptt) cc_final: 0.8711 (tptm) REVERT: H 167 LYS cc_start: 0.8343 (pttp) cc_final: 0.8011 (tttt) REVERT: H 195 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7881 (tm-30) REVERT: H 314 LYS cc_start: 0.9443 (OUTLIER) cc_final: 0.9214 (ttmm) REVERT: H 357 TRP cc_start: 0.9046 (OUTLIER) cc_final: 0.8001 (m-10) REVERT: H 386 LYS cc_start: 0.9506 (mmtp) cc_final: 0.9265 (ttmm) REVERT: H 430 GLU cc_start: 0.9120 (tp30) cc_final: 0.8811 (tm-30) REVERT: J 117 LYS cc_start: 0.8899 (ttmt) cc_final: 0.8534 (tppt) REVERT: J 124 GLU cc_start: 0.8575 (pm20) cc_final: 0.8101 (pm20) REVERT: J 164 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7792 (mtm) REVERT: J 187 ASP cc_start: 0.9141 (t70) cc_final: 0.8392 (t0) REVERT: J 273 GLN cc_start: 0.8966 (mm-40) cc_final: 0.8746 (mm-40) REVERT: J 280 GLN cc_start: 0.7675 (mt0) cc_final: 0.7331 (mt0) REVERT: J 320 GLU cc_start: 0.7904 (tp30) cc_final: 0.7567 (tp30) REVERT: J 346 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8441 (mp0) REVERT: J 360 GLN cc_start: 0.9296 (tt0) cc_final: 0.9063 (tp40) REVERT: K 42 ASP cc_start: 0.8962 (m-30) cc_final: 0.8607 (m-30) REVERT: K 120 ASP cc_start: 0.8651 (p0) cc_final: 0.8275 (p0) REVERT: K 123 LEU cc_start: 0.9639 (mp) cc_final: 0.9370 (mt) REVERT: K 202 MET cc_start: 0.9470 (ptp) cc_final: 0.9141 (pmm) REVERT: L 41 LEU cc_start: 0.9064 (tp) cc_final: 0.8692 (mm) REVERT: L 50 TRP cc_start: 0.8912 (m-10) cc_final: 0.8140 (m-10) REVERT: M 136 THR cc_start: 0.9320 (m) cc_final: 0.9107 (p) REVERT: M 171 ASP cc_start: 0.9091 (t70) cc_final: 0.8742 (t0) REVERT: M 188 TYR cc_start: 0.9440 (m-80) cc_final: 0.9121 (m-80) REVERT: M 193 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8243 (mt-10) REVERT: M 199 MET cc_start: 0.9003 (mmm) cc_final: 0.8698 (mmm) REVERT: N 88 ASP cc_start: 0.8787 (m-30) cc_final: 0.7674 (t70) REVERT: N 106 ASN cc_start: 0.7884 (OUTLIER) cc_final: 0.7621 (t0) REVERT: N 137 ASP cc_start: 0.9013 (t70) cc_final: 0.8615 (p0) REVERT: N 226 LEU cc_start: 0.8967 (mp) cc_final: 0.8672 (tt) REVERT: O 48 SER cc_start: 0.9685 (t) cc_final: 0.9326 (p) REVERT: O 53 ASN cc_start: 0.9420 (m-40) cc_final: 0.9089 (m-40) REVERT: O 54 GLU cc_start: 0.8809 (tp30) cc_final: 0.8543 (pt0) REVERT: O 148 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7274 (pt0) REVERT: O 173 GLU cc_start: 0.9441 (mt-10) cc_final: 0.9165 (mm-30) REVERT: P 6 ARG cc_start: 0.8877 (mtt180) cc_final: 0.8455 (ttm-80) REVERT: P 8 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8082 (tm-30) REVERT: P 157 ILE cc_start: 0.9034 (mt) cc_final: 0.8718 (tp) REVERT: P 162 LYS cc_start: 0.9409 (mttt) cc_final: 0.9191 (mttp) REVERT: P 164 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8320 (tp30) REVERT: S 75 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8415 (tp30) REVERT: S 122 MET cc_start: 0.8564 (mtm) cc_final: 0.8275 (mtp) REVERT: S 124 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8651 (ttt180) REVERT: S 146 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9288 (mt) REVERT: S 156 TYR cc_start: 0.8905 (OUTLIER) cc_final: 0.8442 (t80) REVERT: S 163 GLU cc_start: 0.9354 (mt-10) cc_final: 0.8325 (tm-30) REVERT: S 272 GLU cc_start: 0.9125 (tt0) cc_final: 0.8601 (tm-30) REVERT: S 273 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7743 (mtmt) REVERT: S 287 PHE cc_start: 0.8071 (t80) cc_final: 0.7823 (t80) REVERT: a 99 GLN cc_start: 0.8883 (mm110) cc_final: 0.8543 (pt0) REVERT: a 138 ASP cc_start: 0.9350 (m-30) cc_final: 0.8861 (t0) REVERT: a 154 GLN cc_start: 0.6516 (mt0) cc_final: 0.5989 (mt0) REVERT: a 185 LYS cc_start: 0.9308 (ptmm) cc_final: 0.9018 (tmtt) REVERT: c 181 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8322 (tm-30) REVERT: c 195 ASN cc_start: 0.7073 (t0) cc_final: 0.6710 (t0) REVERT: c 297 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8795 (tp) REVERT: c 301 GLU cc_start: 0.9376 (mt-10) cc_final: 0.8744 (mm-30) REVERT: c 343 ARG cc_start: 0.8279 (ttm-80) cc_final: 0.8067 (ttm-80) REVERT: c 347 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7386 (mm-30) REVERT: o 194 HIS cc_start: 0.8364 (m-70) cc_final: 0.7750 (p90) REVERT: o 385 TYR cc_start: 0.8463 (t80) cc_final: 0.7703 (t80) REVERT: o 431 GLN cc_start: 0.8248 (mt0) cc_final: 0.7876 (tm-30) REVERT: o 443 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7535 (tt) REVERT: y 99 GLN cc_start: 0.9196 (mm110) cc_final: 0.8944 (mp10) REVERT: y 144 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8491 (mm-40) REVERT: y 153 THR cc_start: 0.9418 (m) cc_final: 0.8978 (p) REVERT: y 157 ASP cc_start: 0.8766 (m-30) cc_final: 0.8420 (t0) REVERT: y 162 ASN cc_start: 0.9440 (OUTLIER) cc_final: 0.9118 (m110) REVERT: y 171 GLU cc_start: 0.9301 (tp30) cc_final: 0.9046 (tp30) REVERT: y 182 GLN cc_start: 0.9213 (mt0) cc_final: 0.9004 (mt0) REVERT: b 35 MET cc_start: 0.8598 (mmm) cc_final: 0.8294 (mmm) REVERT: b 41 MET cc_start: 0.9108 (mmm) cc_final: 0.8555 (mtp) REVERT: b 44 VAL cc_start: 0.8596 (t) cc_final: 0.8197 (t) REVERT: b 45 LEU cc_start: 0.8233 (mt) cc_final: 0.7647 (tp) REVERT: b 46 ASN cc_start: 0.8731 (t0) cc_final: 0.8314 (t0) REVERT: b 51 GLU cc_start: 0.8689 (mp0) cc_final: 0.8269 (mp0) REVERT: b 90 GLU cc_start: 0.7313 (tt0) cc_final: 0.7004 (mt-10) REVERT: b 93 LEU cc_start: 0.8796 (mt) cc_final: 0.8321 (mt) REVERT: d 9 LYS cc_start: 0.8651 (mttt) cc_final: 0.8320 (mtpp) REVERT: d 45 ARG cc_start: 0.8838 (mtt-85) cc_final: 0.8594 (tpp80) REVERT: d 60 ASP cc_start: 0.8628 (m-30) cc_final: 0.8364 (p0) REVERT: d 76 ASP cc_start: 0.9007 (m-30) cc_final: 0.8464 (p0) REVERT: d 77 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8435 (mp) REVERT: f 58 GLU cc_start: 0.7716 (pt0) cc_final: 0.7056 (tt0) REVERT: g 32 TYR cc_start: 0.5648 (p90) cc_final: 0.5355 (p90) REVERT: g 56 GLN cc_start: 0.6897 (tt0) cc_final: 0.6081 (pm20) REVERT: g 69 ILE cc_start: 0.6886 (mm) cc_final: 0.6574 (mm) REVERT: g 75 ASP cc_start: 0.6708 (t0) cc_final: 0.6117 (m-30) REVERT: h 17 ILE cc_start: 0.9233 (mp) cc_final: 0.8931 (mp) REVERT: h 18 GLU cc_start: 0.8257 (mp0) cc_final: 0.7712 (pt0) REVERT: j 89 ARG cc_start: 0.8295 (ptt180) cc_final: 0.7991 (mmm-85) outliers start: 244 outliers final: 128 residues processed: 1029 average time/residue: 0.5808 time to fit residues: 1038.5865 Evaluate side-chains 880 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 729 time to evaluate : 4.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 694 ASN Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 832 GLU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1212 ARG Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1337 THR Chi-restraints excluded: chain A residue 1346 PHE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1420 THR Chi-restraints excluded: chain A residue 1440 ILE Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1553 ILE Chi-restraints excluded: chain A residue 1621 VAL Chi-restraints excluded: chain A residue 1650 ARG Chi-restraints excluded: chain A residue 1738 LEU Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1757 LEU Chi-restraints excluded: chain A residue 1893 ILE Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1951 PHE Chi-restraints excluded: chain A residue 1986 MET Chi-restraints excluded: chain A residue 1995 TRP Chi-restraints excluded: chain A residue 1997 ASP Chi-restraints excluded: chain A residue 2017 THR Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 801 TRP Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 182 GLN Chi-restraints excluded: chain H residue 193 SER Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 314 LYS Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 357 TRP Chi-restraints excluded: chain H residue 433 LEU Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 161 ASP Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 257 ILE Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 261 THR Chi-restraints excluded: chain J residue 271 GLN Chi-restraints excluded: chain J residue 301 MET Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain J residue 382 HIS Chi-restraints excluded: chain J residue 408 ASP Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 108 ASN Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 163 VAL Chi-restraints excluded: chain N residue 22 ASN Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain N residue 118 VAL Chi-restraints excluded: chain N residue 288 ILE Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 148 GLU Chi-restraints excluded: chain O residue 181 ARG Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain S residue 58 LEU Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 107 ASP Chi-restraints excluded: chain S residue 124 ARG Chi-restraints excluded: chain S residue 128 THR Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 146 LEU Chi-restraints excluded: chain S residue 156 TYR Chi-restraints excluded: chain S residue 193 VAL Chi-restraints excluded: chain S residue 232 LEU Chi-restraints excluded: chain S residue 273 LYS Chi-restraints excluded: chain S residue 279 LEU Chi-restraints excluded: chain a residue 132 HIS Chi-restraints excluded: chain a residue 158 ASP Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 171 GLN Chi-restraints excluded: chain a residue 177 ASN Chi-restraints excluded: chain c residue 178 SER Chi-restraints excluded: chain c residue 297 LEU Chi-restraints excluded: chain o residue 173 LYS Chi-restraints excluded: chain o residue 331 ILE Chi-restraints excluded: chain o residue 342 LEU Chi-restraints excluded: chain o residue 381 SER Chi-restraints excluded: chain o residue 387 ILE Chi-restraints excluded: chain o residue 443 ILE Chi-restraints excluded: chain y residue 112 LEU Chi-restraints excluded: chain y residue 144 GLN Chi-restraints excluded: chain y residue 161 VAL Chi-restraints excluded: chain y residue 162 ASN Chi-restraints excluded: chain d residue 22 GLU Chi-restraints excluded: chain d residue 77 LEU Chi-restraints excluded: chain d residue 85 LYS Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 15 ASN Chi-restraints excluded: chain f residue 67 THR Chi-restraints excluded: chain f residue 73 ILE Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain h residue 6 PHE Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain j residue 77 THR Chi-restraints excluded: chain j residue 91 ILE Chi-restraints excluded: chain j residue 96 LEU Chi-restraints excluded: chain j residue 100 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 629 optimal weight: 7.9990 chunk 478 optimal weight: 0.9990 chunk 330 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 303 optimal weight: 5.9990 chunk 427 optimal weight: 6.9990 chunk 639 optimal weight: 0.4980 chunk 676 optimal weight: 30.0000 chunk 333 optimal weight: 3.9990 chunk 605 optimal weight: 4.9990 chunk 182 optimal weight: 20.0000 overall best weight: 3.0988 ------------------------------------------------------------------------------- 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 257 ASN ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1532 HIS ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 HIS H 425 GLN K 108 ASN K 140 ASN ** K 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 HIS ** M 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 ASN N 106 ASN ** O 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 158 ASN a 82 GLN ** a 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 60755 Z= 0.331 Angle : 0.694 19.417 84029 Z= 0.346 Chirality : 0.042 0.357 9967 Planarity : 0.005 0.067 9414 Dihedral : 18.231 176.230 12533 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.16 % Favored : 93.79 % Rotamer: Outliers : 5.66 % Allowed : 17.42 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.11), residues: 6554 helix: 1.51 (0.09), residues: 3095 sheet: -2.29 (0.17), residues: 756 loop : -1.93 (0.12), residues: 2703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 933 HIS 0.007 0.001 HIS H 170 PHE 0.036 0.002 PHE C 364 TYR 0.024 0.002 TYR A 391 ARG 0.008 0.001 ARG J 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 755 time to evaluate : 5.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ILE cc_start: 0.9304 (mt) cc_final: 0.8972 (tp) REVERT: A 199 ILE cc_start: 0.9679 (tp) cc_final: 0.9274 (tt) REVERT: A 326 ASN cc_start: 0.9343 (OUTLIER) cc_final: 0.8778 (t0) REVERT: A 493 MET cc_start: 0.9075 (mmt) cc_final: 0.8708 (mmm) REVERT: A 578 MET cc_start: 0.8804 (mtp) cc_final: 0.8528 (mtp) REVERT: A 588 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9022 (pp) REVERT: A 618 SER cc_start: 0.9331 (t) cc_final: 0.8989 (p) REVERT: A 626 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9284 (tp) REVERT: A 674 MET cc_start: 0.9045 (mmp) cc_final: 0.8827 (mmp) REVERT: A 693 LYS cc_start: 0.8061 (mtmt) cc_final: 0.7833 (pttt) REVERT: A 712 LEU cc_start: 0.9584 (mt) cc_final: 0.9299 (mm) REVERT: A 726 ILE cc_start: 0.9557 (tt) cc_final: 0.9352 (mm) REVERT: A 750 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9190 (tt) REVERT: A 754 TYR cc_start: 0.9309 (t80) cc_final: 0.9092 (t80) REVERT: A 832 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8618 (mp0) REVERT: A 852 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9008 (tt) REVERT: A 905 TYR cc_start: 0.7285 (m-80) cc_final: 0.7021 (m-80) REVERT: A 933 GLU cc_start: 0.9460 (mt-10) cc_final: 0.9159 (mp0) REVERT: A 1061 ILE cc_start: 0.9392 (mt) cc_final: 0.9104 (mm) REVERT: A 1085 LYS cc_start: 0.9454 (tptm) cc_final: 0.9110 (tppp) REVERT: A 1101 TYR cc_start: 0.8226 (t80) cc_final: 0.7789 (t80) REVERT: A 1288 LEU cc_start: 0.9457 (mp) cc_final: 0.9139 (mt) REVERT: A 1346 PHE cc_start: 0.9429 (OUTLIER) cc_final: 0.7814 (p90) REVERT: A 1379 MET cc_start: 0.8621 (ttm) cc_final: 0.8365 (ttt) REVERT: A 1450 GLU cc_start: 0.9246 (tp30) cc_final: 0.8638 (tm-30) REVERT: A 1485 ASP cc_start: 0.8793 (m-30) cc_final: 0.8557 (p0) REVERT: A 1545 ASP cc_start: 0.9086 (m-30) cc_final: 0.8684 (m-30) REVERT: A 1687 HIS cc_start: 0.8901 (m-70) cc_final: 0.8520 (p-80) REVERT: A 1778 ASP cc_start: 0.9199 (t0) cc_final: 0.8898 (t0) REVERT: A 1783 MET cc_start: 0.8932 (mmm) cc_final: 0.8516 (mmm) REVERT: A 1807 LYS cc_start: 0.9270 (tptt) cc_final: 0.8640 (mmtt) REVERT: A 1817 GLU cc_start: 0.9529 (tt0) cc_final: 0.9015 (tm-30) REVERT: A 1866 PHE cc_start: 0.8963 (m-10) cc_final: 0.8656 (m-80) REVERT: A 1880 PHE cc_start: 0.7843 (t80) cc_final: 0.7479 (t80) REVERT: A 1903 LYS cc_start: 0.9030 (tppp) cc_final: 0.8758 (tttt) REVERT: A 1948 MET cc_start: 0.9242 (mmm) cc_final: 0.8704 (ppp) REVERT: A 1979 MET cc_start: 0.8817 (mmp) cc_final: 0.8561 (mmp) REVERT: A 1986 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8626 (tpp) REVERT: C 126 MET cc_start: 0.8587 (tpp) cc_final: 0.8022 (tpp) REVERT: C 164 MET cc_start: 0.8806 (ptm) cc_final: 0.8240 (tmm) REVERT: C 179 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.7981 (m-30) REVERT: C 222 MET cc_start: 0.9177 (mmm) cc_final: 0.8703 (mmp) REVERT: C 282 MET cc_start: 0.9356 (tpt) cc_final: 0.8947 (tpp) REVERT: C 295 ILE cc_start: 0.9738 (mt) cc_final: 0.9487 (mt) REVERT: C 391 MET cc_start: 0.8848 (ttp) cc_final: 0.8455 (ttm) REVERT: C 538 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8421 (tm-30) REVERT: C 540 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8791 (mm-30) REVERT: C 545 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9074 (pp) REVERT: C 614 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8815 (tp30) REVERT: C 719 MET cc_start: 0.8712 (ppp) cc_final: 0.8421 (ppp) REVERT: C 880 MET cc_start: 0.9426 (mmm) cc_final: 0.8628 (mmm) REVERT: H 158 CYS cc_start: 0.9010 (p) cc_final: 0.8434 (t) REVERT: H 160 TRP cc_start: 0.7661 (p-90) cc_final: 0.7367 (p-90) REVERT: H 161 LYS cc_start: 0.8972 (tptt) cc_final: 0.8441 (tttt) REVERT: H 167 LYS cc_start: 0.8194 (pttp) cc_final: 0.7892 (tttt) REVERT: H 195 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7667 (tm-30) REVERT: H 350 MET cc_start: 0.8878 (mmm) cc_final: 0.8500 (mmm) REVERT: H 357 TRP cc_start: 0.9207 (OUTLIER) cc_final: 0.7806 (m-10) REVERT: H 386 LYS cc_start: 0.9563 (mmtp) cc_final: 0.9305 (ttmm) REVERT: H 430 GLU cc_start: 0.9190 (tp30) cc_final: 0.8837 (tm-30) REVERT: J 124 GLU cc_start: 0.8543 (pm20) cc_final: 0.8072 (pm20) REVERT: J 164 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7891 (mtm) REVERT: J 187 ASP cc_start: 0.9231 (t0) cc_final: 0.8603 (t0) REVERT: J 203 ASP cc_start: 0.9080 (p0) cc_final: 0.8590 (p0) REVERT: J 273 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8711 (mm-40) REVERT: J 320 GLU cc_start: 0.7985 (tp30) cc_final: 0.7659 (tp30) REVERT: J 346 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8603 (mp0) REVERT: J 360 GLN cc_start: 0.9327 (tt0) cc_final: 0.9067 (tp40) REVERT: K 42 ASP cc_start: 0.8942 (m-30) cc_final: 0.8519 (m-30) REVERT: K 123 LEU cc_start: 0.9686 (mp) cc_final: 0.9455 (mt) REVERT: K 202 MET cc_start: 0.9457 (ptp) cc_final: 0.9172 (pmm) REVERT: L 41 LEU cc_start: 0.9192 (tp) cc_final: 0.8773 (mm) REVERT: M 57 LEU cc_start: 0.9527 (mt) cc_final: 0.9234 (tt) REVERT: M 97 GLU cc_start: 0.9124 (tt0) cc_final: 0.8787 (mt-10) REVERT: M 124 MET cc_start: 0.9455 (mmm) cc_final: 0.8993 (mmt) REVERT: M 171 ASP cc_start: 0.9176 (t70) cc_final: 0.8816 (t0) REVERT: M 188 TYR cc_start: 0.9452 (m-80) cc_final: 0.9176 (m-80) REVERT: M 193 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8345 (mt-10) REVERT: M 199 MET cc_start: 0.9066 (mmm) cc_final: 0.8721 (mmm) REVERT: M 235 GLN cc_start: 0.9537 (tp40) cc_final: 0.9003 (mm110) REVERT: N 88 ASP cc_start: 0.8857 (m-30) cc_final: 0.7718 (t70) REVERT: N 133 ASP cc_start: 0.9449 (t0) cc_final: 0.9125 (t0) REVERT: N 221 ASP cc_start: 0.8855 (m-30) cc_final: 0.8643 (p0) REVERT: O 48 SER cc_start: 0.9690 (t) cc_final: 0.9365 (p) REVERT: O 53 ASN cc_start: 0.9474 (m-40) cc_final: 0.9130 (m-40) REVERT: O 54 GLU cc_start: 0.8926 (tp30) cc_final: 0.8511 (tt0) REVERT: O 173 GLU cc_start: 0.9464 (mt-10) cc_final: 0.9213 (mm-30) REVERT: P 8 GLN cc_start: 0.8476 (tm-30) cc_final: 0.8049 (tm-30) REVERT: P 157 ILE cc_start: 0.9080 (mt) cc_final: 0.8749 (tp) REVERT: P 164 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8251 (tp30) REVERT: S 122 MET cc_start: 0.8598 (mtm) cc_final: 0.8298 (mtp) REVERT: S 146 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9346 (mt) REVERT: S 156 TYR cc_start: 0.9004 (OUTLIER) cc_final: 0.8466 (t80) REVERT: S 163 GLU cc_start: 0.9306 (mt-10) cc_final: 0.8524 (tm-30) REVERT: a 99 GLN cc_start: 0.8937 (mm110) cc_final: 0.8552 (pt0) REVERT: a 138 ASP cc_start: 0.9361 (m-30) cc_final: 0.8855 (t0) REVERT: a 185 LYS cc_start: 0.9289 (ptmm) cc_final: 0.8977 (tmtt) REVERT: c 181 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8244 (tm-30) REVERT: c 195 ASN cc_start: 0.6765 (t0) cc_final: 0.6553 (t0) REVERT: c 297 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8731 (tp) REVERT: c 301 GLU cc_start: 0.9399 (mt-10) cc_final: 0.8805 (mm-30) REVERT: c 347 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7435 (mm-30) REVERT: o 209 ILE cc_start: 0.9197 (mp) cc_final: 0.8875 (tp) REVERT: o 262 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8170 (tt0) REVERT: o 385 TYR cc_start: 0.8498 (t80) cc_final: 0.7634 (t80) REVERT: o 387 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7716 (mt) REVERT: o 431 GLN cc_start: 0.8154 (mt0) cc_final: 0.7789 (tm-30) REVERT: o 443 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7820 (mt) REVERT: o 451 ILE cc_start: 0.7304 (OUTLIER) cc_final: 0.6741 (pp) REVERT: y 99 GLN cc_start: 0.9250 (mm110) cc_final: 0.8999 (mt0) REVERT: y 103 LEU cc_start: 0.9093 (mp) cc_final: 0.8772 (mp) REVERT: y 106 GLU cc_start: 0.9437 (mt-10) cc_final: 0.8967 (pt0) REVERT: y 144 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8694 (mm-40) REVERT: y 157 ASP cc_start: 0.8752 (m-30) cc_final: 0.8344 (t0) REVERT: y 162 ASN cc_start: 0.9399 (OUTLIER) cc_final: 0.9055 (m110) REVERT: y 171 GLU cc_start: 0.9314 (tp30) cc_final: 0.9058 (tp30) REVERT: y 182 GLN cc_start: 0.9183 (mt0) cc_final: 0.8903 (mt0) REVERT: b 35 MET cc_start: 0.8618 (mmm) cc_final: 0.8299 (mmm) REVERT: b 41 MET cc_start: 0.9147 (mmm) cc_final: 0.8332 (mtp) REVERT: b 43 LEU cc_start: 0.9391 (mt) cc_final: 0.8843 (pp) REVERT: b 44 VAL cc_start: 0.8750 (t) cc_final: 0.8466 (t) REVERT: b 46 ASN cc_start: 0.8797 (t0) cc_final: 0.8411 (t0) REVERT: b 90 GLU cc_start: 0.7212 (tt0) cc_final: 0.6959 (mt-10) REVERT: d 9 LYS cc_start: 0.8793 (mttt) cc_final: 0.8477 (mtpp) REVERT: d 22 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7740 (mm-30) REVERT: d 45 ARG cc_start: 0.8874 (mtt-85) cc_final: 0.8649 (tpp80) REVERT: d 76 ASP cc_start: 0.9027 (OUTLIER) cc_final: 0.8650 (p0) REVERT: g 32 TYR cc_start: 0.5650 (p90) cc_final: 0.5370 (p90) REVERT: g 44 MET cc_start: 0.8797 (mmm) cc_final: 0.8553 (tpt) REVERT: g 56 GLN cc_start: 0.6733 (tt0) cc_final: 0.5766 (pm20) REVERT: g 69 ILE cc_start: 0.6878 (mm) cc_final: 0.6604 (mm) REVERT: g 75 ASP cc_start: 0.6744 (t0) cc_final: 0.6126 (m-30) REVERT: h 17 ILE cc_start: 0.9212 (mp) cc_final: 0.8938 (mp) REVERT: h 18 GLU cc_start: 0.8174 (mp0) cc_final: 0.7701 (tm-30) REVERT: j 89 ARG cc_start: 0.8332 (ptt180) cc_final: 0.7997 (mmm-85) outliers start: 290 outliers final: 192 residues processed: 960 average time/residue: 0.5273 time to fit residues: 880.3237 Evaluate side-chains 906 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 692 time to evaluate : 4.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 694 ASN Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 832 GLU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 906 LYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1212 ARG Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1319 ILE Chi-restraints excluded: chain A residue 1337 THR Chi-restraints excluded: chain A residue 1346 PHE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain A residue 1420 THR Chi-restraints excluded: chain A residue 1439 THR Chi-restraints excluded: chain A residue 1440 ILE Chi-restraints excluded: chain A residue 1457 VAL Chi-restraints excluded: chain A residue 1650 ARG Chi-restraints excluded: chain A residue 1738 LEU Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1893 ILE Chi-restraints excluded: chain A residue 1951 PHE Chi-restraints excluded: chain A residue 1986 MET Chi-restraints excluded: chain A residue 1995 TRP Chi-restraints excluded: chain A residue 1997 ASP Chi-restraints excluded: chain A residue 2017 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 283 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 658 ASP Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 783 ILE Chi-restraints excluded: chain C residue 801 TRP Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 830 ASN Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 182 GLN Chi-restraints excluded: chain H residue 193 SER Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 357 TRP Chi-restraints excluded: chain H residue 396 PHE Chi-restraints excluded: chain H residue 433 LEU Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 161 ASP Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 194 HIS Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 232 ILE Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 257 ILE Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 261 THR Chi-restraints excluded: chain J residue 271 GLN Chi-restraints excluded: chain J residue 301 MET Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain J residue 382 HIS Chi-restraints excluded: chain J residue 408 ASP Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 148 HIS Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 92 ILE Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 160 ILE Chi-restraints excluded: chain M residue 163 VAL Chi-restraints excluded: chain M residue 203 THR Chi-restraints excluded: chain N residue 22 ASN Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 95 ASN Chi-restraints excluded: chain N residue 118 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 288 ILE Chi-restraints excluded: chain N residue 291 ILE Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 181 ARG Chi-restraints excluded: chain O residue 185 LEU Chi-restraints excluded: chain O residue 230 THR Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 35 THR Chi-restraints excluded: chain P residue 37 LEU Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 161 THR Chi-restraints excluded: chain R residue 4 ASN Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain S residue 58 LEU Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 107 ASP Chi-restraints excluded: chain S residue 124 ARG Chi-restraints excluded: chain S residue 128 THR Chi-restraints excluded: chain S residue 146 LEU Chi-restraints excluded: chain S residue 156 TYR Chi-restraints excluded: chain S residue 157 THR Chi-restraints excluded: chain S residue 193 VAL Chi-restraints excluded: chain S residue 212 HIS Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 232 LEU Chi-restraints excluded: chain S residue 279 LEU Chi-restraints excluded: chain a residue 111 MET Chi-restraints excluded: chain a residue 132 HIS Chi-restraints excluded: chain a residue 137 LEU Chi-restraints excluded: chain a residue 146 LEU Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 171 GLN Chi-restraints excluded: chain a residue 177 ASN Chi-restraints excluded: chain a residue 237 ILE Chi-restraints excluded: chain a residue 238 THR Chi-restraints excluded: chain c residue 297 LEU Chi-restraints excluded: chain o residue 281 GLU Chi-restraints excluded: chain o residue 296 ILE Chi-restraints excluded: chain o residue 331 ILE Chi-restraints excluded: chain o residue 381 SER Chi-restraints excluded: chain o residue 387 ILE Chi-restraints excluded: chain o residue 419 ASN Chi-restraints excluded: chain o residue 443 ILE Chi-restraints excluded: chain o residue 451 ILE Chi-restraints excluded: chain y residue 96 SER Chi-restraints excluded: chain y residue 112 LEU Chi-restraints excluded: chain y residue 144 GLN Chi-restraints excluded: chain y residue 161 VAL Chi-restraints excluded: chain y residue 162 ASN Chi-restraints excluded: chain b residue 20 LEU Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 86 ILE Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain d residue 22 GLU Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 76 ASP Chi-restraints excluded: chain d residue 85 LYS Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 15 ASN Chi-restraints excluded: chain f residue 67 THR Chi-restraints excluded: chain f residue 73 ILE Chi-restraints excluded: chain g residue 19 ILE Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 39 VAL Chi-restraints excluded: chain h residue 6 PHE Chi-restraints excluded: chain h residue 16 THR Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 42 ASP Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain j residue 96 LEU Chi-restraints excluded: chain j residue 100 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 563 optimal weight: 0.3980 chunk 384 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 503 optimal weight: 1.9990 chunk 279 optimal weight: 2.9990 chunk 577 optimal weight: 30.0000 chunk 467 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 345 optimal weight: 10.0000 chunk 607 optimal weight: 9.9990 chunk 170 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- 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 404 ASN ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 GLN ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 425 GLN ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 ASN ** M 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 91 GLN ** e 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 60755 Z= 0.251 Angle : 0.648 18.381 84029 Z= 0.322 Chirality : 0.041 0.317 9967 Planarity : 0.004 0.070 9414 Dihedral : 18.128 175.835 12530 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.74 % Favored : 94.22 % Rotamer: Outliers : 5.58 % Allowed : 18.02 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.25 (0.11), residues: 6554 helix: 1.66 (0.09), residues: 3092 sheet: -2.07 (0.17), residues: 774 loop : -1.80 (0.12), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP C 933 HIS 0.007 0.001 HIS A 138 PHE 0.026 0.002 PHE S 287 TYR 0.025 0.002 TYR A 391 ARG 0.010 0.000 ARG A2013 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 767 time to evaluate : 4.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ILE cc_start: 0.9319 (mt) cc_final: 0.8965 (tp) REVERT: A 199 ILE cc_start: 0.9683 (tp) cc_final: 0.9267 (tt) REVERT: A 326 ASN cc_start: 0.9268 (OUTLIER) cc_final: 0.8607 (t0) REVERT: A 493 MET cc_start: 0.9011 (mmt) cc_final: 0.8554 (mmm) REVERT: A 551 LEU cc_start: 0.9669 (mt) cc_final: 0.9421 (mp) REVERT: A 588 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.8999 (pp) REVERT: A 618 SER cc_start: 0.9269 (t) cc_final: 0.8960 (p) REVERT: A 626 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.8985 (tp) REVERT: A 629 MET cc_start: 0.8598 (tmm) cc_final: 0.8304 (tmm) REVERT: A 632 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8580 (mt) REVERT: A 693 LYS cc_start: 0.8044 (mtmt) cc_final: 0.7797 (pttt) REVERT: A 712 LEU cc_start: 0.9537 (mt) cc_final: 0.9227 (mm) REVERT: A 750 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9179 (tt) REVERT: A 763 MET cc_start: 0.8554 (ttp) cc_final: 0.8295 (ttt) REVERT: A 832 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8550 (mp0) REVERT: A 852 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9077 (tt) REVERT: A 905 TYR cc_start: 0.7240 (m-80) cc_final: 0.7002 (m-80) REVERT: A 933 GLU cc_start: 0.9452 (mt-10) cc_final: 0.9160 (mp0) REVERT: A 935 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8730 (tm-30) REVERT: A 1004 ASP cc_start: 0.9115 (m-30) cc_final: 0.8894 (m-30) REVERT: A 1085 LYS cc_start: 0.9400 (tptm) cc_final: 0.9103 (tppp) REVERT: A 1086 ASN cc_start: 0.9293 (m-40) cc_final: 0.8959 (t0) REVERT: A 1101 TYR cc_start: 0.8073 (t80) cc_final: 0.7857 (t80) REVERT: A 1199 ILE cc_start: 0.9075 (mm) cc_final: 0.8863 (tt) REVERT: A 1288 LEU cc_start: 0.9429 (mp) cc_final: 0.9125 (mt) REVERT: A 1346 PHE cc_start: 0.9344 (OUTLIER) cc_final: 0.7762 (p90) REVERT: A 1379 MET cc_start: 0.8532 (ttm) cc_final: 0.8266 (ttt) REVERT: A 1485 ASP cc_start: 0.8761 (m-30) cc_final: 0.8496 (p0) REVERT: A 1545 ASP cc_start: 0.8910 (m-30) cc_final: 0.8343 (m-30) REVERT: A 1687 HIS cc_start: 0.8862 (m-70) cc_final: 0.8488 (p-80) REVERT: A 1778 ASP cc_start: 0.9153 (t0) cc_final: 0.8874 (t0) REVERT: A 1783 MET cc_start: 0.8804 (mmm) cc_final: 0.8470 (mmm) REVERT: A 1807 LYS cc_start: 0.9253 (tptt) cc_final: 0.8646 (mmtt) REVERT: A 1817 GLU cc_start: 0.9545 (tt0) cc_final: 0.8981 (tm-30) REVERT: A 1880 PHE cc_start: 0.7837 (t80) cc_final: 0.7457 (t80) REVERT: A 1903 LYS cc_start: 0.9025 (tppp) cc_final: 0.8715 (tttt) REVERT: A 1948 MET cc_start: 0.9256 (mmm) cc_final: 0.8753 (ppp) REVERT: A 1979 MET cc_start: 0.8778 (mmp) cc_final: 0.8486 (mmp) REVERT: C 126 MET cc_start: 0.8658 (tpp) cc_final: 0.8164 (tpp) REVERT: C 164 MET cc_start: 0.8785 (ptm) cc_final: 0.8215 (tmm) REVERT: C 222 MET cc_start: 0.9119 (mmm) cc_final: 0.8630 (mmp) REVERT: C 282 MET cc_start: 0.9359 (tpt) cc_final: 0.8951 (tpp) REVERT: C 295 ILE cc_start: 0.9735 (mt) cc_final: 0.9498 (mt) REVERT: C 391 MET cc_start: 0.8734 (ttp) cc_final: 0.8438 (ttm) REVERT: C 504 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.8092 (t) REVERT: C 538 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8409 (tm-30) REVERT: C 540 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8787 (mm-30) REVERT: C 545 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.8986 (pp) REVERT: C 614 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8555 (tp30) REVERT: C 719 MET cc_start: 0.8726 (ppp) cc_final: 0.8446 (ppp) REVERT: C 880 MET cc_start: 0.9429 (mmm) cc_final: 0.8523 (mmm) REVERT: H 158 CYS cc_start: 0.9128 (p) cc_final: 0.8779 (t) REVERT: H 160 TRP cc_start: 0.7846 (p-90) cc_final: 0.7610 (p-90) REVERT: H 161 LYS cc_start: 0.9036 (tptt) cc_final: 0.8538 (tmtt) REVERT: H 167 LYS cc_start: 0.8121 (pttp) cc_final: 0.7808 (tttt) REVERT: H 195 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7697 (tm-30) REVERT: H 314 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.9089 (ttmm) REVERT: H 350 MET cc_start: 0.8920 (mmm) cc_final: 0.8681 (mmm) REVERT: H 357 TRP cc_start: 0.9258 (OUTLIER) cc_final: 0.7756 (m-10) REVERT: H 386 LYS cc_start: 0.9570 (mmtp) cc_final: 0.9270 (ttmm) REVERT: H 396 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.8284 (m-10) REVERT: H 430 GLU cc_start: 0.9147 (tp30) cc_final: 0.8809 (tm-30) REVERT: J 117 LYS cc_start: 0.8922 (ttmt) cc_final: 0.8550 (tppt) REVERT: J 124 GLU cc_start: 0.8353 (pm20) cc_final: 0.7949 (pm20) REVERT: J 164 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7878 (mtm) REVERT: J 187 ASP cc_start: 0.9205 (t0) cc_final: 0.8675 (t0) REVERT: J 203 ASP cc_start: 0.8977 (p0) cc_final: 0.8537 (p0) REVERT: J 232 ILE cc_start: 0.9341 (OUTLIER) cc_final: 0.9092 (mt) REVERT: J 253 MET cc_start: 0.8462 (mtp) cc_final: 0.7999 (mtp) REVERT: J 273 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8682 (mm-40) REVERT: J 280 GLN cc_start: 0.7678 (mt0) cc_final: 0.7162 (mt0) REVERT: J 320 GLU cc_start: 0.7913 (tp30) cc_final: 0.7608 (tp30) REVERT: J 346 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8589 (mp0) REVERT: J 360 GLN cc_start: 0.9316 (tt0) cc_final: 0.9089 (tp40) REVERT: K 42 ASP cc_start: 0.8860 (m-30) cc_final: 0.8460 (m-30) REVERT: K 123 LEU cc_start: 0.9664 (mp) cc_final: 0.9341 (mt) REVERT: K 202 MET cc_start: 0.9466 (ptp) cc_final: 0.9163 (pmm) REVERT: L 41 LEU cc_start: 0.9122 (tp) cc_final: 0.8704 (mm) REVERT: L 50 TRP cc_start: 0.8920 (m-10) cc_final: 0.8084 (m-90) REVERT: M 97 GLU cc_start: 0.9128 (tt0) cc_final: 0.8781 (mt-10) REVERT: M 124 MET cc_start: 0.9407 (mmm) cc_final: 0.9033 (mmt) REVERT: M 171 ASP cc_start: 0.9075 (t70) cc_final: 0.8676 (t0) REVERT: M 188 TYR cc_start: 0.9425 (m-80) cc_final: 0.9136 (m-80) REVERT: M 193 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8196 (mt-10) REVERT: M 199 MET cc_start: 0.9072 (mmm) cc_final: 0.8706 (mmm) REVERT: M 235 GLN cc_start: 0.9523 (tp40) cc_final: 0.9048 (mm110) REVERT: N 221 ASP cc_start: 0.8770 (m-30) cc_final: 0.8558 (p0) REVERT: O 48 SER cc_start: 0.9677 (t) cc_final: 0.9351 (p) REVERT: O 53 ASN cc_start: 0.9464 (m-40) cc_final: 0.9247 (m-40) REVERT: O 54 GLU cc_start: 0.8912 (tp30) cc_final: 0.8540 (pt0) REVERT: O 90 MET cc_start: 0.8956 (mmm) cc_final: 0.8259 (mmm) REVERT: O 173 GLU cc_start: 0.9468 (mt-10) cc_final: 0.9184 (mm-30) REVERT: P 157 ILE cc_start: 0.9072 (mt) cc_final: 0.8727 (tp) REVERT: P 160 MET cc_start: 0.9003 (mmm) cc_final: 0.8733 (tpp) REVERT: S 122 MET cc_start: 0.8619 (mtm) cc_final: 0.8327 (mtp) REVERT: S 146 LEU cc_start: 0.9663 (OUTLIER) cc_final: 0.9383 (mt) REVERT: S 156 TYR cc_start: 0.9011 (OUTLIER) cc_final: 0.8374 (t80) REVERT: S 163 GLU cc_start: 0.9334 (mt-10) cc_final: 0.8377 (tm-30) REVERT: a 99 GLN cc_start: 0.9053 (mm110) cc_final: 0.8669 (pt0) REVERT: a 111 MET cc_start: 0.8970 (tpp) cc_final: 0.8663 (mmm) REVERT: a 138 ASP cc_start: 0.9331 (m-30) cc_final: 0.8782 (t0) REVERT: a 186 LEU cc_start: 0.8740 (tt) cc_final: 0.8479 (tt) REVERT: c 181 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8345 (tm-30) REVERT: c 195 ASN cc_start: 0.6699 (t0) cc_final: 0.6481 (t0) REVERT: c 303 ASN cc_start: 0.9607 (m-40) cc_final: 0.9394 (m110) REVERT: c 347 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7401 (mm-30) REVERT: o 209 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8927 (tp) REVERT: o 262 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8168 (tt0) REVERT: o 342 LEU cc_start: 0.9024 (mt) cc_final: 0.8731 (tp) REVERT: o 385 TYR cc_start: 0.8447 (t80) cc_final: 0.7535 (t80) REVERT: o 387 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7617 (mt) REVERT: o 431 GLN cc_start: 0.8131 (mt0) cc_final: 0.7805 (tm-30) REVERT: o 443 ILE cc_start: 0.7838 (OUTLIER) cc_final: 0.7388 (mt) REVERT: o 451 ILE cc_start: 0.7320 (OUTLIER) cc_final: 0.7107 (pp) REVERT: y 99 GLN cc_start: 0.9231 (mm110) cc_final: 0.8947 (mt0) REVERT: y 103 LEU cc_start: 0.9056 (mp) cc_final: 0.8745 (mp) REVERT: y 106 GLU cc_start: 0.9422 (mt-10) cc_final: 0.8984 (pt0) REVERT: y 144 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8710 (mm-40) REVERT: y 157 ASP cc_start: 0.8728 (m-30) cc_final: 0.8442 (t0) REVERT: y 162 ASN cc_start: 0.9416 (OUTLIER) cc_final: 0.9079 (m110) REVERT: y 169 GLN cc_start: 0.9533 (mt0) cc_final: 0.9270 (tp40) REVERT: y 182 GLN cc_start: 0.9165 (mt0) cc_final: 0.8898 (mt0) REVERT: b 35 MET cc_start: 0.8616 (mmm) cc_final: 0.8272 (mmm) REVERT: b 41 MET cc_start: 0.9145 (mmm) cc_final: 0.8639 (mtp) REVERT: b 43 LEU cc_start: 0.9445 (mt) cc_final: 0.9227 (mt) REVERT: b 46 ASN cc_start: 0.8754 (t0) cc_final: 0.8344 (t0) REVERT: d 9 LYS cc_start: 0.8798 (mttt) cc_final: 0.8481 (mtpp) REVERT: d 44 LEU cc_start: 0.8981 (mp) cc_final: 0.8659 (mt) REVERT: d 45 ARG cc_start: 0.8846 (mtt-85) cc_final: 0.8592 (tpp80) REVERT: d 61 GLN cc_start: 0.8952 (mt0) cc_final: 0.8328 (mp10) REVERT: d 76 ASP cc_start: 0.9081 (OUTLIER) cc_final: 0.8749 (p0) REVERT: f 58 GLU cc_start: 0.7749 (pt0) cc_final: 0.7094 (tt0) REVERT: g 56 GLN cc_start: 0.6675 (tt0) cc_final: 0.5799 (pm20) REVERT: g 69 ILE cc_start: 0.6775 (mm) cc_final: 0.6500 (mm) REVERT: g 75 ASP cc_start: 0.6962 (t0) cc_final: 0.6372 (m-30) REVERT: h 18 GLU cc_start: 0.8281 (mp0) cc_final: 0.7683 (tm-30) REVERT: j 70 GLU cc_start: 0.8088 (tp30) cc_final: 0.7855 (tp30) REVERT: j 89 ARG cc_start: 0.8277 (ptt180) cc_final: 0.8042 (mmm-85) outliers start: 286 outliers final: 171 residues processed: 973 average time/residue: 0.5336 time to fit residues: 905.4321 Evaluate side-chains 881 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 686 time to evaluate : 4.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 694 ASN Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 832 GLU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 906 LYS Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1212 ARG Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1285 VAL Chi-restraints excluded: chain A residue 1319 ILE Chi-restraints excluded: chain A residue 1337 THR Chi-restraints excluded: chain A residue 1346 PHE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1440 ILE Chi-restraints excluded: chain A residue 1449 ASN Chi-restraints excluded: chain A residue 1553 ILE Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1650 ARG Chi-restraints excluded: chain A residue 1738 LEU Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1779 LEU Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1893 ILE Chi-restraints excluded: chain A residue 1951 PHE Chi-restraints excluded: chain A residue 1995 TRP Chi-restraints excluded: chain A residue 1997 ASP Chi-restraints excluded: chain A residue 2017 THR Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 658 ASP Chi-restraints excluded: chain C residue 783 ILE Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 182 GLN Chi-restraints excluded: chain H residue 193 SER Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 314 LYS Chi-restraints excluded: chain H residue 357 TRP Chi-restraints excluded: chain H residue 396 PHE Chi-restraints excluded: chain H residue 419 PHE Chi-restraints excluded: chain H residue 433 LEU Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 161 ASP Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 194 HIS Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 232 ILE Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 257 ILE Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 261 THR Chi-restraints excluded: chain J residue 271 GLN Chi-restraints excluded: chain J residue 301 MET Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain J residue 382 HIS Chi-restraints excluded: chain J residue 393 VAL Chi-restraints excluded: chain J residue 408 ASP Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 92 ILE Chi-restraints excluded: chain L residue 153 CYS Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 203 THR Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 118 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 288 ILE Chi-restraints excluded: chain N residue 291 ILE Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 181 ARG Chi-restraints excluded: chain O residue 185 LEU Chi-restraints excluded: chain O residue 230 THR Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 35 THR Chi-restraints excluded: chain P residue 37 LEU Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 161 THR Chi-restraints excluded: chain R residue 4 ASN Chi-restraints excluded: chain S residue 58 LEU Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 107 ASP Chi-restraints excluded: chain S residue 124 ARG Chi-restraints excluded: chain S residue 128 THR Chi-restraints excluded: chain S residue 146 LEU Chi-restraints excluded: chain S residue 156 TYR Chi-restraints excluded: chain S residue 157 THR Chi-restraints excluded: chain S residue 193 VAL Chi-restraints excluded: chain S residue 212 HIS Chi-restraints excluded: chain S residue 232 LEU Chi-restraints excluded: chain S residue 279 LEU Chi-restraints excluded: chain a residue 132 HIS Chi-restraints excluded: chain a residue 137 LEU Chi-restraints excluded: chain a residue 146 LEU Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 171 GLN Chi-restraints excluded: chain a residue 177 ASN Chi-restraints excluded: chain a residue 231 THR Chi-restraints excluded: chain a residue 237 ILE Chi-restraints excluded: chain a residue 238 THR Chi-restraints excluded: chain c residue 186 ILE Chi-restraints excluded: chain o residue 209 ILE Chi-restraints excluded: chain o residue 274 HIS Chi-restraints excluded: chain o residue 281 GLU Chi-restraints excluded: chain o residue 331 ILE Chi-restraints excluded: chain o residue 381 SER Chi-restraints excluded: chain o residue 387 ILE Chi-restraints excluded: chain o residue 419 ASN Chi-restraints excluded: chain o residue 443 ILE Chi-restraints excluded: chain o residue 451 ILE Chi-restraints excluded: chain y residue 96 SER Chi-restraints excluded: chain y residue 144 GLN Chi-restraints excluded: chain y residue 161 VAL Chi-restraints excluded: chain y residue 162 ASN Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 15 LEU Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 48 CYS Chi-restraints excluded: chain b residue 86 ILE Chi-restraints excluded: chain b residue 97 VAL Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain d residue 22 GLU Chi-restraints excluded: chain d residue 76 ASP Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain f residue 67 THR Chi-restraints excluded: chain g residue 19 ILE Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain h residue 6 PHE Chi-restraints excluded: chain h residue 16 THR Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain j residue 77 THR Chi-restraints excluded: chain j residue 96 LEU Chi-restraints excluded: chain j residue 100 SER Chi-restraints excluded: chain j residue 101 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 227 optimal weight: 3.9990 chunk 609 optimal weight: 20.0000 chunk 133 optimal weight: 4.9990 chunk 397 optimal weight: 7.9990 chunk 167 optimal weight: 4.9990 chunk 677 optimal weight: 0.6980 chunk 562 optimal weight: 20.0000 chunk 313 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 224 optimal weight: 2.9990 chunk 355 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 343 ASN ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 371 GLN ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 ASN ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 170 ASN a 149 GLN a 171 GLN ** c 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 50 ASN f 77 ASN ** h 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 60755 Z= 0.245 Angle : 0.648 17.604 84029 Z= 0.319 Chirality : 0.041 0.346 9967 Planarity : 0.004 0.069 9414 Dihedral : 18.060 175.863 12526 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.74 % Favored : 94.22 % Rotamer: Outliers : 5.17 % Allowed : 19.23 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.14 (0.11), residues: 6554 helix: 1.73 (0.09), residues: 3084 sheet: -1.92 (0.18), residues: 767 loop : -1.75 (0.12), residues: 2703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP C 933 HIS 0.007 0.001 HIS A 138 PHE 0.022 0.002 PHE C 212 TYR 0.027 0.002 TYR A 391 ARG 0.009 0.000 ARG A 709 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 994 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 729 time to evaluate : 5.090 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: A 134 MET cc_start: 0.9272 (mmm) cc_final: 0.8696 (mmm) REVERT: A 142 ILE cc_start: 0.9337 (mt) cc_final: 0.8983 (tp) REVERT: A 199 ILE cc_start: 0.9684 (tp) cc_final: 0.9275 (tt) REVERT: A 224 MET cc_start: 0.8757 (mtt) cc_final: 0.8393 (mtm) REVERT: A 326 ASN cc_start: 0.9253 (OUTLIER) cc_final: 0.8591 (t0) REVERT: A 422 LEU cc_start: 0.9565 (tp) cc_final: 0.9232 (tt) REVERT: A 493 MET cc_start: 0.8930 (mmt) cc_final: 0.8509 (mmm) REVERT: A 551 LEU cc_start: 0.9665 (mt) cc_final: 0.9417 (mp) REVERT: A 588 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9006 (pp) REVERT: A 618 SER cc_start: 0.9269 (t) cc_final: 0.9000 (p) REVERT: A 626 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.8977 (tp) REVERT: A 629 MET cc_start: 0.8523 (tmm) cc_final: 0.8169 (tmm) REVERT: A 693 LYS cc_start: 0.8041 (mtmt) cc_final: 0.7795 (pttt) REVERT: A 712 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9249 (mm) REVERT: A 750 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9147 (tt) REVERT: A 832 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8586 (mp0) REVERT: A 852 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.8959 (tt) REVERT: A 905 TYR cc_start: 0.7217 (m-80) cc_final: 0.6979 (m-80) REVERT: A 933 GLU cc_start: 0.9444 (mt-10) cc_final: 0.9132 (mp0) REVERT: A 935 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8766 (tm-30) REVERT: A 1004 ASP cc_start: 0.9129 (m-30) cc_final: 0.8620 (t0) REVERT: A 1085 LYS cc_start: 0.9388 (tptm) cc_final: 0.9084 (tppp) REVERT: A 1086 ASN cc_start: 0.9268 (m-40) cc_final: 0.8923 (t0) REVERT: A 1262 MET cc_start: 0.8864 (ttp) cc_final: 0.8600 (tmm) REVERT: A 1288 LEU cc_start: 0.9426 (mp) cc_final: 0.9139 (mt) REVERT: A 1346 PHE cc_start: 0.9339 (OUTLIER) cc_final: 0.7690 (p90) REVERT: A 1379 MET cc_start: 0.8504 (ttm) cc_final: 0.8247 (ttt) REVERT: A 1485 ASP cc_start: 0.8745 (m-30) cc_final: 0.8482 (p0) REVERT: A 1513 GLU cc_start: 0.8856 (tt0) cc_final: 0.8517 (mt-10) REVERT: A 1545 ASP cc_start: 0.8977 (m-30) cc_final: 0.8530 (m-30) REVERT: A 1687 HIS cc_start: 0.8860 (m-70) cc_final: 0.8473 (p-80) REVERT: A 1778 ASP cc_start: 0.9123 (t0) cc_final: 0.8857 (t0) REVERT: A 1783 MET cc_start: 0.8735 (mmm) cc_final: 0.8371 (mmm) REVERT: A 1807 LYS cc_start: 0.9238 (tptt) cc_final: 0.8646 (mmtt) REVERT: A 1817 GLU cc_start: 0.9513 (tt0) cc_final: 0.8915 (tm-30) REVERT: A 1866 PHE cc_start: 0.8935 (m-10) cc_final: 0.8648 (m-80) REVERT: A 1880 PHE cc_start: 0.7852 (t80) cc_final: 0.7458 (t80) REVERT: A 1903 LYS cc_start: 0.9022 (tppp) cc_final: 0.8678 (tttt) REVERT: A 1948 MET cc_start: 0.9216 (mmm) cc_final: 0.8704 (ppp) REVERT: C 126 MET cc_start: 0.8677 (tpp) cc_final: 0.8219 (tpp) REVERT: C 164 MET cc_start: 0.8799 (ptm) cc_final: 0.8248 (tmm) REVERT: C 179 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.7906 (m-30) REVERT: C 222 MET cc_start: 0.9131 (mmm) cc_final: 0.8615 (mmp) REVERT: C 282 MET cc_start: 0.9371 (tpt) cc_final: 0.8970 (tpp) REVERT: C 391 MET cc_start: 0.8716 (ttp) cc_final: 0.8440 (ttm) REVERT: C 504 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8097 (t) REVERT: C 538 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8430 (tm-30) REVERT: C 540 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8809 (mm-30) REVERT: C 545 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.8985 (pp) REVERT: C 614 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8546 (tp30) REVERT: C 652 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.7910 (tpp) REVERT: C 719 MET cc_start: 0.8726 (ppp) cc_final: 0.8478 (ppp) REVERT: C 820 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6492 (mt) REVERT: C 880 MET cc_start: 0.9422 (mmm) cc_final: 0.8439 (mmm) REVERT: C 933 TRP cc_start: 0.8096 (p-90) cc_final: 0.7869 (p-90) REVERT: C 968 MET cc_start: 0.9069 (mmm) cc_final: 0.8786 (mmm) REVERT: H 155 MET cc_start: 0.8414 (mmm) cc_final: 0.8075 (tpp) REVERT: H 158 CYS cc_start: 0.9050 (p) cc_final: 0.8713 (t) REVERT: H 160 TRP cc_start: 0.7884 (p-90) cc_final: 0.7611 (p-90) REVERT: H 161 LYS cc_start: 0.8971 (tptt) cc_final: 0.8583 (tptm) REVERT: H 167 LYS cc_start: 0.8216 (pttp) cc_final: 0.7944 (tttt) REVERT: H 195 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7704 (tm-30) REVERT: H 350 MET cc_start: 0.8934 (mmm) cc_final: 0.8642 (mmm) REVERT: H 357 TRP cc_start: 0.9316 (OUTLIER) cc_final: 0.7764 (m-10) REVERT: H 386 LYS cc_start: 0.9580 (mmtp) cc_final: 0.9277 (ttmm) REVERT: H 396 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.8232 (m-10) REVERT: H 430 GLU cc_start: 0.9180 (tp30) cc_final: 0.8816 (tm-30) REVERT: J 117 LYS cc_start: 0.8895 (ttmt) cc_final: 0.8538 (tppt) REVERT: J 124 GLU cc_start: 0.8288 (pm20) cc_final: 0.7911 (pm20) REVERT: J 164 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7889 (mtm) REVERT: J 187 ASP cc_start: 0.9141 (t0) cc_final: 0.8579 (t0) REVERT: J 203 ASP cc_start: 0.8982 (p0) cc_final: 0.8759 (p0) REVERT: J 253 MET cc_start: 0.8475 (mtp) cc_final: 0.8059 (mtp) REVERT: J 273 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8704 (mm-40) REVERT: J 280 GLN cc_start: 0.7737 (mt0) cc_final: 0.7284 (mt0) REVERT: J 320 GLU cc_start: 0.7981 (tp30) cc_final: 0.7667 (tp30) REVERT: J 360 GLN cc_start: 0.9317 (tt0) cc_final: 0.9021 (tp40) REVERT: K 42 ASP cc_start: 0.8851 (m-30) cc_final: 0.8460 (m-30) REVERT: K 123 LEU cc_start: 0.9661 (mp) cc_final: 0.9320 (mt) REVERT: K 202 MET cc_start: 0.9481 (ptp) cc_final: 0.9161 (pmm) REVERT: L 41 LEU cc_start: 0.9131 (tp) cc_final: 0.8716 (mm) REVERT: L 50 TRP cc_start: 0.8883 (m-10) cc_final: 0.8156 (m-90) REVERT: M 97 GLU cc_start: 0.9128 (tt0) cc_final: 0.8784 (mt-10) REVERT: M 124 MET cc_start: 0.9390 (mmm) cc_final: 0.8945 (mmt) REVERT: M 171 ASP cc_start: 0.9088 (t70) cc_final: 0.8738 (t0) REVERT: M 188 TYR cc_start: 0.9446 (m-80) cc_final: 0.9146 (m-80) REVERT: M 193 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8165 (mt-10) REVERT: M 199 MET cc_start: 0.9074 (mmm) cc_final: 0.8676 (mmm) REVERT: M 235 GLN cc_start: 0.9489 (tp40) cc_final: 0.8923 (mm110) REVERT: N 67 GLN cc_start: 0.9362 (OUTLIER) cc_final: 0.8742 (mp10) REVERT: N 87 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8344 (ppt-90) REVERT: N 88 ASP cc_start: 0.8960 (m-30) cc_final: 0.7696 (t0) REVERT: O 48 SER cc_start: 0.9671 (t) cc_final: 0.9356 (p) REVERT: O 53 ASN cc_start: 0.9476 (m-40) cc_final: 0.9102 (m-40) REVERT: O 54 GLU cc_start: 0.8990 (tp30) cc_final: 0.8522 (tt0) REVERT: O 90 MET cc_start: 0.8926 (mmm) cc_final: 0.8354 (mmm) REVERT: O 154 GLU cc_start: 0.9151 (tp30) cc_final: 0.8762 (tp30) REVERT: O 173 GLU cc_start: 0.9467 (mt-10) cc_final: 0.9187 (mm-30) REVERT: O 175 MET cc_start: 0.8436 (tmm) cc_final: 0.8177 (tmm) REVERT: P 157 ILE cc_start: 0.9068 (mt) cc_final: 0.8723 (tp) REVERT: P 160 MET cc_start: 0.9009 (mmm) cc_final: 0.8743 (tpp) REVERT: S 89 GLU cc_start: 0.9362 (mm-30) cc_final: 0.8872 (mm-30) REVERT: S 122 MET cc_start: 0.8619 (mtm) cc_final: 0.8345 (mtp) REVERT: S 146 LEU cc_start: 0.9657 (OUTLIER) cc_final: 0.9355 (mt) REVERT: S 163 GLU cc_start: 0.9426 (mt-10) cc_final: 0.8665 (tm-30) REVERT: a 99 GLN cc_start: 0.9061 (mm110) cc_final: 0.8526 (tt0) REVERT: a 111 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8652 (mmm) REVERT: a 186 LEU cc_start: 0.8717 (tt) cc_final: 0.8509 (tt) REVERT: c 181 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8342 (tm-30) REVERT: c 195 ASN cc_start: 0.6702 (t0) cc_final: 0.6497 (t0) REVERT: c 301 GLU cc_start: 0.9317 (mt-10) cc_final: 0.9116 (tp30) REVERT: c 303 ASN cc_start: 0.9633 (m-40) cc_final: 0.9388 (m110) REVERT: c 347 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7461 (mm-30) REVERT: o 262 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8171 (tt0) REVERT: o 385 TYR cc_start: 0.8449 (t80) cc_final: 0.7528 (t80) REVERT: o 387 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7584 (mt) REVERT: o 431 GLN cc_start: 0.8127 (mt0) cc_final: 0.7781 (tm-30) REVERT: o 443 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7598 (mt) REVERT: y 99 GLN cc_start: 0.9228 (mm110) cc_final: 0.8952 (mt0) REVERT: y 103 LEU cc_start: 0.9056 (mp) cc_final: 0.8743 (mp) REVERT: y 106 GLU cc_start: 0.9413 (mt-10) cc_final: 0.8967 (pt0) REVERT: y 144 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8691 (mm-40) REVERT: y 162 ASN cc_start: 0.9424 (OUTLIER) cc_final: 0.9067 (m110) REVERT: y 169 GLN cc_start: 0.9535 (mt0) cc_final: 0.9278 (tp40) REVERT: y 182 GLN cc_start: 0.9150 (mt0) cc_final: 0.8758 (mt0) REVERT: b 35 MET cc_start: 0.8577 (mmm) cc_final: 0.8102 (mmm) REVERT: b 41 MET cc_start: 0.9156 (mmm) cc_final: 0.8668 (mtp) REVERT: b 46 ASN cc_start: 0.8726 (t0) cc_final: 0.8416 (t0) REVERT: d 9 LYS cc_start: 0.8806 (mttt) cc_final: 0.8452 (mtpp) REVERT: d 22 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7514 (mm-30) REVERT: d 23 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8820 (tp) REVERT: d 44 LEU cc_start: 0.8985 (mp) cc_final: 0.8696 (mt) REVERT: d 61 GLN cc_start: 0.8970 (mt0) cc_final: 0.8378 (mp-120) REVERT: d 76 ASP cc_start: 0.9122 (OUTLIER) cc_final: 0.8697 (p0) REVERT: e 10 MET cc_start: 0.6289 (mmm) cc_final: 0.6077 (tmm) REVERT: f 58 GLU cc_start: 0.7755 (pt0) cc_final: 0.7093 (tt0) REVERT: g 44 MET cc_start: 0.8785 (mmm) cc_final: 0.8461 (tpp) REVERT: g 56 GLN cc_start: 0.6771 (tt0) cc_final: 0.6171 (pm20) REVERT: g 69 ILE cc_start: 0.6870 (mm) cc_final: 0.6610 (mm) REVERT: g 75 ASP cc_start: 0.6956 (t0) cc_final: 0.6368 (m-30) REVERT: h 18 GLU cc_start: 0.8274 (mp0) cc_final: 0.7616 (tm-30) REVERT: j 89 ARG cc_start: 0.8456 (ptt180) cc_final: 0.8082 (mmm-85) outliers start: 265 outliers final: 184 residues processed: 921 average time/residue: 0.5594 time to fit residues: 904.7754 Evaluate side-chains 896 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 685 time to evaluate : 4.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 694 ASN Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 832 GLU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 906 LYS Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1212 ARG Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1285 VAL Chi-restraints excluded: chain A residue 1319 ILE Chi-restraints excluded: chain A residue 1346 PHE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1399 MET Chi-restraints excluded: chain A residue 1440 ILE Chi-restraints excluded: chain A residue 1449 ASN Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1621 VAL Chi-restraints excluded: chain A residue 1650 ARG Chi-restraints excluded: chain A residue 1738 LEU Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1779 LEU Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1893 ILE Chi-restraints excluded: chain A residue 1898 VAL Chi-restraints excluded: chain A residue 1951 PHE Chi-restraints excluded: chain A residue 1995 TRP Chi-restraints excluded: chain A residue 1997 ASP Chi-restraints excluded: chain A residue 2017 THR Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 652 MET Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 658 ASP Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 783 ILE Chi-restraints excluded: chain C residue 801 TRP Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 182 GLN Chi-restraints excluded: chain H residue 193 SER Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 357 TRP Chi-restraints excluded: chain H residue 396 PHE Chi-restraints excluded: chain H residue 419 PHE Chi-restraints excluded: chain H residue 433 LEU Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 194 HIS Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 257 ILE Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 261 THR Chi-restraints excluded: chain J residue 271 GLN Chi-restraints excluded: chain J residue 301 MET Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain J residue 382 HIS Chi-restraints excluded: chain J residue 408 ASP Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 92 ILE Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 153 CYS Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 160 ILE Chi-restraints excluded: chain M residue 203 THR Chi-restraints excluded: chain N residue 22 ASN Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 67 GLN Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 87 ARG Chi-restraints excluded: chain N residue 118 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 288 ILE Chi-restraints excluded: chain N residue 291 ILE Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 18 ASP Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 181 ARG Chi-restraints excluded: chain O residue 230 THR Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 35 THR Chi-restraints excluded: chain P residue 37 LEU Chi-restraints excluded: chain P residue 161 THR Chi-restraints excluded: chain R residue 4 ASN Chi-restraints excluded: chain S residue 58 LEU Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 107 ASP Chi-restraints excluded: chain S residue 124 ARG Chi-restraints excluded: chain S residue 128 THR Chi-restraints excluded: chain S residue 146 LEU Chi-restraints excluded: chain S residue 156 TYR Chi-restraints excluded: chain S residue 157 THR Chi-restraints excluded: chain S residue 212 HIS Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 232 LEU Chi-restraints excluded: chain S residue 279 LEU Chi-restraints excluded: chain a residue 111 MET Chi-restraints excluded: chain a residue 132 HIS Chi-restraints excluded: chain a residue 137 LEU Chi-restraints excluded: chain a residue 146 LEU Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 171 GLN Chi-restraints excluded: chain a residue 177 ASN Chi-restraints excluded: chain a residue 237 ILE Chi-restraints excluded: chain a residue 238 THR Chi-restraints excluded: chain c residue 186 ILE Chi-restraints excluded: chain o residue 177 LEU Chi-restraints excluded: chain o residue 274 HIS Chi-restraints excluded: chain o residue 281 GLU Chi-restraints excluded: chain o residue 331 ILE Chi-restraints excluded: chain o residue 381 SER Chi-restraints excluded: chain o residue 387 ILE Chi-restraints excluded: chain o residue 443 ILE Chi-restraints excluded: chain y residue 96 SER Chi-restraints excluded: chain y residue 112 LEU Chi-restraints excluded: chain y residue 144 GLN Chi-restraints excluded: chain y residue 161 VAL Chi-restraints excluded: chain y residue 162 ASN Chi-restraints excluded: chain y residue 208 SER Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 15 LEU Chi-restraints excluded: chain b residue 20 LEU Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 86 ILE Chi-restraints excluded: chain b residue 97 VAL Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain d residue 22 GLU Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 76 ASP Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain f residue 67 THR Chi-restraints excluded: chain f residue 73 ILE Chi-restraints excluded: chain g residue 19 ILE Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 39 VAL Chi-restraints excluded: chain h residue 6 PHE Chi-restraints excluded: chain h residue 16 THR Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain j residue 67 MET Chi-restraints excluded: chain j residue 77 THR Chi-restraints excluded: chain j residue 96 LEU Chi-restraints excluded: chain j residue 100 SER Chi-restraints excluded: chain j residue 101 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 652 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 chunk 385 optimal weight: 0.0980 chunk 494 optimal weight: 3.9990 chunk 383 optimal weight: 5.9990 chunk 570 optimal weight: 40.0000 chunk 378 optimal weight: 2.9990 chunk 674 optimal weight: 20.0000 chunk 422 optimal weight: 2.9990 chunk 411 optimal weight: 0.6980 chunk 311 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 558 GLN ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 371 GLN H 390 HIS ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 283 GLN ** o 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 60755 Z= 0.242 Angle : 0.649 18.842 84029 Z= 0.317 Chirality : 0.040 0.302 9967 Planarity : 0.004 0.090 9414 Dihedral : 18.000 176.007 12524 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.71 % Favored : 94.25 % Rotamer: Outliers : 5.11 % Allowed : 20.32 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.06 (0.11), residues: 6554 helix: 1.74 (0.09), residues: 3092 sheet: -1.74 (0.18), residues: 755 loop : -1.69 (0.12), residues: 2707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP C 933 HIS 0.008 0.001 HIS A 138 PHE 0.021 0.002 PHE e 18 TYR 0.025 0.002 TYR A 391 ARG 0.013 0.000 ARG P 6 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 990 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 728 time to evaluate : 5.037 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: A 142 ILE cc_start: 0.9341 (mt) cc_final: 0.8984 (tp) REVERT: A 199 ILE cc_start: 0.9712 (tp) cc_final: 0.9323 (tt) REVERT: A 326 ASN cc_start: 0.9217 (OUTLIER) cc_final: 0.8518 (t0) REVERT: A 331 PHE cc_start: 0.9226 (OUTLIER) cc_final: 0.8572 (m-80) REVERT: A 422 LEU cc_start: 0.9532 (tp) cc_final: 0.9198 (tt) REVERT: A 493 MET cc_start: 0.8896 (mmt) cc_final: 0.8479 (mmm) REVERT: A 551 LEU cc_start: 0.9667 (mt) cc_final: 0.9413 (mp) REVERT: A 588 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9037 (pp) REVERT: A 618 SER cc_start: 0.9365 (t) cc_final: 0.8911 (p) REVERT: A 626 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9044 (tp) REVERT: A 629 MET cc_start: 0.8508 (tmm) cc_final: 0.8111 (tmm) REVERT: A 693 LYS cc_start: 0.8039 (mtmt) cc_final: 0.7787 (pttt) REVERT: A 712 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9264 (mm) REVERT: A 750 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9147 (tt) REVERT: A 832 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8571 (mp0) REVERT: A 852 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8933 (tt) REVERT: A 905 TYR cc_start: 0.7201 (m-80) cc_final: 0.6959 (m-80) REVERT: A 933 GLU cc_start: 0.9431 (mt-10) cc_final: 0.9143 (mp0) REVERT: A 935 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8771 (tm-30) REVERT: A 972 MET cc_start: 0.8329 (mtt) cc_final: 0.7810 (ttt) REVERT: A 1004 ASP cc_start: 0.9145 (m-30) cc_final: 0.8631 (t0) REVERT: A 1085 LYS cc_start: 0.9381 (tptm) cc_final: 0.9077 (tppp) REVERT: A 1086 ASN cc_start: 0.9240 (m-40) cc_final: 0.8888 (t0) REVERT: A 1288 LEU cc_start: 0.9422 (mp) cc_final: 0.9139 (mt) REVERT: A 1346 PHE cc_start: 0.9348 (OUTLIER) cc_final: 0.7667 (p90) REVERT: A 1379 MET cc_start: 0.8477 (ttm) cc_final: 0.8257 (ttt) REVERT: A 1485 ASP cc_start: 0.8734 (m-30) cc_final: 0.8469 (p0) REVERT: A 1513 GLU cc_start: 0.8846 (tt0) cc_final: 0.8548 (mt-10) REVERT: A 1545 ASP cc_start: 0.8858 (m-30) cc_final: 0.8499 (m-30) REVERT: A 1616 ARG cc_start: 0.9281 (ttm-80) cc_final: 0.8882 (ttm170) REVERT: A 1632 ILE cc_start: 0.9429 (mm) cc_final: 0.9198 (pt) REVERT: A 1687 HIS cc_start: 0.8948 (m-70) cc_final: 0.8507 (p-80) REVERT: A 1703 MET cc_start: 0.7027 (mmm) cc_final: 0.6747 (mmm) REVERT: A 1778 ASP cc_start: 0.9129 (t0) cc_final: 0.8862 (t0) REVERT: A 1783 MET cc_start: 0.8812 (mmm) cc_final: 0.8510 (mmm) REVERT: A 1807 LYS cc_start: 0.9241 (tptt) cc_final: 0.8650 (mmtt) REVERT: A 1817 GLU cc_start: 0.9540 (tt0) cc_final: 0.8966 (tm-30) REVERT: A 1866 PHE cc_start: 0.8918 (m-10) cc_final: 0.8629 (m-80) REVERT: A 1880 PHE cc_start: 0.7866 (t80) cc_final: 0.7455 (t80) REVERT: A 1903 LYS cc_start: 0.8986 (tppp) cc_final: 0.8690 (tttt) REVERT: A 1948 MET cc_start: 0.9195 (mmm) cc_final: 0.8706 (ppp) REVERT: A 1986 MET cc_start: 0.9268 (tpp) cc_final: 0.9066 (tpt) REVERT: C 126 MET cc_start: 0.8636 (tpp) cc_final: 0.8313 (tpp) REVERT: C 150 MET cc_start: 0.9488 (mmm) cc_final: 0.9182 (mmm) REVERT: C 164 MET cc_start: 0.8820 (ptm) cc_final: 0.8248 (tmm) REVERT: C 179 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.7934 (m-30) REVERT: C 222 MET cc_start: 0.9141 (mmm) cc_final: 0.8616 (mmp) REVERT: C 282 MET cc_start: 0.9397 (tpt) cc_final: 0.9024 (tpp) REVERT: C 391 MET cc_start: 0.8715 (ttp) cc_final: 0.8445 (ttm) REVERT: C 504 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8118 (t) REVERT: C 538 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8422 (tm-30) REVERT: C 540 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8820 (mm-30) REVERT: C 545 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9081 (pp) REVERT: C 614 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8669 (tp30) REVERT: C 652 MET cc_start: 0.8741 (tpp) cc_final: 0.7935 (tpp) REVERT: C 719 MET cc_start: 0.8733 (ppp) cc_final: 0.8477 (ppp) REVERT: C 820 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6484 (mt) REVERT: C 859 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8514 (pm20) REVERT: C 968 MET cc_start: 0.9078 (mmm) cc_final: 0.8777 (mmm) REVERT: H 101 MET cc_start: 0.6835 (ptp) cc_final: 0.5856 (tmm) REVERT: H 155 MET cc_start: 0.8468 (mmm) cc_final: 0.8053 (tpp) REVERT: H 158 CYS cc_start: 0.9069 (p) cc_final: 0.8753 (t) REVERT: H 160 TRP cc_start: 0.7888 (p-90) cc_final: 0.7617 (p-90) REVERT: H 161 LYS cc_start: 0.8995 (tptt) cc_final: 0.8580 (tptm) REVERT: H 167 LYS cc_start: 0.8226 (pttp) cc_final: 0.7935 (tttt) REVERT: H 195 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7708 (tm-30) REVERT: H 350 MET cc_start: 0.8984 (mmm) cc_final: 0.8631 (mmm) REVERT: H 357 TRP cc_start: 0.9317 (OUTLIER) cc_final: 0.7801 (m-10) REVERT: H 386 LYS cc_start: 0.9576 (mmtp) cc_final: 0.9284 (ttmm) REVERT: H 396 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8195 (m-10) REVERT: J 117 LYS cc_start: 0.8883 (ttmt) cc_final: 0.8526 (tppt) REVERT: J 164 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7914 (mtm) REVERT: J 187 ASP cc_start: 0.9130 (t0) cc_final: 0.8583 (t0) REVERT: J 273 GLN cc_start: 0.9020 (mm-40) cc_final: 0.8700 (mm-40) REVERT: J 280 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7174 (mt0) REVERT: J 303 VAL cc_start: 0.9251 (OUTLIER) cc_final: 0.9018 (m) REVERT: J 320 GLU cc_start: 0.7958 (tp30) cc_final: 0.7715 (tp30) REVERT: J 360 GLN cc_start: 0.9320 (tt0) cc_final: 0.9049 (tp40) REVERT: K 42 ASP cc_start: 0.8899 (m-30) cc_final: 0.8558 (m-30) REVERT: K 123 LEU cc_start: 0.9660 (mp) cc_final: 0.9300 (mt) REVERT: K 149 MET cc_start: 0.8756 (ttp) cc_final: 0.7947 (pmm) REVERT: K 202 MET cc_start: 0.9485 (ptp) cc_final: 0.9159 (pmm) REVERT: L 41 LEU cc_start: 0.9128 (tp) cc_final: 0.8708 (mm) REVERT: L 50 TRP cc_start: 0.8840 (m-10) cc_final: 0.8105 (m-90) REVERT: M 97 GLU cc_start: 0.9138 (tt0) cc_final: 0.8717 (tm-30) REVERT: M 124 MET cc_start: 0.9358 (mmm) cc_final: 0.8883 (mmt) REVERT: M 171 ASP cc_start: 0.9095 (t70) cc_final: 0.8754 (t0) REVERT: M 188 TYR cc_start: 0.9443 (m-80) cc_final: 0.9176 (m-80) REVERT: M 193 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8155 (mt-10) REVERT: M 235 GLN cc_start: 0.9480 (tp40) cc_final: 0.8902 (mm110) REVERT: N 33 GLU cc_start: 0.8658 (pt0) cc_final: 0.8183 (tt0) REVERT: N 67 GLN cc_start: 0.9383 (OUTLIER) cc_final: 0.8755 (mp10) REVERT: N 87 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8427 (ppt-90) REVERT: N 88 ASP cc_start: 0.8870 (m-30) cc_final: 0.7590 (t0) REVERT: O 48 SER cc_start: 0.9665 (t) cc_final: 0.9358 (p) REVERT: O 53 ASN cc_start: 0.9579 (m-40) cc_final: 0.9372 (m-40) REVERT: O 54 GLU cc_start: 0.9027 (tp30) cc_final: 0.8529 (tt0) REVERT: O 90 MET cc_start: 0.8923 (mmm) cc_final: 0.8491 (mmm) REVERT: O 91 MET cc_start: 0.8936 (mmm) cc_final: 0.8717 (mmm) REVERT: O 154 GLU cc_start: 0.9181 (tp30) cc_final: 0.8786 (tp30) REVERT: O 173 GLU cc_start: 0.9464 (mt-10) cc_final: 0.9189 (mm-30) REVERT: O 175 MET cc_start: 0.8435 (tmm) cc_final: 0.8168 (tmm) REVERT: P 157 ILE cc_start: 0.9075 (mt) cc_final: 0.8729 (tp) REVERT: S 39 ASP cc_start: 0.7837 (m-30) cc_final: 0.7512 (t0) REVERT: S 87 ILE cc_start: 0.9443 (mm) cc_final: 0.9219 (tt) REVERT: S 89 GLU cc_start: 0.9371 (mm-30) cc_final: 0.8978 (mt-10) REVERT: S 122 MET cc_start: 0.8581 (mtm) cc_final: 0.8278 (mtp) REVERT: S 146 LEU cc_start: 0.9632 (OUTLIER) cc_final: 0.9356 (mt) REVERT: S 163 GLU cc_start: 0.9432 (mt-10) cc_final: 0.8846 (tm-30) REVERT: a 99 GLN cc_start: 0.9055 (mm110) cc_final: 0.8512 (tt0) REVERT: a 111 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8642 (mmm) REVERT: a 186 LEU cc_start: 0.8724 (tt) cc_final: 0.8524 (tt) REVERT: c 301 GLU cc_start: 0.9315 (mt-10) cc_final: 0.9114 (tp30) REVERT: c 303 ASN cc_start: 0.9646 (m-40) cc_final: 0.9423 (m110) REVERT: c 347 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7359 (mm-30) REVERT: o 262 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8147 (tt0) REVERT: o 385 TYR cc_start: 0.8433 (t80) cc_final: 0.7452 (t80) REVERT: o 387 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7523 (mt) REVERT: o 431 GLN cc_start: 0.8118 (mt0) cc_final: 0.7809 (tm-30) REVERT: o 443 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7685 (mt) REVERT: y 99 GLN cc_start: 0.9210 (mm110) cc_final: 0.8845 (mt0) REVERT: y 103 LEU cc_start: 0.9104 (mp) cc_final: 0.8812 (mp) REVERT: y 106 GLU cc_start: 0.9391 (mt-10) cc_final: 0.8962 (pt0) REVERT: y 144 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.8694 (mm-40) REVERT: y 162 ASN cc_start: 0.9490 (OUTLIER) cc_final: 0.9099 (m110) REVERT: y 169 GLN cc_start: 0.9519 (mt0) cc_final: 0.9283 (tp40) REVERT: y 171 GLU cc_start: 0.9311 (tp30) cc_final: 0.8971 (tp30) REVERT: y 182 GLN cc_start: 0.9205 (mt0) cc_final: 0.8766 (mt0) REVERT: b 35 MET cc_start: 0.8514 (mmm) cc_final: 0.8014 (mmm) REVERT: b 41 MET cc_start: 0.9129 (mmm) cc_final: 0.8617 (mtp) REVERT: b 46 ASN cc_start: 0.8780 (t0) cc_final: 0.8553 (t0) REVERT: d 9 LYS cc_start: 0.8812 (mttt) cc_final: 0.8467 (mtpp) REVERT: d 23 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8798 (tp) REVERT: d 44 LEU cc_start: 0.9020 (mp) cc_final: 0.8804 (mt) REVERT: d 61 GLN cc_start: 0.9015 (mt0) cc_final: 0.8354 (mp10) REVERT: e 10 MET cc_start: 0.6729 (mmm) cc_final: 0.6403 (tmm) REVERT: f 58 GLU cc_start: 0.7826 (pt0) cc_final: 0.7172 (tt0) REVERT: g 11 MET cc_start: 0.8142 (mmm) cc_final: 0.7913 (mtt) REVERT: g 44 MET cc_start: 0.8826 (mmm) cc_final: 0.8578 (tpt) REVERT: g 56 GLN cc_start: 0.6767 (tt0) cc_final: 0.5848 (pm20) REVERT: g 69 ILE cc_start: 0.6834 (mm) cc_final: 0.6599 (mm) REVERT: g 75 ASP cc_start: 0.6868 (t0) cc_final: 0.6357 (m-30) REVERT: h 18 GLU cc_start: 0.8041 (mp0) cc_final: 0.7567 (tm-30) REVERT: j 89 ARG cc_start: 0.8471 (ptt180) cc_final: 0.8070 (mmm-85) outliers start: 262 outliers final: 190 residues processed: 921 average time/residue: 0.5334 time to fit residues: 855.2349 Evaluate side-chains 896 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 678 time to evaluate : 4.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 694 ASN Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 832 GLU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 906 LYS Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1212 ARG Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1285 VAL Chi-restraints excluded: chain A residue 1313 ASP Chi-restraints excluded: chain A residue 1319 ILE Chi-restraints excluded: chain A residue 1337 THR Chi-restraints excluded: chain A residue 1346 PHE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1399 MET Chi-restraints excluded: chain A residue 1440 ILE Chi-restraints excluded: chain A residue 1449 ASN Chi-restraints excluded: chain A residue 1469 ILE Chi-restraints excluded: chain A residue 1553 ILE Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1621 VAL Chi-restraints excluded: chain A residue 1650 ARG Chi-restraints excluded: chain A residue 1738 LEU Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1779 LEU Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1893 ILE Chi-restraints excluded: chain A residue 1951 PHE Chi-restraints excluded: chain A residue 1995 TRP Chi-restraints excluded: chain A residue 1997 ASP Chi-restraints excluded: chain A residue 2017 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 658 ASP Chi-restraints excluded: chain C residue 783 ILE Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 859 GLU Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 182 GLN Chi-restraints excluded: chain H residue 193 SER Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 357 TRP Chi-restraints excluded: chain H residue 383 ILE Chi-restraints excluded: chain H residue 396 PHE Chi-restraints excluded: chain H residue 419 PHE Chi-restraints excluded: chain H residue 433 LEU Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 161 ASP Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 194 HIS Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 257 ILE Chi-restraints excluded: chain J residue 261 THR Chi-restraints excluded: chain J residue 271 GLN Chi-restraints excluded: chain J residue 280 GLN Chi-restraints excluded: chain J residue 301 MET Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain J residue 393 VAL Chi-restraints excluded: chain J residue 408 ASP Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 92 ILE Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 153 CYS Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 203 THR Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 67 GLN Chi-restraints excluded: chain N residue 74 CYS Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 87 ARG Chi-restraints excluded: chain N residue 95 ASN Chi-restraints excluded: chain N residue 118 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 288 ILE Chi-restraints excluded: chain N residue 291 ILE Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 18 ASP Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 151 MET Chi-restraints excluded: chain O residue 181 ARG Chi-restraints excluded: chain O residue 230 THR Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 35 THR Chi-restraints excluded: chain P residue 37 LEU Chi-restraints excluded: chain P residue 161 THR Chi-restraints excluded: chain R residue 4 ASN Chi-restraints excluded: chain S residue 58 LEU Chi-restraints excluded: chain S residue 107 ASP Chi-restraints excluded: chain S residue 124 ARG Chi-restraints excluded: chain S residue 128 THR Chi-restraints excluded: chain S residue 146 LEU Chi-restraints excluded: chain S residue 156 TYR Chi-restraints excluded: chain S residue 157 THR Chi-restraints excluded: chain S residue 193 VAL Chi-restraints excluded: chain S residue 212 HIS Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 232 LEU Chi-restraints excluded: chain S residue 279 LEU Chi-restraints excluded: chain a residue 111 MET Chi-restraints excluded: chain a residue 132 HIS Chi-restraints excluded: chain a residue 137 LEU Chi-restraints excluded: chain a residue 146 LEU Chi-restraints excluded: chain a residue 177 ASN Chi-restraints excluded: chain a residue 231 THR Chi-restraints excluded: chain a residue 237 ILE Chi-restraints excluded: chain a residue 238 THR Chi-restraints excluded: chain c residue 186 ILE Chi-restraints excluded: chain c residue 216 ILE Chi-restraints excluded: chain o residue 177 LEU Chi-restraints excluded: chain o residue 281 GLU Chi-restraints excluded: chain o residue 331 ILE Chi-restraints excluded: chain o residue 381 SER Chi-restraints excluded: chain o residue 387 ILE Chi-restraints excluded: chain o residue 419 ASN Chi-restraints excluded: chain o residue 443 ILE Chi-restraints excluded: chain y residue 96 SER Chi-restraints excluded: chain y residue 112 LEU Chi-restraints excluded: chain y residue 144 GLN Chi-restraints excluded: chain y residue 161 VAL Chi-restraints excluded: chain y residue 162 ASN Chi-restraints excluded: chain y residue 208 SER Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 15 LEU Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 86 ILE Chi-restraints excluded: chain b residue 97 VAL Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain d residue 22 GLU Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain f residue 73 ILE Chi-restraints excluded: chain g residue 19 ILE Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 39 VAL Chi-restraints excluded: chain h residue 6 PHE Chi-restraints excluded: chain h residue 16 THR Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain j residue 77 THR Chi-restraints excluded: chain j residue 96 LEU Chi-restraints excluded: chain j residue 100 SER Chi-restraints excluded: chain j residue 101 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 417 optimal weight: 1.9990 chunk 269 optimal weight: 0.9990 chunk 402 optimal weight: 10.0000 chunk 203 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 428 optimal weight: 0.8980 chunk 459 optimal weight: 7.9990 chunk 333 optimal weight: 0.0060 chunk 62 optimal weight: 0.9990 chunk 530 optimal weight: 10.0000 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1516 GLN A1532 HIS ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 306 HIS ** J 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 360 GLN K 111 HIS N 72 GLN ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 154 GLN ** a 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 309 HIS ** o 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 204 ASN ** e 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 60755 Z= 0.188 Angle : 0.640 18.424 84029 Z= 0.309 Chirality : 0.040 0.443 9967 Planarity : 0.004 0.105 9414 Dihedral : 17.906 175.031 12524 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.20 % Favored : 94.75 % Rotamer: Outliers : 4.35 % Allowed : 21.65 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.07 (0.11), residues: 6554 helix: 1.85 (0.09), residues: 3086 sheet: -1.58 (0.18), residues: 757 loop : -1.65 (0.12), residues: 2711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP C 933 HIS 0.007 0.001 HIS A 138 PHE 0.019 0.001 PHE H 342 TYR 0.028 0.001 TYR A 391 ARG 0.007 0.000 ARG A1163 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 997 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 774 time to evaluate : 5.030 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: A 142 ILE cc_start: 0.9331 (mt) cc_final: 0.8984 (tp) REVERT: A 199 ILE cc_start: 0.9718 (tp) cc_final: 0.9317 (tt) REVERT: A 224 MET cc_start: 0.8785 (mtt) cc_final: 0.8540 (mtm) REVERT: A 326 ASN cc_start: 0.8966 (OUTLIER) cc_final: 0.8491 (t0) REVERT: A 331 PHE cc_start: 0.9228 (OUTLIER) cc_final: 0.8741 (m-80) REVERT: A 422 LEU cc_start: 0.9523 (tp) cc_final: 0.9204 (tt) REVERT: A 551 LEU cc_start: 0.9663 (mt) cc_final: 0.9405 (mp) REVERT: A 588 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9013 (pp) REVERT: A 618 SER cc_start: 0.9384 (t) cc_final: 0.8987 (p) REVERT: A 629 MET cc_start: 0.8452 (tmm) cc_final: 0.8034 (tmm) REVERT: A 674 MET cc_start: 0.9145 (mmp) cc_final: 0.8791 (mmp) REVERT: A 693 LYS cc_start: 0.8107 (mtmt) cc_final: 0.7881 (pttt) REVERT: A 712 LEU cc_start: 0.9494 (mt) cc_final: 0.9194 (mm) REVERT: A 750 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9027 (tt) REVERT: A 832 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8567 (mp0) REVERT: A 852 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8905 (tt) REVERT: A 933 GLU cc_start: 0.9419 (mt-10) cc_final: 0.9149 (mp0) REVERT: A 935 GLU cc_start: 0.9031 (tm-30) cc_final: 0.8705 (tm-30) REVERT: A 1004 ASP cc_start: 0.9128 (m-30) cc_final: 0.8616 (t0) REVERT: A 1085 LYS cc_start: 0.9399 (tptm) cc_final: 0.9115 (tppp) REVERT: A 1086 ASN cc_start: 0.9230 (m-40) cc_final: 0.8908 (t0) REVERT: A 1101 TYR cc_start: 0.7822 (t80) cc_final: 0.7423 (t80) REVERT: A 1202 ASN cc_start: 0.8664 (m110) cc_final: 0.8393 (m110) REVERT: A 1288 LEU cc_start: 0.9370 (mp) cc_final: 0.9089 (mt) REVERT: A 1346 PHE cc_start: 0.9292 (OUTLIER) cc_final: 0.7551 (p90) REVERT: A 1485 ASP cc_start: 0.8704 (m-30) cc_final: 0.8440 (p0) REVERT: A 1513 GLU cc_start: 0.8865 (tt0) cc_final: 0.8605 (mt-10) REVERT: A 1522 ASN cc_start: 0.8563 (t0) cc_final: 0.8102 (t0) REVERT: A 1545 ASP cc_start: 0.8875 (m-30) cc_final: 0.8523 (m-30) REVERT: A 1632 ILE cc_start: 0.9389 (mm) cc_final: 0.9173 (pt) REVERT: A 1687 HIS cc_start: 0.8931 (m-70) cc_final: 0.8520 (p-80) REVERT: A 1778 ASP cc_start: 0.9077 (t0) cc_final: 0.8867 (t0) REVERT: A 1783 MET cc_start: 0.8785 (mmm) cc_final: 0.8562 (mmm) REVERT: A 1807 LYS cc_start: 0.9196 (tptt) cc_final: 0.8636 (mmtt) REVERT: A 1817 GLU cc_start: 0.9502 (tt0) cc_final: 0.8884 (tm-30) REVERT: A 1866 PHE cc_start: 0.8931 (m-10) cc_final: 0.8655 (m-80) REVERT: A 1880 PHE cc_start: 0.7879 (t80) cc_final: 0.7487 (t80) REVERT: A 1903 LYS cc_start: 0.8997 (tppp) cc_final: 0.8695 (tttt) REVERT: A 1986 MET cc_start: 0.9107 (tpp) cc_final: 0.8761 (tpp) REVERT: C 126 MET cc_start: 0.8569 (tpp) cc_final: 0.8267 (tpp) REVERT: C 150 MET cc_start: 0.9442 (mmm) cc_final: 0.9140 (mmm) REVERT: C 164 MET cc_start: 0.8802 (ptm) cc_final: 0.8163 (tmm) REVERT: C 179 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8006 (m-30) REVERT: C 194 ASN cc_start: 0.8086 (m-40) cc_final: 0.7861 (t0) REVERT: C 222 MET cc_start: 0.9111 (mmm) cc_final: 0.8588 (mmp) REVERT: C 282 MET cc_start: 0.9425 (tpt) cc_final: 0.9043 (tpp) REVERT: C 478 TYR cc_start: 0.8349 (t80) cc_final: 0.8072 (t80) REVERT: C 504 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8165 (t) REVERT: C 538 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8448 (tm-30) REVERT: C 545 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8817 (pp) REVERT: C 614 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8508 (tp30) REVERT: C 652 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.7914 (tpp) REVERT: C 719 MET cc_start: 0.8724 (ppp) cc_final: 0.8448 (ppp) REVERT: C 820 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6474 (mt) REVERT: C 859 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8535 (pm20) REVERT: C 968 MET cc_start: 0.9086 (mmm) cc_final: 0.8781 (mmm) REVERT: H 102 PHE cc_start: 0.7772 (t80) cc_final: 0.7041 (t80) REVERT: H 155 MET cc_start: 0.8440 (mmm) cc_final: 0.7941 (tpp) REVERT: H 158 CYS cc_start: 0.9067 (p) cc_final: 0.8711 (t) REVERT: H 161 LYS cc_start: 0.9018 (tptt) cc_final: 0.8467 (tttt) REVERT: H 167 LYS cc_start: 0.8196 (pttp) cc_final: 0.7950 (tttt) REVERT: H 195 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7699 (tm-30) REVERT: H 334 LEU cc_start: 0.9603 (mt) cc_final: 0.9399 (mt) REVERT: H 350 MET cc_start: 0.8880 (mmm) cc_final: 0.8637 (mmm) REVERT: H 357 TRP cc_start: 0.9305 (OUTLIER) cc_final: 0.7810 (m-10) REVERT: H 386 LYS cc_start: 0.9576 (mmtp) cc_final: 0.9237 (ttmm) REVERT: H 433 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8870 (pt) REVERT: J 117 LYS cc_start: 0.8867 (ttmt) cc_final: 0.8504 (tppt) REVERT: J 143 ARG cc_start: 0.8809 (mtp85) cc_final: 0.8545 (mtp85) REVERT: J 164 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7883 (mtm) REVERT: J 187 ASP cc_start: 0.9083 (t0) cc_final: 0.8512 (t0) REVERT: J 253 MET cc_start: 0.8216 (mtp) cc_final: 0.7763 (mtp) REVERT: J 273 GLN cc_start: 0.9012 (mm-40) cc_final: 0.8723 (mm-40) REVERT: J 280 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7390 (mt0) REVERT: J 320 GLU cc_start: 0.7949 (tp30) cc_final: 0.7718 (tp30) REVERT: J 360 GLN cc_start: 0.9332 (tt0) cc_final: 0.8973 (tp40) REVERT: K 42 ASP cc_start: 0.8940 (m-30) cc_final: 0.8719 (m-30) REVERT: K 112 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8317 (mm) REVERT: K 123 LEU cc_start: 0.9659 (mp) cc_final: 0.9294 (mt) REVERT: K 149 MET cc_start: 0.8768 (ttp) cc_final: 0.8196 (pmm) REVERT: K 178 TYR cc_start: 0.8822 (m-10) cc_final: 0.8193 (m-80) REVERT: K 199 ASP cc_start: 0.8898 (OUTLIER) cc_final: 0.8465 (p0) REVERT: L 41 LEU cc_start: 0.9025 (tp) cc_final: 0.8640 (mm) REVERT: L 50 TRP cc_start: 0.8630 (m-10) cc_final: 0.7821 (m-90) REVERT: L 53 MET cc_start: 0.8923 (tpp) cc_final: 0.8700 (mmm) REVERT: M 97 GLU cc_start: 0.9126 (tt0) cc_final: 0.8699 (tm-30) REVERT: M 124 MET cc_start: 0.9283 (mmm) cc_final: 0.8833 (mmt) REVERT: M 171 ASP cc_start: 0.9148 (t70) cc_final: 0.8805 (t0) REVERT: M 188 TYR cc_start: 0.9386 (m-80) cc_final: 0.9164 (m-80) REVERT: M 193 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8007 (mt-10) REVERT: M 235 GLN cc_start: 0.9467 (tp40) cc_final: 0.8888 (mm110) REVERT: N 33 GLU cc_start: 0.8690 (pt0) cc_final: 0.8244 (tt0) REVERT: N 67 GLN cc_start: 0.9384 (OUTLIER) cc_final: 0.8747 (mp10) REVERT: N 87 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8506 (ptt-90) REVERT: N 88 ASP cc_start: 0.8833 (m-30) cc_final: 0.7277 (t0) REVERT: O 48 SER cc_start: 0.9652 (t) cc_final: 0.9344 (p) REVERT: O 53 ASN cc_start: 0.9563 (m-40) cc_final: 0.9198 (m-40) REVERT: O 54 GLU cc_start: 0.8991 (tp30) cc_final: 0.8455 (tt0) REVERT: O 90 MET cc_start: 0.8873 (mmm) cc_final: 0.8400 (mmm) REVERT: O 91 MET cc_start: 0.8891 (mmm) cc_final: 0.8689 (mmm) REVERT: O 154 GLU cc_start: 0.9188 (tp30) cc_final: 0.8803 (tp30) REVERT: O 173 GLU cc_start: 0.9494 (mt-10) cc_final: 0.9194 (mm-30) REVERT: O 175 MET cc_start: 0.8423 (tmm) cc_final: 0.8135 (tmm) REVERT: P 157 ILE cc_start: 0.9045 (mt) cc_final: 0.8716 (tp) REVERT: S 39 ASP cc_start: 0.7735 (m-30) cc_final: 0.7477 (t0) REVERT: S 89 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8984 (mm-30) REVERT: S 122 MET cc_start: 0.8507 (mtm) cc_final: 0.8241 (mtp) REVERT: S 146 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9354 (mt) REVERT: S 163 GLU cc_start: 0.9378 (mt-10) cc_final: 0.9021 (tm-30) REVERT: S 180 LYS cc_start: 0.8864 (mtmm) cc_final: 0.8386 (mmmt) REVERT: a 99 GLN cc_start: 0.8950 (mm110) cc_final: 0.8420 (tt0) REVERT: a 111 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8658 (mmm) REVERT: a 186 LEU cc_start: 0.8735 (tt) cc_final: 0.8507 (tt) REVERT: c 301 GLU cc_start: 0.9303 (mt-10) cc_final: 0.8741 (tp30) REVERT: c 347 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7622 (mm-30) REVERT: o 173 LYS cc_start: 0.8023 (pttm) cc_final: 0.7165 (mmmt) REVERT: o 194 HIS cc_start: 0.8242 (m-70) cc_final: 0.7649 (p90) REVERT: o 209 ILE cc_start: 0.8915 (mp) cc_final: 0.8504 (tp) REVERT: o 342 LEU cc_start: 0.9080 (mt) cc_final: 0.8787 (tp) REVERT: o 385 TYR cc_start: 0.8527 (t80) cc_final: 0.7501 (t80) REVERT: o 387 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7489 (mt) REVERT: o 431 GLN cc_start: 0.8189 (mt0) cc_final: 0.7814 (tm-30) REVERT: y 99 GLN cc_start: 0.9231 (mm110) cc_final: 0.8883 (mt0) REVERT: y 103 LEU cc_start: 0.9097 (mp) cc_final: 0.8808 (mp) REVERT: y 106 GLU cc_start: 0.9388 (mt-10) cc_final: 0.8945 (pt0) REVERT: y 144 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8665 (mm-40) REVERT: y 162 ASN cc_start: 0.9410 (OUTLIER) cc_final: 0.9054 (m110) REVERT: y 169 GLN cc_start: 0.9500 (mt0) cc_final: 0.9254 (tp40) REVERT: y 182 GLN cc_start: 0.9165 (mt0) cc_final: 0.8680 (mt0) REVERT: y 200 ASN cc_start: 0.8241 (OUTLIER) cc_final: 0.7383 (t0) REVERT: b 35 MET cc_start: 0.8486 (mmm) cc_final: 0.8009 (mmm) REVERT: b 41 MET cc_start: 0.9104 (mmm) cc_final: 0.8582 (mtp) REVERT: b 46 ASN cc_start: 0.8814 (t0) cc_final: 0.8533 (t0) REVERT: b 90 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7274 (mm-30) REVERT: d 9 LYS cc_start: 0.8795 (mttt) cc_final: 0.8453 (mtpp) REVERT: d 22 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7556 (mm-30) REVERT: d 29 TYR cc_start: 0.8320 (m-80) cc_final: 0.8048 (m-80) REVERT: e 10 MET cc_start: 0.6452 (mmm) cc_final: 0.6246 (tmm) REVERT: f 55 GLU cc_start: 0.7046 (pp20) cc_final: 0.6843 (pp20) REVERT: g 11 MET cc_start: 0.8073 (mmm) cc_final: 0.7856 (mtt) REVERT: g 44 MET cc_start: 0.8891 (mmm) cc_final: 0.8649 (tpt) REVERT: g 56 GLN cc_start: 0.6806 (tt0) cc_final: 0.5890 (pm20) REVERT: g 69 ILE cc_start: 0.7032 (mm) cc_final: 0.6772 (mm) REVERT: g 75 ASP cc_start: 0.6624 (t0) cc_final: 0.6021 (m-30) REVERT: h 18 GLU cc_start: 0.8024 (mp0) cc_final: 0.7513 (tm-30) REVERT: j 89 ARG cc_start: 0.8552 (ptt180) cc_final: 0.8144 (mmm-85) outliers start: 223 outliers final: 158 residues processed: 938 average time/residue: 0.5259 time to fit residues: 860.2607 Evaluate side-chains 896 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 710 time to evaluate : 5.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 694 ASN Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 832 GLU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 906 LYS Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1212 ARG Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1319 ILE Chi-restraints excluded: chain A residue 1337 THR Chi-restraints excluded: chain A residue 1346 PHE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1358 ASP Chi-restraints excluded: chain A residue 1399 MET Chi-restraints excluded: chain A residue 1440 ILE Chi-restraints excluded: chain A residue 1449 ASN Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1650 ARG Chi-restraints excluded: chain A residue 1738 LEU Chi-restraints excluded: chain A residue 1779 LEU Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1893 ILE Chi-restraints excluded: chain A residue 1951 PHE Chi-restraints excluded: chain A residue 1995 TRP Chi-restraints excluded: chain A residue 1997 ASP Chi-restraints excluded: chain A residue 2017 THR Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 652 MET Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 658 ASP Chi-restraints excluded: chain C residue 783 ILE Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 859 GLU Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 182 GLN Chi-restraints excluded: chain H residue 193 SER Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 357 TRP Chi-restraints excluded: chain H residue 396 PHE Chi-restraints excluded: chain H residue 419 PHE Chi-restraints excluded: chain H residue 433 LEU Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 161 ASP Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 194 HIS Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 257 ILE Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 261 THR Chi-restraints excluded: chain J residue 271 GLN Chi-restraints excluded: chain J residue 280 GLN Chi-restraints excluded: chain J residue 301 MET Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain J residue 382 HIS Chi-restraints excluded: chain J residue 393 VAL Chi-restraints excluded: chain J residue 408 ASP Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 153 CYS Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain M residue 203 THR Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 67 GLN Chi-restraints excluded: chain N residue 74 CYS Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain N residue 87 ARG Chi-restraints excluded: chain N residue 118 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 288 ILE Chi-restraints excluded: chain N residue 291 ILE Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 18 ASP Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 151 MET Chi-restraints excluded: chain O residue 181 ARG Chi-restraints excluded: chain O residue 230 THR Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 37 LEU Chi-restraints excluded: chain S residue 58 LEU Chi-restraints excluded: chain S residue 107 ASP Chi-restraints excluded: chain S residue 124 ARG Chi-restraints excluded: chain S residue 128 THR Chi-restraints excluded: chain S residue 146 LEU Chi-restraints excluded: chain S residue 156 TYR Chi-restraints excluded: chain S residue 193 VAL Chi-restraints excluded: chain S residue 212 HIS Chi-restraints excluded: chain S residue 232 LEU Chi-restraints excluded: chain S residue 279 LEU Chi-restraints excluded: chain a residue 111 MET Chi-restraints excluded: chain a residue 132 HIS Chi-restraints excluded: chain a residue 146 LEU Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 177 ASN Chi-restraints excluded: chain a residue 231 THR Chi-restraints excluded: chain a residue 237 ILE Chi-restraints excluded: chain a residue 238 THR Chi-restraints excluded: chain c residue 186 ILE Chi-restraints excluded: chain c residue 216 ILE Chi-restraints excluded: chain o residue 177 LEU Chi-restraints excluded: chain o residue 281 GLU Chi-restraints excluded: chain o residue 285 LEU Chi-restraints excluded: chain o residue 331 ILE Chi-restraints excluded: chain o residue 381 SER Chi-restraints excluded: chain o residue 387 ILE Chi-restraints excluded: chain o residue 419 ASN Chi-restraints excluded: chain o residue 443 ILE Chi-restraints excluded: chain y residue 96 SER Chi-restraints excluded: chain y residue 144 GLN Chi-restraints excluded: chain y residue 161 VAL Chi-restraints excluded: chain y residue 162 ASN Chi-restraints excluded: chain y residue 200 ASN Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 15 LEU Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 81 VAL Chi-restraints excluded: chain b residue 86 ILE Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 22 GLU Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain f residue 73 ILE Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain h residue 6 PHE Chi-restraints excluded: chain h residue 16 THR Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain j residue 67 MET Chi-restraints excluded: chain j residue 96 LEU Chi-restraints excluded: chain j residue 100 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 613 optimal weight: 0.0570 chunk 646 optimal weight: 3.9990 chunk 589 optimal weight: 8.9990 chunk 628 optimal weight: 6.9990 chunk 378 optimal weight: 4.9990 chunk 273 optimal weight: 4.9990 chunk 493 optimal weight: 20.0000 chunk 192 optimal weight: 0.8980 chunk 568 optimal weight: 40.0000 chunk 594 optimal weight: 10.0000 chunk 626 optimal weight: 6.9990 overall best weight: 2.9904 ------------------------------------------------------------------------------- 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 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 300 ASN c 304 GLN ** o 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 60755 Z= 0.318 Angle : 0.692 18.143 84029 Z= 0.338 Chirality : 0.041 0.314 9967 Planarity : 0.005 0.073 9414 Dihedral : 17.914 177.130 12522 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.23 % Favored : 93.73 % Rotamer: Outliers : 4.41 % Allowed : 22.04 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.02 (0.11), residues: 6554 helix: 1.75 (0.09), residues: 3091 sheet: -1.54 (0.19), residues: 739 loop : -1.63 (0.12), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 933 HIS 0.008 0.001 HIS H 310 PHE 0.025 0.002 PHE S 287 TYR 0.031 0.002 TYR A 391 ARG 0.008 0.001 ARG N 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 703 time to evaluate : 5.044 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: A 134 MET cc_start: 0.9127 (mmm) cc_final: 0.8916 (mmm) REVERT: A 142 ILE cc_start: 0.9371 (mt) cc_final: 0.9051 (tp) REVERT: A 199 ILE cc_start: 0.9693 (tp) cc_final: 0.9294 (tt) REVERT: A 326 ASN cc_start: 0.9230 (OUTLIER) cc_final: 0.8538 (t0) REVERT: A 331 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.8678 (m-80) REVERT: A 422 LEU cc_start: 0.9533 (tp) cc_final: 0.9212 (tt) REVERT: A 493 MET cc_start: 0.8872 (mmt) cc_final: 0.8002 (mmt) REVERT: A 551 LEU cc_start: 0.9680 (mt) cc_final: 0.9432 (mp) REVERT: A 578 MET cc_start: 0.8995 (ptp) cc_final: 0.8739 (ptp) REVERT: A 588 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9071 (pp) REVERT: A 618 SER cc_start: 0.9402 (t) cc_final: 0.8835 (p) REVERT: A 629 MET cc_start: 0.8465 (tmm) cc_final: 0.8090 (tmm) REVERT: A 693 LYS cc_start: 0.8050 (mtmt) cc_final: 0.7828 (pttt) REVERT: A 750 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9049 (tt) REVERT: A 775 ARG cc_start: 0.9017 (tpp-160) cc_final: 0.8780 (mmm160) REVERT: A 832 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8765 (mp0) REVERT: A 852 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9001 (tt) REVERT: A 933 GLU cc_start: 0.9428 (mt-10) cc_final: 0.9131 (mp0) REVERT: A 935 GLU cc_start: 0.9067 (tm-30) cc_final: 0.8800 (tm-30) REVERT: A 973 GLU cc_start: 0.8753 (tp30) cc_final: 0.8379 (tp30) REVERT: A 1004 ASP cc_start: 0.9175 (m-30) cc_final: 0.8917 (m-30) REVERT: A 1085 LYS cc_start: 0.9428 (tptm) cc_final: 0.9124 (tppp) REVERT: A 1086 ASN cc_start: 0.9296 (m-40) cc_final: 0.8886 (t0) REVERT: A 1101 TYR cc_start: 0.7860 (t80) cc_final: 0.7473 (t80) REVERT: A 1288 LEU cc_start: 0.9438 (mp) cc_final: 0.9204 (mt) REVERT: A 1346 PHE cc_start: 0.9417 (OUTLIER) cc_final: 0.7677 (p90) REVERT: A 1522 ASN cc_start: 0.8886 (t0) cc_final: 0.8661 (t0) REVERT: A 1545 ASP cc_start: 0.8977 (m-30) cc_final: 0.8634 (m-30) REVERT: A 1687 HIS cc_start: 0.8902 (m-70) cc_final: 0.8522 (p-80) REVERT: A 1778 ASP cc_start: 0.9106 (t0) cc_final: 0.8859 (t0) REVERT: A 1783 MET cc_start: 0.8815 (mmm) cc_final: 0.8443 (mmm) REVERT: A 1802 MET cc_start: 0.9597 (mmm) cc_final: 0.9394 (mmp) REVERT: A 1807 LYS cc_start: 0.9213 (tptt) cc_final: 0.8660 (mmtt) REVERT: A 1817 GLU cc_start: 0.9543 (tt0) cc_final: 0.8983 (tm-30) REVERT: A 1866 PHE cc_start: 0.8988 (m-10) cc_final: 0.8737 (m-80) REVERT: A 1880 PHE cc_start: 0.7909 (t80) cc_final: 0.7469 (t80) REVERT: A 1948 MET cc_start: 0.9229 (mmm) cc_final: 0.8627 (ppp) REVERT: A 1979 MET cc_start: 0.8604 (mmt) cc_final: 0.8277 (mmp) REVERT: C 126 MET cc_start: 0.8574 (tpp) cc_final: 0.8324 (tpp) REVERT: C 150 MET cc_start: 0.9484 (mmm) cc_final: 0.9183 (mmm) REVERT: C 164 MET cc_start: 0.8812 (ptm) cc_final: 0.8226 (tmm) REVERT: C 179 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8010 (m-30) REVERT: C 222 MET cc_start: 0.9104 (mmm) cc_final: 0.8596 (mmp) REVERT: C 282 MET cc_start: 0.9435 (tpt) cc_final: 0.9058 (tpp) REVERT: C 504 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8114 (t) REVERT: C 537 CYS cc_start: 0.9116 (t) cc_final: 0.8693 (t) REVERT: C 538 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8372 (tt0) REVERT: C 545 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8918 (pp) REVERT: C 614 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8705 (tp30) REVERT: C 719 MET cc_start: 0.8743 (ppp) cc_final: 0.8478 (ppp) REVERT: C 820 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6567 (mt) REVERT: C 859 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8472 (pm20) REVERT: C 880 MET cc_start: 0.9306 (mmm) cc_final: 0.8734 (mmm) REVERT: C 931 TYR cc_start: 0.9125 (p90) cc_final: 0.8654 (p90) REVERT: C 968 MET cc_start: 0.9106 (mmm) cc_final: 0.8854 (mmm) REVERT: H 155 MET cc_start: 0.8505 (mmm) cc_final: 0.8144 (tpp) REVERT: H 158 CYS cc_start: 0.9167 (p) cc_final: 0.8833 (t) REVERT: H 161 LYS cc_start: 0.8961 (tptt) cc_final: 0.8490 (tttt) REVERT: H 167 LYS cc_start: 0.8209 (pttp) cc_final: 0.7898 (tttt) REVERT: H 195 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7846 (tm-30) REVERT: H 334 LEU cc_start: 0.9528 (mt) cc_final: 0.9311 (mt) REVERT: H 357 TRP cc_start: 0.9371 (OUTLIER) cc_final: 0.7935 (m-10) REVERT: H 386 LYS cc_start: 0.9595 (mmtp) cc_final: 0.9286 (ttmm) REVERT: J 117 LYS cc_start: 0.8888 (ttmt) cc_final: 0.8529 (tppt) REVERT: J 164 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.7981 (mtm) REVERT: J 187 ASP cc_start: 0.9206 (t0) cc_final: 0.8742 (t0) REVERT: J 253 MET cc_start: 0.8454 (mtp) cc_final: 0.7974 (mtp) REVERT: J 280 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7216 (mt0) REVERT: J 360 GLN cc_start: 0.9363 (tt0) cc_final: 0.9062 (tp40) REVERT: K 42 ASP cc_start: 0.8961 (m-30) cc_final: 0.8723 (m-30) REVERT: K 48 GLN cc_start: 0.8000 (pp30) cc_final: 0.7436 (pp30) REVERT: K 123 LEU cc_start: 0.9693 (mp) cc_final: 0.9393 (mt) REVERT: K 149 MET cc_start: 0.8770 (ttp) cc_final: 0.7910 (pmm) REVERT: L 41 LEU cc_start: 0.9160 (tp) cc_final: 0.8745 (mm) REVERT: M 57 LEU cc_start: 0.9553 (mt) cc_final: 0.9261 (tt) REVERT: M 97 GLU cc_start: 0.9138 (tt0) cc_final: 0.8705 (tm-30) REVERT: M 124 MET cc_start: 0.9247 (mmm) cc_final: 0.8868 (mmt) REVERT: M 188 TYR cc_start: 0.9477 (m-80) cc_final: 0.9163 (m-80) REVERT: M 193 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8253 (mt-10) REVERT: N 67 GLN cc_start: 0.9395 (OUTLIER) cc_final: 0.8762 (mp10) REVERT: N 88 ASP cc_start: 0.9021 (m-30) cc_final: 0.7819 (t0) REVERT: N 100 MET cc_start: 0.8233 (tpt) cc_final: 0.7529 (pmm) REVERT: O 48 SER cc_start: 0.9651 (t) cc_final: 0.9353 (p) REVERT: O 90 MET cc_start: 0.8905 (mmm) cc_final: 0.8397 (mmm) REVERT: O 154 GLU cc_start: 0.9176 (tp30) cc_final: 0.8778 (tp30) REVERT: O 173 GLU cc_start: 0.9494 (mt-10) cc_final: 0.9202 (mm-30) REVERT: P 157 ILE cc_start: 0.9094 (mt) cc_final: 0.8730 (tp) REVERT: P 160 MET cc_start: 0.9048 (mmm) cc_final: 0.8744 (tpp) REVERT: S 39 ASP cc_start: 0.7745 (m-30) cc_final: 0.7495 (t0) REVERT: S 89 GLU cc_start: 0.9311 (mm-30) cc_final: 0.8980 (mt-10) REVERT: S 122 MET cc_start: 0.8595 (mtm) cc_final: 0.8334 (mtp) REVERT: S 146 LEU cc_start: 0.9628 (OUTLIER) cc_final: 0.9318 (mt) REVERT: S 163 GLU cc_start: 0.9410 (mt-10) cc_final: 0.8876 (tm-30) REVERT: a 99 GLN cc_start: 0.9000 (mm110) cc_final: 0.8452 (tt0) REVERT: a 111 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8641 (mmm) REVERT: a 186 LEU cc_start: 0.8690 (tt) cc_final: 0.8478 (tt) REVERT: c 347 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7594 (mm-30) REVERT: o 173 LYS cc_start: 0.8187 (pttm) cc_final: 0.7268 (mmmt) REVERT: o 194 HIS cc_start: 0.8274 (m-70) cc_final: 0.7689 (p90) REVERT: o 342 LEU cc_start: 0.9092 (mt) cc_final: 0.8821 (tp) REVERT: o 385 TYR cc_start: 0.8251 (t80) cc_final: 0.7399 (t80) REVERT: o 387 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.7621 (mt) REVERT: o 431 GLN cc_start: 0.8112 (mt0) cc_final: 0.7807 (tm-30) REVERT: y 99 GLN cc_start: 0.9230 (mm110) cc_final: 0.8960 (mt0) REVERT: y 144 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8624 (mm-40) REVERT: y 162 ASN cc_start: 0.9431 (OUTLIER) cc_final: 0.9066 (m110) REVERT: y 169 GLN cc_start: 0.9489 (mt0) cc_final: 0.9243 (tp40) REVERT: y 171 GLU cc_start: 0.9330 (tp30) cc_final: 0.8996 (tp30) REVERT: y 182 GLN cc_start: 0.9184 (mt0) cc_final: 0.8720 (mt0) REVERT: y 200 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8101 (t0) REVERT: b 35 MET cc_start: 0.8367 (mmm) cc_final: 0.7793 (mmm) REVERT: b 41 MET cc_start: 0.9120 (mmm) cc_final: 0.8523 (mtp) REVERT: b 46 ASN cc_start: 0.8789 (t0) cc_final: 0.8453 (t0) REVERT: d 9 LYS cc_start: 0.8831 (mttt) cc_final: 0.8484 (mtpp) REVERT: d 22 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7496 (mm-30) REVERT: d 23 LEU cc_start: 0.8816 (tp) cc_final: 0.8280 (tp) REVERT: d 29 TYR cc_start: 0.8221 (m-80) cc_final: 0.7972 (m-80) REVERT: d 61 GLN cc_start: 0.9035 (mt0) cc_final: 0.8363 (mp10) REVERT: f 55 GLU cc_start: 0.6937 (pp20) cc_final: 0.6678 (pp20) REVERT: f 58 GLU cc_start: 0.7750 (pt0) cc_final: 0.7086 (tt0) REVERT: g 44 MET cc_start: 0.8750 (mmm) cc_final: 0.8395 (tpp) REVERT: g 56 GLN cc_start: 0.6865 (tt0) cc_final: 0.6179 (pm20) REVERT: g 69 ILE cc_start: 0.7133 (mm) cc_final: 0.6850 (mm) REVERT: g 75 ASP cc_start: 0.6899 (t0) cc_final: 0.6300 (m-30) REVERT: h 18 GLU cc_start: 0.8042 (mp0) cc_final: 0.7463 (tm-30) REVERT: j 89 ARG cc_start: 0.8575 (ptt180) cc_final: 0.8175 (mmm-85) outliers start: 226 outliers final: 178 residues processed: 867 average time/residue: 0.5255 time to fit residues: 794.9618 Evaluate side-chains 869 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 668 time to evaluate : 4.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 694 ASN Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 832 GLU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 906 LYS Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1212 ARG Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1285 VAL Chi-restraints excluded: chain A residue 1313 ASP Chi-restraints excluded: chain A residue 1319 ILE Chi-restraints excluded: chain A residue 1337 THR Chi-restraints excluded: chain A residue 1346 PHE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1440 ILE Chi-restraints excluded: chain A residue 1449 ASN Chi-restraints excluded: chain A residue 1553 ILE Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1621 VAL Chi-restraints excluded: chain A residue 1650 ARG Chi-restraints excluded: chain A residue 1738 LEU Chi-restraints excluded: chain A residue 1779 LEU Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1893 ILE Chi-restraints excluded: chain A residue 1951 PHE Chi-restraints excluded: chain A residue 1995 TRP Chi-restraints excluded: chain A residue 1997 ASP Chi-restraints excluded: chain A residue 2017 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 658 ASP Chi-restraints excluded: chain C residue 783 ILE Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 859 GLU Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 182 GLN Chi-restraints excluded: chain H residue 193 SER Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 357 TRP Chi-restraints excluded: chain H residue 383 ILE Chi-restraints excluded: chain H residue 396 PHE Chi-restraints excluded: chain H residue 419 PHE Chi-restraints excluded: chain H residue 433 LEU Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 161 ASP Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 194 HIS Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 257 ILE Chi-restraints excluded: chain J residue 261 THR Chi-restraints excluded: chain J residue 271 GLN Chi-restraints excluded: chain J residue 280 GLN Chi-restraints excluded: chain J residue 301 MET Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain J residue 382 HIS Chi-restraints excluded: chain J residue 393 VAL Chi-restraints excluded: chain J residue 408 ASP Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 142 PHE Chi-restraints excluded: chain L residue 153 CYS Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain M residue 203 THR Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 67 GLN Chi-restraints excluded: chain N residue 74 CYS Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain N residue 95 ASN Chi-restraints excluded: chain N residue 118 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 288 ILE Chi-restraints excluded: chain N residue 291 ILE Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 18 ASP Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 230 THR Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 37 LEU Chi-restraints excluded: chain R residue 4 ASN Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain S residue 58 LEU Chi-restraints excluded: chain S residue 107 ASP Chi-restraints excluded: chain S residue 124 ARG Chi-restraints excluded: chain S residue 128 THR Chi-restraints excluded: chain S residue 146 LEU Chi-restraints excluded: chain S residue 156 TYR Chi-restraints excluded: chain S residue 157 THR Chi-restraints excluded: chain S residue 212 HIS Chi-restraints excluded: chain S residue 232 LEU Chi-restraints excluded: chain S residue 246 LEU Chi-restraints excluded: chain S residue 279 LEU Chi-restraints excluded: chain a residue 111 MET Chi-restraints excluded: chain a residue 132 HIS Chi-restraints excluded: chain a residue 146 LEU Chi-restraints excluded: chain a residue 177 ASN Chi-restraints excluded: chain a residue 231 THR Chi-restraints excluded: chain a residue 237 ILE Chi-restraints excluded: chain a residue 238 THR Chi-restraints excluded: chain c residue 216 ILE Chi-restraints excluded: chain o residue 177 LEU Chi-restraints excluded: chain o residue 281 GLU Chi-restraints excluded: chain o residue 285 LEU Chi-restraints excluded: chain o residue 331 ILE Chi-restraints excluded: chain o residue 381 SER Chi-restraints excluded: chain o residue 387 ILE Chi-restraints excluded: chain o residue 419 ASN Chi-restraints excluded: chain o residue 443 ILE Chi-restraints excluded: chain y residue 96 SER Chi-restraints excluded: chain y residue 144 GLN Chi-restraints excluded: chain y residue 161 VAL Chi-restraints excluded: chain y residue 162 ASN Chi-restraints excluded: chain y residue 200 ASN Chi-restraints excluded: chain b residue 15 LEU Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 86 ILE Chi-restraints excluded: chain b residue 97 VAL Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain d residue 22 GLU Chi-restraints excluded: chain d residue 83 LEU Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 19 ASN Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain h residue 6 PHE Chi-restraints excluded: chain h residue 16 THR Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain j residue 67 MET Chi-restraints excluded: chain j residue 96 LEU Chi-restraints excluded: chain j residue 100 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 412 optimal weight: 10.0000 chunk 664 optimal weight: 5.9990 chunk 405 optimal weight: 0.7980 chunk 315 optimal weight: 2.9990 chunk 462 optimal weight: 4.9990 chunk 697 optimal weight: 5.9990 chunk 641 optimal weight: 9.9990 chunk 555 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 428 optimal weight: 0.9980 chunk 340 optimal weight: 5.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 82 GLN ** a 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 60755 Z= 0.259 Angle : 0.675 17.721 84029 Z= 0.329 Chirality : 0.041 0.362 9967 Planarity : 0.004 0.070 9414 Dihedral : 17.921 177.197 12522 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.71 % Favored : 94.25 % Rotamer: Outliers : 4.17 % Allowed : 22.37 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.02 (0.11), residues: 6554 helix: 1.75 (0.09), residues: 3082 sheet: -1.56 (0.18), residues: 748 loop : -1.61 (0.12), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP o 320 HIS 0.006 0.001 HIS A 138 PHE 0.026 0.002 PHE S 287 TYR 0.032 0.002 TYR A 391 ARG 0.013 0.000 ARG A2013 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 710 time to evaluate : 5.017 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: A 142 ILE cc_start: 0.9340 (mt) cc_final: 0.9029 (tp) REVERT: A 179 MET cc_start: 0.9034 (ttp) cc_final: 0.8814 (tmm) REVERT: A 199 ILE cc_start: 0.9692 (tp) cc_final: 0.9286 (tt) REVERT: A 326 ASN cc_start: 0.9206 (OUTLIER) cc_final: 0.8513 (t0) REVERT: A 331 PHE cc_start: 0.9215 (OUTLIER) cc_final: 0.8629 (m-80) REVERT: A 422 LEU cc_start: 0.9517 (tp) cc_final: 0.9189 (tt) REVERT: A 493 MET cc_start: 0.8831 (mmt) cc_final: 0.7949 (mmt) REVERT: A 551 LEU cc_start: 0.9668 (mt) cc_final: 0.9406 (mp) REVERT: A 578 MET cc_start: 0.8955 (ptp) cc_final: 0.8656 (ptp) REVERT: A 588 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9093 (pp) REVERT: A 618 SER cc_start: 0.9391 (t) cc_final: 0.8927 (p) REVERT: A 626 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8942 (tp) REVERT: A 629 MET cc_start: 0.8477 (tmm) cc_final: 0.8079 (tmm) REVERT: A 693 LYS cc_start: 0.8041 (mtmt) cc_final: 0.7820 (pttt) REVERT: A 712 LEU cc_start: 0.9483 (mt) cc_final: 0.9230 (mm) REVERT: A 750 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9055 (tt) REVERT: A 775 ARG cc_start: 0.9083 (tpp-160) cc_final: 0.8797 (mmm160) REVERT: A 832 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8636 (mp0) REVERT: A 933 GLU cc_start: 0.9417 (mt-10) cc_final: 0.9120 (mp0) REVERT: A 935 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8746 (tm-30) REVERT: A 973 GLU cc_start: 0.8735 (tp30) cc_final: 0.8371 (tp30) REVERT: A 1004 ASP cc_start: 0.9157 (m-30) cc_final: 0.8893 (m-30) REVERT: A 1085 LYS cc_start: 0.9425 (tptm) cc_final: 0.9132 (tppp) REVERT: A 1086 ASN cc_start: 0.9206 (m-40) cc_final: 0.8809 (t0) REVERT: A 1101 TYR cc_start: 0.7830 (t80) cc_final: 0.7287 (t80) REVERT: A 1288 LEU cc_start: 0.9431 (mp) cc_final: 0.9199 (mt) REVERT: A 1346 PHE cc_start: 0.9382 (OUTLIER) cc_final: 0.7596 (p90) REVERT: A 1379 MET cc_start: 0.8847 (tpp) cc_final: 0.8381 (tpp) REVERT: A 1522 ASN cc_start: 0.8836 (t0) cc_final: 0.8628 (t0) REVERT: A 1545 ASP cc_start: 0.8867 (m-30) cc_final: 0.8510 (m-30) REVERT: A 1632 ILE cc_start: 0.9408 (mm) cc_final: 0.9178 (pt) REVERT: A 1687 HIS cc_start: 0.8922 (m-70) cc_final: 0.8539 (p-80) REVERT: A 1778 ASP cc_start: 0.9142 (t0) cc_final: 0.8852 (t0) REVERT: A 1783 MET cc_start: 0.8825 (mmm) cc_final: 0.8516 (mmm) REVERT: A 1807 LYS cc_start: 0.9211 (tptt) cc_final: 0.8662 (mmtt) REVERT: A 1866 PHE cc_start: 0.8988 (m-10) cc_final: 0.8743 (m-80) REVERT: A 1880 PHE cc_start: 0.7887 (t80) cc_final: 0.7456 (t80) REVERT: A 1948 MET cc_start: 0.9228 (mmm) cc_final: 0.8654 (ppp) REVERT: A 1979 MET cc_start: 0.8555 (mmt) cc_final: 0.8173 (mmp) REVERT: A 1986 MET cc_start: 0.9021 (tpp) cc_final: 0.8600 (tpp) REVERT: C 78 MET cc_start: 0.5355 (ptt) cc_final: 0.4460 (ptt) REVERT: C 126 MET cc_start: 0.8603 (tpp) cc_final: 0.8378 (tpp) REVERT: C 150 MET cc_start: 0.9466 (mmm) cc_final: 0.9165 (mmm) REVERT: C 164 MET cc_start: 0.8789 (ptm) cc_final: 0.8222 (tmm) REVERT: C 179 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8005 (m-30) REVERT: C 222 MET cc_start: 0.9071 (mmm) cc_final: 0.8521 (mmp) REVERT: C 282 MET cc_start: 0.9439 (tpt) cc_final: 0.9057 (tpp) REVERT: C 504 THR cc_start: 0.8663 (OUTLIER) cc_final: 0.8134 (t) REVERT: C 537 CYS cc_start: 0.9105 (t) cc_final: 0.8683 (t) REVERT: C 538 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8466 (tt0) REVERT: C 540 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8485 (mm-30) REVERT: C 545 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.8970 (pp) REVERT: C 614 GLU cc_start: 0.9143 (mm-30) cc_final: 0.8710 (tp30) REVERT: C 652 MET cc_start: 0.8741 (tpp) cc_final: 0.8023 (tpp) REVERT: C 719 MET cc_start: 0.8746 (ppp) cc_final: 0.8473 (ppp) REVERT: C 820 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6538 (mt) REVERT: C 859 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8465 (pm20) REVERT: C 880 MET cc_start: 0.9285 (mmm) cc_final: 0.8722 (mmm) REVERT: C 931 TYR cc_start: 0.9092 (p90) cc_final: 0.8501 (p90) REVERT: C 968 MET cc_start: 0.9105 (mmm) cc_final: 0.8848 (mmm) REVERT: H 155 MET cc_start: 0.8520 (mmm) cc_final: 0.8117 (tpp) REVERT: H 158 CYS cc_start: 0.9189 (p) cc_final: 0.8832 (t) REVERT: H 161 LYS cc_start: 0.8892 (tptt) cc_final: 0.8480 (tttt) REVERT: H 167 LYS cc_start: 0.8194 (pttp) cc_final: 0.7870 (tttt) REVERT: H 195 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7773 (tm-30) REVERT: H 334 LEU cc_start: 0.9496 (mt) cc_final: 0.9251 (mt) REVERT: H 357 TRP cc_start: 0.9348 (OUTLIER) cc_final: 0.8402 (m-10) REVERT: H 386 LYS cc_start: 0.9595 (mmtp) cc_final: 0.9272 (ttmm) REVERT: J 117 LYS cc_start: 0.8881 (ttmt) cc_final: 0.8521 (tppt) REVERT: J 164 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7936 (mtm) REVERT: J 187 ASP cc_start: 0.9122 (t0) cc_final: 0.8576 (t0) REVERT: J 253 MET cc_start: 0.8396 (mtp) cc_final: 0.7932 (mtp) REVERT: J 280 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7174 (mt0) REVERT: K 42 ASP cc_start: 0.8962 (m-30) cc_final: 0.8725 (m-30) REVERT: K 48 GLN cc_start: 0.8066 (pp30) cc_final: 0.7478 (pp30) REVERT: K 123 LEU cc_start: 0.9690 (mp) cc_final: 0.9371 (mt) REVERT: K 149 MET cc_start: 0.8834 (ttp) cc_final: 0.8227 (pmm) REVERT: K 199 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8496 (p0) REVERT: L 41 LEU cc_start: 0.9107 (tp) cc_final: 0.8724 (mm) REVERT: L 50 TRP cc_start: 0.8778 (m-10) cc_final: 0.8055 (m-90) REVERT: M 97 GLU cc_start: 0.9135 (tt0) cc_final: 0.8695 (tm-30) REVERT: M 124 MET cc_start: 0.9189 (mmm) cc_final: 0.8837 (mmt) REVERT: M 188 TYR cc_start: 0.9445 (m-80) cc_final: 0.9173 (m-80) REVERT: M 193 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8100 (mt-10) REVERT: N 33 GLU cc_start: 0.8687 (pt0) cc_final: 0.8205 (tt0) REVERT: N 67 GLN cc_start: 0.9390 (OUTLIER) cc_final: 0.8744 (mp10) REVERT: N 88 ASP cc_start: 0.9008 (m-30) cc_final: 0.7763 (t0) REVERT: N 100 MET cc_start: 0.8238 (tpt) cc_final: 0.7537 (pmm) REVERT: O 48 SER cc_start: 0.9649 (t) cc_final: 0.9351 (p) REVERT: O 154 GLU cc_start: 0.9190 (tp30) cc_final: 0.8799 (tp30) REVERT: O 162 THR cc_start: 0.9127 (p) cc_final: 0.8713 (t) REVERT: O 173 GLU cc_start: 0.9489 (mt-10) cc_final: 0.9190 (mm-30) REVERT: O 213 TYR cc_start: 0.8921 (m-80) cc_final: 0.8106 (m-10) REVERT: P 157 ILE cc_start: 0.9095 (mt) cc_final: 0.8755 (tp) REVERT: P 160 MET cc_start: 0.9042 (mmm) cc_final: 0.8741 (tpp) REVERT: S 39 ASP cc_start: 0.7713 (m-30) cc_final: 0.7465 (t0) REVERT: S 89 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8886 (mt-10) REVERT: S 122 MET cc_start: 0.8526 (mtm) cc_final: 0.8260 (mtp) REVERT: S 146 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9371 (mt) REVERT: S 163 GLU cc_start: 0.9381 (mt-10) cc_final: 0.9041 (tm-30) REVERT: S 291 PHE cc_start: 0.7369 (OUTLIER) cc_final: 0.6848 (m-80) REVERT: a 99 GLN cc_start: 0.8998 (mm110) cc_final: 0.8452 (tt0) REVERT: a 111 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8700 (mmm) REVERT: a 186 LEU cc_start: 0.8746 (tt) cc_final: 0.8542 (tt) REVERT: o 173 LYS cc_start: 0.8234 (pttm) cc_final: 0.7365 (mmmt) REVERT: o 194 HIS cc_start: 0.8261 (m-70) cc_final: 0.7678 (p90) REVERT: o 342 LEU cc_start: 0.9119 (mt) cc_final: 0.8839 (tp) REVERT: o 385 TYR cc_start: 0.8239 (t80) cc_final: 0.7380 (t80) REVERT: o 387 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.7567 (mt) REVERT: o 431 GLN cc_start: 0.8133 (mt0) cc_final: 0.7853 (tm-30) REVERT: y 99 GLN cc_start: 0.9416 (mm110) cc_final: 0.9182 (mt0) REVERT: y 106 GLU cc_start: 0.9377 (mt-10) cc_final: 0.8933 (pt0) REVERT: y 144 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8676 (mm-40) REVERT: y 162 ASN cc_start: 0.9399 (OUTLIER) cc_final: 0.9056 (m110) REVERT: y 169 GLN cc_start: 0.9499 (mt0) cc_final: 0.9270 (tp40) REVERT: y 171 GLU cc_start: 0.9302 (tp30) cc_final: 0.8981 (tp30) REVERT: y 182 GLN cc_start: 0.9151 (mt0) cc_final: 0.8681 (mt0) REVERT: y 200 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.7973 (t0) REVERT: b 35 MET cc_start: 0.8352 (mmm) cc_final: 0.7752 (mmm) REVERT: b 41 MET cc_start: 0.9117 (mmm) cc_final: 0.8602 (mtp) REVERT: b 46 ASN cc_start: 0.8724 (t0) cc_final: 0.8516 (t0) REVERT: d 9 LYS cc_start: 0.8832 (mttt) cc_final: 0.8480 (mtpp) REVERT: d 22 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7707 (mm-30) REVERT: d 23 LEU cc_start: 0.8798 (tp) cc_final: 0.8273 (tp) REVERT: d 29 TYR cc_start: 0.8280 (m-80) cc_final: 0.7771 (m-80) REVERT: d 61 GLN cc_start: 0.9006 (mt0) cc_final: 0.8345 (mp10) REVERT: f 55 GLU cc_start: 0.7093 (pp20) cc_final: 0.6840 (pp20) REVERT: f 58 GLU cc_start: 0.7756 (pt0) cc_final: 0.7091 (tt0) REVERT: g 44 MET cc_start: 0.8826 (mmm) cc_final: 0.8499 (tpp) REVERT: g 56 GLN cc_start: 0.6857 (tt0) cc_final: 0.6160 (pm20) REVERT: g 69 ILE cc_start: 0.7126 (mm) cc_final: 0.6862 (mm) REVERT: g 75 ASP cc_start: 0.6889 (t0) cc_final: 0.6288 (m-30) REVERT: h 18 GLU cc_start: 0.8191 (mp0) cc_final: 0.7472 (tm-30) REVERT: j 42 THR cc_start: 0.8268 (p) cc_final: 0.8030 (p) REVERT: j 89 ARG cc_start: 0.8587 (ptt180) cc_final: 0.8209 (mmm-85) outliers start: 214 outliers final: 172 residues processed: 866 average time/residue: 0.5387 time to fit residues: 818.0026 Evaluate side-chains 877 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 680 time to evaluate : 5.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 694 ASN Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 832 GLU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 906 LYS Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1212 ARG Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1321 MET Chi-restraints excluded: chain A residue 1337 THR Chi-restraints excluded: chain A residue 1346 PHE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1358 ASP Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain A residue 1440 ILE Chi-restraints excluded: chain A residue 1449 ASN Chi-restraints excluded: chain A residue 1553 ILE Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1650 ARG Chi-restraints excluded: chain A residue 1738 LEU Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1779 LEU Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1893 ILE Chi-restraints excluded: chain A residue 1951 PHE Chi-restraints excluded: chain A residue 1995 TRP Chi-restraints excluded: chain A residue 1997 ASP Chi-restraints excluded: chain A residue 2017 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 658 ASP Chi-restraints excluded: chain C residue 783 ILE Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 859 GLU Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 182 GLN Chi-restraints excluded: chain H residue 193 SER Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 357 TRP Chi-restraints excluded: chain H residue 396 PHE Chi-restraints excluded: chain H residue 419 PHE Chi-restraints excluded: chain H residue 433 LEU Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 161 ASP Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 194 HIS Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 257 ILE Chi-restraints excluded: chain J residue 261 THR Chi-restraints excluded: chain J residue 271 GLN Chi-restraints excluded: chain J residue 280 GLN Chi-restraints excluded: chain J residue 301 MET Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain J residue 382 HIS Chi-restraints excluded: chain J residue 393 VAL Chi-restraints excluded: chain J residue 408 ASP Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 142 PHE Chi-restraints excluded: chain L residue 153 CYS Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 203 THR Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 67 GLN Chi-restraints excluded: chain N residue 74 CYS Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain N residue 95 ASN Chi-restraints excluded: chain N residue 118 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 288 ILE Chi-restraints excluded: chain N residue 291 ILE Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 18 ASP Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 230 THR Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 37 LEU Chi-restraints excluded: chain R residue 4 ASN Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain S residue 58 LEU Chi-restraints excluded: chain S residue 81 MET Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 107 ASP Chi-restraints excluded: chain S residue 124 ARG Chi-restraints excluded: chain S residue 128 THR Chi-restraints excluded: chain S residue 146 LEU Chi-restraints excluded: chain S residue 156 TYR Chi-restraints excluded: chain S residue 157 THR Chi-restraints excluded: chain S residue 212 HIS Chi-restraints excluded: chain S residue 232 LEU Chi-restraints excluded: chain S residue 246 LEU Chi-restraints excluded: chain S residue 279 LEU Chi-restraints excluded: chain S residue 291 PHE Chi-restraints excluded: chain a residue 111 MET Chi-restraints excluded: chain a residue 132 HIS Chi-restraints excluded: chain a residue 146 LEU Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 177 ASN Chi-restraints excluded: chain a residue 231 THR Chi-restraints excluded: chain a residue 237 ILE Chi-restraints excluded: chain a residue 238 THR Chi-restraints excluded: chain c residue 216 ILE Chi-restraints excluded: chain o residue 177 LEU Chi-restraints excluded: chain o residue 281 GLU Chi-restraints excluded: chain o residue 285 LEU Chi-restraints excluded: chain o residue 331 ILE Chi-restraints excluded: chain o residue 381 SER Chi-restraints excluded: chain o residue 387 ILE Chi-restraints excluded: chain o residue 419 ASN Chi-restraints excluded: chain o residue 443 ILE Chi-restraints excluded: chain y residue 96 SER Chi-restraints excluded: chain y residue 144 GLN Chi-restraints excluded: chain y residue 161 VAL Chi-restraints excluded: chain y residue 162 ASN Chi-restraints excluded: chain y residue 183 MET Chi-restraints excluded: chain y residue 200 ASN Chi-restraints excluded: chain b residue 15 LEU Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 86 ILE Chi-restraints excluded: chain b residue 97 VAL Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 22 GLU Chi-restraints excluded: chain d residue 83 LEU Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain f residue 73 ILE Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain h residue 6 PHE Chi-restraints excluded: chain h residue 16 THR Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain j residue 96 LEU Chi-restraints excluded: chain j residue 100 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 441 optimal weight: 5.9990 chunk 591 optimal weight: 5.9990 chunk 170 optimal weight: 0.7980 chunk 512 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 556 optimal weight: 0.0770 chunk 232 optimal weight: 2.9990 chunk 571 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 ASN ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 GLN H 105 GLN H 362 ASN ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN L 112 ASN ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.087795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.067160 restraints weight = 236562.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.068960 restraints weight = 121617.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.069135 restraints weight = 74321.821| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 60755 Z= 0.192 Angle : 0.656 18.515 84029 Z= 0.316 Chirality : 0.040 0.263 9967 Planarity : 0.004 0.072 9414 Dihedral : 17.818 175.946 12522 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.46 % Favored : 94.49 % Rotamer: Outliers : 3.98 % Allowed : 22.63 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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 (0.11), residues: 6554 helix: 1.81 (0.09), residues: 3084 sheet: -1.48 (0.18), residues: 752 loop : -1.57 (0.12), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP o 320 HIS 0.007 0.001 HIS H 170 PHE 0.026 0.001 PHE A1388 TYR 0.031 0.001 TYR A 391 ARG 0.012 0.000 ARG A2013 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14276.53 seconds wall clock time: 251 minutes 58.85 seconds (15118.85 seconds total)