Starting phenix.real_space_refine on Sat Dec 9 22:01:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g90_4364/12_2023/6g90_4364_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g90_4364/12_2023/6g90_4364.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g90_4364/12_2023/6g90_4364_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g90_4364/12_2023/6g90_4364_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g90_4364/12_2023/6g90_4364_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g90_4364/12_2023/6g90_4364.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g90_4364/12_2023/6g90_4364.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g90_4364/12_2023/6g90_4364_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g90_4364/12_2023/6g90_4364_neut_updated.pdb" } resolution = 4.0 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 288 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 9 6.06 5 P 508 5.49 5 S 255 5.16 5 C 39535 2.51 5 N 11135 2.21 5 O 13608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 35": "NH1" <-> "NH2" Residue "B TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 84": "NH1" <-> "NH2" Residue "D ARG 341": "NH1" <-> "NH2" Residue "D ARG 378": "NH1" <-> "NH2" Residue "D ARG 492": "NH1" <-> "NH2" Residue "E ARG 427": "NH1" <-> "NH2" Residue "E ARG 492": "NH1" <-> "NH2" Residue "F ARG 330": "NH1" <-> "NH2" Residue "F ARG 377": "NH1" <-> "NH2" Residue "G ARG 138": "NH1" <-> "NH2" Residue "G PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 12": "NH1" <-> "NH2" Residue "H ARG 215": "NH1" <-> "NH2" Residue "H ARG 216": "NH1" <-> "NH2" Residue "J ARG 2": "NH1" <-> "NH2" Residue "J ARG 38": "NH1" <-> "NH2" Residue "O ARG 186": "NH1" <-> "NH2" Residue "O ARG 476": "NH1" <-> "NH2" Residue "O ARG 496": "NH1" <-> "NH2" Residue "O ARG 556": "NH1" <-> "NH2" Residue "O ARG 593": "NH1" <-> "NH2" Residue "O ARG 849": "NH1" <-> "NH2" Residue "O ARG 898": "NH1" <-> "NH2" Residue "O ARG 931": "NH1" <-> "NH2" Residue "O ARG 936": "NH1" <-> "NH2" Residue "P ARG 170": "NH1" <-> "NH2" Residue "P ARG 181": "NH1" <-> "NH2" Residue "P ARG 185": "NH1" <-> "NH2" Residue "P ARG 186": "NH1" <-> "NH2" Residue "P ARG 200": "NH1" <-> "NH2" Residue "P ARG 223": "NH1" <-> "NH2" Residue "P ARG 232": "NH1" <-> "NH2" Residue "P ARG 400": "NH1" <-> "NH2" Residue "P ARG 608": "NH1" <-> "NH2" Residue "P ARG 617": "NH1" <-> "NH2" Residue "P ARG 631": "NH1" <-> "NH2" Residue "P ARG 732": "NH1" <-> "NH2" Residue "P ARG 767": "NH1" <-> "NH2" Residue "P ARG 768": "NH1" <-> "NH2" Residue "P ARG 781": "NH1" <-> "NH2" Residue "P ARG 839": "NH1" <-> "NH2" Residue "P ARG 870": "NH1" <-> "NH2" Residue "P ARG 875": "NH1" <-> "NH2" Residue "P ARG 952": "NH1" <-> "NH2" Residue "P ARG 989": "NH1" <-> "NH2" Residue "P ARG 1002": "NH1" <-> "NH2" Residue "P ARG 1061": "NH1" <-> "NH2" Residue "P ARG 1084": "NH1" <-> "NH2" Residue "P ARG 1116": "NH1" <-> "NH2" Residue "P ARG 1134": "NH1" <-> "NH2" Residue "P ARG 1308": "NH1" <-> "NH2" Residue "P ARG 1315": "NH1" <-> "NH2" Residue "P ARG 1328": "NH1" <-> "NH2" Residue "P ARG 1357": "NH1" <-> "NH2" Residue "Q ARG 155": "NH1" <-> "NH2" Residue "R TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 183": "OE1" <-> "OE2" Residue "T ARG 228": "NH1" <-> "NH2" Residue "T GLU 318": "OE1" <-> "OE2" Residue "T ARG 341": "NH1" <-> "NH2" Residue "T ARG 445": "NH1" <-> "NH2" Residue "U GLU 222": "OE1" <-> "OE2" Residue "V GLU 172": "OE1" <-> "OE2" Residue "V GLU 180": "OE1" <-> "OE2" Residue "Z ARG 6": "NH1" <-> "NH2" Residue "Z ARG 36": "NH1" <-> "NH2" Residue "b ARG 62": "NH1" <-> "NH2" Residue "b ARG 80": "NH1" <-> "NH2" Residue "d ARG 30": "NH1" <-> "NH2" Residue "d ARG 90": "NH1" <-> "NH2" Residue "g ARG 23": "NH1" <-> "NH2" Residue "i ARG 15": "NH1" <-> "NH2" Residue "i ARG 41": "NH1" <-> "NH2" Residue "i ARG 89": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 65050 Number of models: 1 Model: "" Number of chains: 43 Chain: "1" Number of atoms: 6625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 6625 Classifications: {'RNA': 327} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 21, 'rna3p': 36, 'rna3p_pur': 133, 'rna3p_pyr': 126} Link IDs: {'rna2p': 31, 'rna3p': 295} Chain breaks: 14 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 34 Chain: "2" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 3025 Classifications: {'RNA': 143} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 7, 'rna3p': 3, 'rna3p_pur': 60, 'rna3p_pyr': 68} Link IDs: {'rna2p': 12, 'rna3p': 130} Chain breaks: 7 Chain: "A" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 492 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 296 Unresolved non-hydrogen angles: 382 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'UNK:plan-1': 20, 'ASP:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 7, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 150 Chain: "B" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1450 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 13, 'TRANS': 179} Chain breaks: 2 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'UNK:plan-1': 31, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "C" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1323 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 8, 'TRANS': 168} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "D" Number of atoms: 3462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3462 Classifications: {'peptide': 509} Incomplete info: {'truncation_to_alanine': 228} Link IDs: {'PTRANS': 16, 'TRANS': 492} Chain breaks: 16 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 938 Unresolved non-hydrogen angles: 1218 Unresolved non-hydrogen dihedrals: 819 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 4, 'TYR:plan': 12, 'ASN:plan1': 13, 'TRP:plan': 10, 'ASP:plan': 15, 'PHE:plan': 21, 'GLU:plan': 16, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 559 Chain: "E" Number of atoms: 4574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4574 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 529} 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: "F" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1337 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain breaks: 4 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: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1684 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain breaks: 5 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "H" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1083 Classifications: {'peptide': 158} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 64} Link IDs: {'PTRANS': 4, 'TRANS': 153} Chain breaks: 6 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 213 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'UNK:plan-1': 56, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 77 Chain: "I" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 789 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 15, 'rna3p_pyr': 18} Link IDs: {'rna2p': 4, 'rna3p': 33} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' A%rna3p_pur:plan2': 1, ' A%rna3p_pur:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "J" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 324 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 39} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "O" Number of atoms: 6612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 6612 Classifications: {'peptide': 833} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 789} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "P" Number of atoms: 9437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1186, 9437 Classifications: {'peptide': 1186} Link IDs: {'PTRANS': 45, 'TRANS': 1140} Chain breaks: 7 Chain: "Q" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1786 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 201} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "R" Number of atoms: 1429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1429 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 5, 'TRANS': 167} Chain breaks: 3 Chain: "S" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 814 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "T" Number of atoms: 3915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3915 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 451} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "U" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1489 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain breaks: 3 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 22} Unresolved non-hydrogen planarities: 22 Chain: "V" Number of atoms: 1084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1084 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 2, 'TRANS': 124} Chain breaks: 1 Chain: "W" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1383 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "X" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 255 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'TRANS': 50} Chain breaks: 1 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'UNK:plan-1': 51} Unresolved non-hydrogen planarities: 51 Chain: "Y" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 683 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "Z" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 685 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "b" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 972 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "d" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 714 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 85} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "e" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 600 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 5, 'TRANS': 71} Chain breaks: 1 Chain: "f" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 585 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "g" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 556 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain breaks: 1 Chain: "h" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 834 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "i" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 805 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "s" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 518 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "t" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 569 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain breaks: 1 Chain: "u" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 752 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 88} 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: "v" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 632 Classifications: {'peptide': 82} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 77} Chain: "w" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 602 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 5, 'TRANS': 71} Chain breaks: 1 Chain: "x" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 585 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "y" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 577 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" 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} Chain: "S" 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: "T" 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} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11640 SG CYS C 6 141.824 70.087 96.020 1.00 63.83 S ATOM 11667 SG CYS C 9 140.224 72.187 98.237 1.00 62.91 S ATOM 24149 SG CYS H 45 137.739 36.490 117.092 1.00107.66 S ATOM 24206 SG CYS H 53 137.114 39.281 114.523 1.00120.50 S ATOM 24734 SG CYS H 201 125.170 57.088 119.902 1.00115.67 S ATOM 24756 SG CYS H 204 128.684 56.423 120.366 1.00111.70 S ATOM 45517 SG CYS S 11 175.370 212.802 89.781 1.00 22.96 S ATOM 45786 SG CYS S 46 178.826 213.872 89.041 1.00128.12 S ATOM 45809 SG CYS S 49 177.086 215.062 91.955 1.00 77.51 S ATOM 46092 SG CYS S 86 178.182 211.586 91.943 1.00 50.49 S ATOM 45603 SG CYS S 23 177.488 213.749 108.366 1.00131.11 S ATOM 45627 SG CYS S 26 175.057 211.083 107.439 1.00215.57 S ATOM 45876 SG CYS S 58 177.265 212.560 104.879 1.00219.50 S ATOM 45898 SG CYS S 61 174.580 214.525 106.288 1.00349.17 S ATOM 45654 SG CYS S 30 177.670 200.544 100.378 1.00193.00 S ATOM 45675 SG CYS S 33 174.878 198.671 101.741 1.00 59.79 S ATOM 45990 SG CYS S 73 177.819 196.956 100.912 1.00214.84 S ATOM 46019 SG CYS S 76 175.734 198.202 98.332 1.00 95.38 S ATOM 48518 SG CYS T 282 37.625 225.242 93.443 1.00 0.00 S ATOM 48542 SG CYS T 285 34.319 225.541 90.477 1.00 0.00 S ATOM 49480 SG CYS T 423 133.221 171.724 74.426 1.00201.73 S ATOM 49503 SG CYS T 426 132.020 168.057 75.147 1.00192.30 S ATOM 50422 SG CYS U 68 136.201 182.317 111.848 1.00 94.55 S ATOM 50445 SG CYS U 71 134.402 183.675 109.396 1.00108.64 S Time building chain proxies: 27.57, per 1000 atoms: 0.42 Number of scatterers: 65050 At special positions: 0 Unit cell: (263.29, 264.42, 169.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 9 29.99 S 255 16.00 P 508 15.00 O 13608 8.00 N 11135 7.00 C 39535 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS O 321 " - pdb=" SG CYS O 358 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 23.60 Conformation dependent library (CDL) restraints added in 8.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C1000 " pdb="ZN ZN C1000 " - pdb=" ND1 HIS C 30 " pdb="ZN ZN C1000 " - pdb=" NE2 HIS C 24 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 6 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 9 " pdb=" ZN H1000 " pdb="ZN ZN H1000 " - pdb=" NE2 HIS H 72 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 53 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 45 " pdb=" ZN H1001 " pdb="ZN ZN H1001 " - pdb=" ND1 HIS H 226 " pdb="ZN ZN H1001 " - pdb=" NE2 HIS H 220 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 201 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 204 " pdb=" ZN S1000 " pdb="ZN ZN S1000 " - pdb=" SG CYS S 49 " pdb="ZN ZN S1000 " - pdb=" SG CYS S 46 " pdb="ZN ZN S1000 " - pdb=" SG CYS S 11 " pdb="ZN ZN S1000 " - pdb=" SG CYS S 86 " pdb=" ZN S1001 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 61 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 58 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 23 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 26 " pdb=" ZN S1002 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 73 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 33 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 76 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 30 " pdb=" ZN T1000 " pdb="ZN ZN T1000 " - pdb=" NE2 HIS T 298 " pdb="ZN ZN T1000 " - pdb=" ND1 HIS T 304 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 282 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 285 " pdb=" ZN T1001 " pdb="ZN ZN T1001 " - pdb=" NE2 HIS T 446 " pdb="ZN ZN T1001 " - pdb=" ND1 HIS T 440 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 423 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 426 " pdb=" ZN U1000 " pdb="ZN ZN U1000 " - pdb=" SG CYS U 71 " pdb="ZN ZN U1000 " - pdb=" NE2 HIS U 84 " pdb="ZN ZN U1000 " - pdb=" ND1 HIS U 90 " pdb="ZN ZN U1000 " - pdb=" SG CYS U 68 " Number of angles added : 25 13208 Ramachandran restraints generated. 6604 Oldfield, 0 Emsley, 6604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13376 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 253 helices and 70 sheets defined 41.6% alpha, 13.9% beta 137 base pairs and 266 stacking pairs defined. Time for finding SS restraints: 23.39 Creating SS restraints... Processing helix chain 'A' and resid 31 through 40 Proline residue: A 37 - end of helix Proline residue: A 40 - end of helix Processing helix chain 'A' and resid 85 through 93 Processing helix chain 'A' and resid 116 through 122 Processing helix chain 'A' and resid 135 through 147 Processing helix chain 'B' and resid 10 through 13 No H-bonds generated for 'chain 'B' and resid 10 through 13' Processing helix chain 'B' and resid 44 through 54 removed outlier: 3.644A pdb=" N LEU B 48 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER B 51 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 87 removed outlier: 3.921A pdb=" N UNK B 71 " --> pdb=" O UNK B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 107 No H-bonds generated for 'chain 'B' and resid 105 through 107' Processing helix chain 'B' and resid 120 through 127 Processing helix chain 'B' and resid 159 through 165 Processing helix chain 'C' and resid 18 through 25 Processing helix chain 'C' and resid 28 through 47 Processing helix chain 'C' and resid 80 through 99 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 115 through 118 No H-bonds generated for 'chain 'C' and resid 115 through 118' Processing helix chain 'C' and resid 128 through 133 removed outlier: 4.073A pdb=" N LYS C 132 " --> pdb=" O GLY C 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 62 Processing helix chain 'D' and resid 68 through 84 Processing helix chain 'D' and resid 89 through 101 Processing helix chain 'D' and resid 109 through 118 removed outlier: 4.378A pdb=" N SER D 114 " --> pdb=" O LEU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 135 Processing helix chain 'D' and resid 140 through 153 Processing helix chain 'D' and resid 161 through 171 Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 218 through 235 Processing helix chain 'D' and resid 251 through 265 Processing helix chain 'D' and resid 272 through 285 Proline residue: D 285 - end of helix Processing helix chain 'D' and resid 290 through 303 Processing helix chain 'D' and resid 308 through 320 Processing helix chain 'D' and resid 326 through 336 Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 345 through 359 Processing helix chain 'D' and resid 366 through 380 removed outlier: 4.211A pdb=" N THR D 370 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS D 374 " --> pdb=" O GLU D 371 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS D 377 " --> pdb=" O CYS D 374 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG D 378 " --> pdb=" O MET D 375 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER D 380 " --> pdb=" O LYS D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 412 removed outlier: 3.860A pdb=" N LEU D 403 " --> pdb=" O PHE D 399 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER D 406 " --> pdb=" O ILE D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 423 Processing helix chain 'D' and resid 430 through 445 removed outlier: 3.668A pdb=" N VAL D 444 " --> pdb=" O THR D 440 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU D 445 " --> pdb=" O THR D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 458 Processing helix chain 'D' and resid 468 through 480 Processing helix chain 'D' and resid 484 through 492 Processing helix chain 'D' and resid 494 through 497 No H-bonds generated for 'chain 'D' and resid 494 through 497' Processing helix chain 'D' and resid 502 through 517 Processing helix chain 'D' and resid 522 through 528 Processing helix chain 'D' and resid 540 through 543 No H-bonds generated for 'chain 'D' and resid 540 through 543' Processing helix chain 'D' and resid 566 through 569 No H-bonds generated for 'chain 'D' and resid 566 through 569' Processing helix chain 'D' and resid 593 through 597 Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'E' and resid 3 through 9 Processing helix chain 'E' and resid 11 through 22 Processing helix chain 'E' and resid 27 through 40 Processing helix chain 'E' and resid 50 through 64 Processing helix chain 'E' and resid 71 through 84 removed outlier: 3.663A pdb=" N LEU E 84 " --> pdb=" O LEU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 100 Processing helix chain 'E' and resid 107 through 119 removed outlier: 3.956A pdb=" N ASN E 118 " --> pdb=" O LYS E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 137 removed outlier: 3.792A pdb=" N TYR E 136 " --> pdb=" O THR E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 157 Processing helix chain 'E' and resid 161 through 171 removed outlier: 3.523A pdb=" N TRP E 165 " --> pdb=" O LYS E 162 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN E 166 " --> pdb=" O LYS E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 192 Processing helix chain 'E' and resid 199 through 202 No H-bonds generated for 'chain 'E' and resid 199 through 202' Processing helix chain 'E' and resid 205 through 210 Processing helix chain 'E' and resid 223 through 254 removed outlier: 3.719A pdb=" N LYS E 235 " --> pdb=" O LYS E 231 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE E 236 " --> pdb=" O LYS E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 289 removed outlier: 3.617A pdb=" N LYS E 281 " --> pdb=" O GLU E 277 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR E 288 " --> pdb=" O ASP E 284 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU E 289 " --> pdb=" O TYR E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 302 Processing helix chain 'E' and resid 312 through 322 removed outlier: 3.592A pdb=" N ASN E 322 " --> pdb=" O LYS E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 338 Processing helix chain 'E' and resid 345 through 358 Processing helix chain 'E' and resid 361 through 375 Processing helix chain 'E' and resid 379 through 381 No H-bonds generated for 'chain 'E' and resid 379 through 381' Processing helix chain 'E' and resid 385 through 402 Processing helix chain 'E' and resid 418 through 428 Processing helix chain 'E' and resid 438 through 445 removed outlier: 3.545A pdb=" N ASN E 442 " --> pdb=" O ILE E 439 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL E 445 " --> pdb=" O ASN E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 467 removed outlier: 3.891A pdb=" N GLN E 462 " --> pdb=" O LYS E 458 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS E 463 " --> pdb=" O ASN E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 473 No H-bonds generated for 'chain 'E' and resid 470 through 473' Processing helix chain 'E' and resid 476 through 487 Processing helix chain 'E' and resid 495 through 506 Processing helix chain 'E' and resid 517 through 528 Processing helix chain 'E' and resid 531 through 541 Processing helix chain 'F' and resid 325 through 333 removed outlier: 4.188A pdb=" N LEU F 329 " --> pdb=" O THR F 325 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG F 330 " --> pdb=" O GLU F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 368 Processing helix chain 'F' and resid 388 through 397 Processing helix chain 'F' and resid 502 through 514 Processing helix chain 'G' and resid 47 through 57 Processing helix chain 'G' and resid 79 through 92 removed outlier: 3.870A pdb=" N GLU G 88 " --> pdb=" O GLU G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 141 removed outlier: 3.644A pdb=" N VAL G 128 " --> pdb=" O ASP G 124 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER G 130 " --> pdb=" O CYS G 126 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL G 131 " --> pdb=" O PHE G 127 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG G 138 " --> pdb=" O ALA G 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU G 139 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TRP G 140 " --> pdb=" O GLN G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 219 Processing helix chain 'G' and resid 231 through 252 removed outlier: 3.647A pdb=" N ASN G 240 " --> pdb=" O LYS G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 292 removed outlier: 4.004A pdb=" N LYS G 269 " --> pdb=" O SER G 265 " (cutoff:3.500A) Proline residue: G 272 - end of helix Processing helix chain 'H' and resid 7 through 19 Processing helix chain 'H' and resid 46 through 50 Processing helix chain 'H' and resid 54 through 57 No H-bonds generated for 'chain 'H' and resid 54 through 57' Processing helix chain 'H' and resid 74 through 83 Processing helix chain 'H' and resid 92 through 119 Processing helix chain 'H' and resid 127 through 137 Processing helix chain 'H' and resid 176 through 186 Processing helix chain 'H' and resid 216 through 221 Processing helix chain 'H' and resid 224 through 240 Processing helix chain 'J' and resid 9 through 13 Processing helix chain 'J' and resid 36 through 42 Processing helix chain 'O' and resid 138 through 144 Processing helix chain 'O' and resid 158 through 174 removed outlier: 3.601A pdb=" N SER O 167 " --> pdb=" O GLU O 163 " (cutoff:3.500A) Processing helix chain 'O' and resid 178 through 190 removed outlier: 3.555A pdb=" N THR O 183 " --> pdb=" O ALA O 179 " (cutoff:3.500A) Processing helix chain 'O' and resid 197 through 209 Proline residue: O 206 - end of helix removed outlier: 4.121A pdb=" N LEU O 209 " --> pdb=" O LEU O 205 " (cutoff:3.500A) Processing helix chain 'O' and resid 215 through 232 removed outlier: 3.647A pdb=" N THR O 224 " --> pdb=" O LEU O 220 " (cutoff:3.500A) Processing helix chain 'O' and resid 237 through 252 Proline residue: O 249 - end of helix removed outlier: 4.865A pdb=" N ILE O 252 " --> pdb=" O ALA O 248 " (cutoff:3.500A) Processing helix chain 'O' and resid 256 through 273 removed outlier: 3.618A pdb=" N THR O 261 " --> pdb=" O MET O 257 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE O 266 " --> pdb=" O GLY O 262 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR O 271 " --> pdb=" O THR O 267 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL O 272 " --> pdb=" O ASN O 268 " (cutoff:3.500A) Processing helix chain 'O' and resid 275 through 286 Proline residue: O 284 - end of helix Processing helix chain 'O' and resid 291 through 307 Processing helix chain 'O' and resid 310 through 322 Proline residue: O 315 - end of helix Processing helix chain 'O' and resid 327 through 348 removed outlier: 4.045A pdb=" N VAL O 337 " --> pdb=" O GLY O 333 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE O 346 " --> pdb=" O ILE O 342 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLY O 347 " --> pdb=" O LEU O 343 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL O 348 " --> pdb=" O LEU O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 352 through 363 removed outlier: 3.569A pdb=" N CYS O 358 " --> pdb=" O GLY O 354 " (cutoff:3.500A) Processing helix chain 'O' and resid 368 through 383 Processing helix chain 'O' and resid 387 through 407 removed outlier: 3.659A pdb=" N ILE O 390 " --> pdb=" O PRO O 387 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU O 391 " --> pdb=" O TYR O 388 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN O 394 " --> pdb=" O GLU O 391 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU O 397 " --> pdb=" O ASN O 394 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU O 398 " --> pdb=" O VAL O 395 " (cutoff:3.500A) Proline residue: O 399 - end of helix removed outlier: 4.045A pdb=" N ARG O 405 " --> pdb=" O LYS O 402 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N HIS O 407 " --> pdb=" O ILE O 404 " (cutoff:3.500A) Processing helix chain 'O' and resid 409 through 425 Proline residue: O 424 - end of helix Processing helix chain 'O' and resid 428 through 447 removed outlier: 4.092A pdb=" N ARG O 440 " --> pdb=" O THR O 436 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE O 441 " --> pdb=" O GLU O 437 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ASP O 447 " --> pdb=" O ARG O 443 " (cutoff:3.500A) Processing helix chain 'O' and resid 451 through 466 removed outlier: 4.383A pdb=" N ALA O 466 " --> pdb=" O GLN O 462 " (cutoff:3.500A) Processing helix chain 'O' and resid 472 through 477 Processing helix chain 'O' and resid 479 through 487 removed outlier: 3.525A pdb=" N GLN O 485 " --> pdb=" O PRO O 481 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS O 486 " --> pdb=" O GLU O 482 " (cutoff:3.500A) Processing helix chain 'O' and resid 490 through 494 Processing helix chain 'O' and resid 496 through 512 removed outlier: 4.029A pdb=" N VAL O 501 " --> pdb=" O PRO O 497 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS O 511 " --> pdb=" O VAL O 507 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS O 512 " --> pdb=" O THR O 508 " (cutoff:3.500A) Processing helix chain 'O' and resid 515 through 527 removed outlier: 4.571A pdb=" N THR O 524 " --> pdb=" O ASP O 520 " (cutoff:3.500A) Proline residue: O 525 - end of helix Processing helix chain 'O' and resid 531 through 547 Processing helix chain 'O' and resid 555 through 570 Processing helix chain 'O' and resid 578 through 589 Processing helix chain 'O' and resid 592 through 609 removed outlier: 3.712A pdb=" N LYS O 595 " --> pdb=" O ILE O 592 " (cutoff:3.500A) Proline residue: O 596 - end of helix removed outlier: 4.205A pdb=" N ALA O 599 " --> pdb=" O PRO O 596 " (cutoff:3.500A) Proline residue: O 600 - end of helix Processing helix chain 'O' and resid 614 through 634 Proline residue: O 629 - end of helix removed outlier: 3.686A pdb=" N LYS O 632 " --> pdb=" O ILE O 628 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN O 633 " --> pdb=" O PRO O 629 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS O 634 " --> pdb=" O VAL O 630 " (cutoff:3.500A) Processing helix chain 'O' and resid 638 through 652 removed outlier: 4.798A pdb=" N GLY O 652 " --> pdb=" O TYR O 648 " (cutoff:3.500A) Processing helix chain 'O' and resid 656 through 672 removed outlier: 3.899A pdb=" N SER O 661 " --> pdb=" O GLU O 657 " (cutoff:3.500A) Processing helix chain 'O' and resid 682 through 695 Proline residue: O 687 - end of helix Proline residue: O 691 - end of helix removed outlier: 4.886A pdb=" N ARG O 694 " --> pdb=" O THR O 690 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASN O 695 " --> pdb=" O PRO O 691 " (cutoff:3.500A) Processing helix chain 'O' and resid 699 through 714 Processing helix chain 'O' and resid 721 through 736 removed outlier: 5.188A pdb=" N LYS O 736 " --> pdb=" O LEU O 732 " (cutoff:3.500A) Processing helix chain 'O' and resid 740 through 756 removed outlier: 3.742A pdb=" N PHE O 750 " --> pdb=" O ALA O 746 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY O 751 " --> pdb=" O ASN O 747 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE O 752 " --> pdb=" O ALA O 748 " (cutoff:3.500A) Processing helix chain 'O' and resid 759 through 770 removed outlier: 3.841A pdb=" N ALA O 765 " --> pdb=" O ASP O 761 " (cutoff:3.500A) Processing helix chain 'O' and resid 775 through 792 Processing helix chain 'O' and resid 794 through 806 Proline residue: O 799 - end of helix Processing helix chain 'O' and resid 810 through 825 Processing helix chain 'O' and resid 831 through 847 removed outlier: 5.476A pdb=" N TYR O 836 " --> pdb=" O LYS O 832 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N PHE O 837 " --> pdb=" O ASP O 833 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE O 838 " --> pdb=" O TYR O 834 " (cutoff:3.500A) Proline residue: O 840 - end of helix removed outlier: 3.888A pdb=" N ASP O 844 " --> pdb=" O PRO O 840 " (cutoff:3.500A) Processing helix chain 'O' and resid 851 through 868 removed outlier: 3.580A pdb=" N HIS O 863 " --> pdb=" O ASN O 859 " (cutoff:3.500A) Processing helix chain 'O' and resid 874 through 889 Proline residue: O 886 - end of helix removed outlier: 4.808A pdb=" N PHE O 889 " --> pdb=" O ILE O 885 " (cutoff:3.500A) Processing helix chain 'O' and resid 893 through 910 Processing helix chain 'O' and resid 912 through 921 Processing helix chain 'O' and resid 930 through 944 removed outlier: 3.663A pdb=" N ARG O 936 " --> pdb=" O LYS O 932 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL O 937 " --> pdb=" O ALA O 933 " (cutoff:3.500A) Processing helix chain 'O' and resid 947 through 952 Proline residue: O 951 - end of helix No H-bonds generated for 'chain 'O' and resid 947 through 952' Processing helix chain 'P' and resid 746 through 748 No H-bonds generated for 'chain 'P' and resid 746 through 748' Processing helix chain 'P' and resid 1145 through 1153 removed outlier: 3.536A pdb=" N ILE P1150 " --> pdb=" O GLU P1146 " (cutoff:3.500A) Processing helix chain 'P' and resid 1156 through 1160 removed outlier: 4.255A pdb=" N SER P1160 " --> pdb=" O SER P1157 " (cutoff:3.500A) Processing helix chain 'P' and resid 1168 through 1176 Processing helix chain 'P' and resid 1181 through 1183 No H-bonds generated for 'chain 'P' and resid 1181 through 1183' Processing helix chain 'P' and resid 1235 through 1264 removed outlier: 3.803A pdb=" N GLU P1249 " --> pdb=" O ASN P1245 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASP P1251 " --> pdb=" O MET P1247 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ASP P1252 " --> pdb=" O ALA P1248 " (cutoff:3.500A) Processing helix chain 'P' and resid 1304 through 1309 Processing helix chain 'P' and resid 1320 through 1328 removed outlier: 3.938A pdb=" N ASN P1325 " --> pdb=" O ASP P1321 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE P1326 " --> pdb=" O LEU P1322 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU P1327 " --> pdb=" O CYS P1323 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG P1328 " --> pdb=" O GLU P1324 " (cutoff:3.500A) Processing helix chain 'P' and resid 1331 through 1340 removed outlier: 3.656A pdb=" N LYS P1339 " --> pdb=" O GLU P1335 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ASN P1340 " --> pdb=" O PHE P1336 " (cutoff:3.500A) Processing helix chain 'P' and resid 1346 through 1359 removed outlier: 4.010A pdb=" N VAL P1356 " --> pdb=" O THR P1352 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ARG P1357 " --> pdb=" O ILE P1353 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR P1358 " --> pdb=" O ASN P1354 " (cutoff:3.500A) Processing helix chain 'Q' and resid 134 through 140 removed outlier: 3.668A pdb=" N SER Q 139 " --> pdb=" O SER Q 135 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLN Q 140 " --> pdb=" O GLN Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 149 through 153 Processing helix chain 'Q' and resid 157 through 164 Processing helix chain 'Q' and resid 186 through 190 removed outlier: 3.979A pdb=" N GLY Q 190 " --> pdb=" O ARG Q 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 186 through 190' Processing helix chain 'Q' and resid 198 through 203 removed outlier: 3.945A pdb=" N THR Q 203 " --> pdb=" O ILE Q 199 " (cutoff:3.500A) Processing helix chain 'Q' and resid 205 through 208 No H-bonds generated for 'chain 'Q' and resid 205 through 208' Processing helix chain 'Q' and resid 244 through 251 Processing helix chain 'Q' and resid 276 through 288 Processing helix chain 'Q' and resid 296 through 302 Processing helix chain 'Q' and resid 311 through 319 removed outlier: 3.611A pdb=" N MET Q 314 " --> pdb=" O PRO Q 311 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS Q 315 " --> pdb=" O TRP Q 312 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP Q 318 " --> pdb=" O LYS Q 315 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE Q 319 " --> pdb=" O MET Q 316 " (cutoff:3.500A) Processing helix chain 'Q' and resid 337 through 339 No H-bonds generated for 'chain 'Q' and resid 337 through 339' Processing helix chain 'Q' and resid 362 through 364 No H-bonds generated for 'chain 'Q' and resid 362 through 364' Processing helix chain 'R' and resid 22 through 31 removed outlier: 3.977A pdb=" N GLN R 31 " --> pdb=" O GLU R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 70 Processing helix chain 'R' and resid 121 through 129 Processing helix chain 'R' and resid 158 through 168 Processing helix chain 'R' and resid 192 through 202 Processing helix chain 'S' and resid 24 through 26 No H-bonds generated for 'chain 'S' and resid 24 through 26' Processing helix chain 'S' and resid 47 through 49 No H-bonds generated for 'chain 'S' and resid 47 through 49' Processing helix chain 'S' and resid 53 through 56 Processing helix chain 'S' and resid 74 through 79 Processing helix chain 'S' and resid 81 through 83 No H-bonds generated for 'chain 'S' and resid 81 through 83' Processing helix chain 'S' and resid 94 through 103 Processing helix chain 'T' and resid 3 through 27 Processing helix chain 'T' and resid 29 through 42 removed outlier: 4.413A pdb=" N HIS T 34 " --> pdb=" O LEU T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 56 Processing helix chain 'T' and resid 69 through 96 Processing helix chain 'T' and resid 113 through 124 removed outlier: 3.556A pdb=" N GLU T 122 " --> pdb=" O GLN T 118 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS T 124 " --> pdb=" O GLU T 120 " (cutoff:3.500A) Processing helix chain 'T' and resid 137 through 144 Processing helix chain 'T' and resid 159 through 161 No H-bonds generated for 'chain 'T' and resid 159 through 161' Processing helix chain 'T' and resid 166 through 168 No H-bonds generated for 'chain 'T' and resid 166 through 168' Processing helix chain 'T' and resid 175 through 177 No H-bonds generated for 'chain 'T' and resid 175 through 177' Processing helix chain 'T' and resid 183 through 193 Processing helix chain 'T' and resid 200 through 211 removed outlier: 3.996A pdb=" N LEU T 209 " --> pdb=" O ASP T 205 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE T 210 " --> pdb=" O ILE T 206 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU T 211 " --> pdb=" O LEU T 207 " (cutoff:3.500A) Processing helix chain 'T' and resid 215 through 218 No H-bonds generated for 'chain 'T' and resid 215 through 218' Processing helix chain 'T' and resid 227 through 247 Processing helix chain 'T' and resid 253 through 266 Processing helix chain 'T' and resid 268 through 270 No H-bonds generated for 'chain 'T' and resid 268 through 270' Processing helix chain 'T' and resid 292 through 296 Processing helix chain 'T' and resid 302 through 310 Processing helix chain 'T' and resid 312 through 327 Processing helix chain 'T' and resid 329 through 344 Processing helix chain 'T' and resid 347 through 361 Processing helix chain 'T' and resid 409 through 415 Processing helix chain 'T' and resid 434 through 440 Processing helix chain 'T' and resid 444 through 453 Processing helix chain 'T' and resid 469 through 477 Processing helix chain 'T' and resid 513 through 515 No H-bonds generated for 'chain 'T' and resid 513 through 515' Processing helix chain 'T' and resid 518 through 527 Processing helix chain 'U' and resid 43 through 45 No H-bonds generated for 'chain 'U' and resid 43 through 45' Processing helix chain 'U' and resid 78 through 86 Processing helix chain 'U' and resid 88 through 104 Processing helix chain 'U' and resid 235 through 239 Processing helix chain 'V' and resid 90 through 103 Processing helix chain 'V' and resid 109 through 116 removed outlier: 4.100A pdb=" N SER V 115 " --> pdb=" O GLU V 111 " (cutoff:3.500A) Processing helix chain 'V' and resid 123 through 125 No H-bonds generated for 'chain 'V' and resid 123 through 125' Processing helix chain 'V' and resid 130 through 145 removed outlier: 4.145A pdb=" N VAL V 139 " --> pdb=" O THR V 136 " (cutoff:3.500A) Processing helix chain 'V' and resid 157 through 194 Processing helix chain 'W' and resid 5 through 8 No H-bonds generated for 'chain 'W' and resid 5 through 8' Processing helix chain 'W' and resid 47 through 50 Processing helix chain 'W' and resid 112 through 119 removed outlier: 4.141A pdb=" N ARG W 116 " --> pdb=" O ASP W 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 133 through 136 Processing helix chain 'W' and resid 140 through 147 Processing helix chain 'W' and resid 161 through 169 Processing helix chain 'X' and resid 2 through 43 Processing helix chain 'X' and resid 51 through 54 No H-bonds generated for 'chain 'X' and resid 51 through 54' Processing helix chain 'Y' and resid 41 through 54 removed outlier: 4.298A pdb=" N THR Y 54 " --> pdb=" O LEU Y 50 " (cutoff:3.500A) Processing helix chain 'Y' and resid 79 through 88 Processing helix chain 'Z' and resid 3 through 18 Processing helix chain 'Z' and resid 28 through 45 Processing helix chain 'Z' and resid 47 through 57 Processing helix chain 'Z' and resid 62 through 73 Processing helix chain 'Z' and resid 75 through 82 Processing helix chain 'b' and resid 55 through 61 removed outlier: 3.893A pdb=" N ASP b 59 " --> pdb=" O LYS b 55 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS b 60 " --> pdb=" O THR b 56 " (cutoff:3.500A) Processing helix chain 'b' and resid 105 through 130 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 'd' and resid 76 through 79 Processing helix chain 'e' and resid 13 through 22 Processing helix chain 'f' and resid 15 through 22 Processing helix chain 'f' and resid 60 through 62 No H-bonds generated for 'chain 'f' and resid 60 through 62' Processing helix chain 'g' and resid 8 through 10 No H-bonds generated for 'chain 'g' and resid 8 through 10' Processing helix chain 'h' and resid 4 through 10 removed outlier: 4.006A pdb=" N LEU h 10 " --> pdb=" O PHE h 6 " (cutoff:3.500A) Processing helix chain 'h' and resid 60 through 68 Processing helix chain 'h' and resid 89 through 91 No H-bonds generated for 'chain 'h' and resid 89 through 91' Processing helix chain 'h' and resid 103 through 106 No H-bonds generated for 'chain 'h' and resid 103 through 106' Processing helix chain 'h' and resid 110 through 118 Processing helix chain 'i' and resid 18 through 27 Processing helix chain 'i' and resid 30 through 39 removed outlier: 3.754A pdb=" N LEU i 33 " --> pdb=" O PRO i 30 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN i 35 " --> pdb=" O SER i 32 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA i 37 " --> pdb=" O ILE i 34 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET i 38 " --> pdb=" O ASN i 35 " (cutoff:3.500A) Processing helix chain 't' and resid 3 through 10 removed outlier: 3.905A pdb=" N LEU t 10 " --> pdb=" O PHE t 6 " (cutoff:3.500A) Processing helix chain 't' and resid 89 through 91 No H-bonds generated for 'chain 't' and resid 89 through 91' Processing helix chain 'u' and resid 18 through 28 Processing helix chain 'u' and resid 30 through 40 removed outlier: 3.605A pdb=" N ASN u 35 " --> pdb=" O SER u 32 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP u 36 " --> pdb=" O LEU u 33 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR u 40 " --> pdb=" O ALA u 37 " (cutoff:3.500A) Processing helix chain 'v' and resid 6 through 13 Processing helix chain 'v' and resid 76 through 80 removed outlier: 3.731A pdb=" N ASN v 80 " --> pdb=" O LEU v 77 " (cutoff:3.500A) Processing helix chain 'w' and resid 13 through 23 Processing helix chain 'w' and resid 84 through 86 No H-bonds generated for 'chain 'w' and resid 84 through 86' Processing helix chain 'x' and resid 15 through 22 Processing helix chain 'x' and resid 75 through 77 No H-bonds generated for 'chain 'x' and resid 75 through 77' Processing helix chain 'y' and resid 8 through 10 No H-bonds generated for 'chain 'y' and resid 8 through 10' Processing helix chain 'y' and resid 65 through 67 No H-bonds generated for 'chain 'y' and resid 65 through 67' Processing sheet with id= A, first strand: chain 'A' and resid 107 through 110 removed outlier: 3.521A pdb=" N ARG A 107 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.579A pdb=" N ALA A 98 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 100 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ARG A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 182 through 185 Processing sheet with id= D, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.608A pdb=" N SER C 11 " --> pdb=" O CYS C 6 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 582 through 584 Processing sheet with id= F, first strand: chain 'F' and resid 379 through 382 removed outlier: 3.722A pdb=" N TYR F 341 " --> pdb=" O GLN F 354 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 444 through 447 Processing sheet with id= H, first strand: chain 'G' and resid 69 through 76 removed outlier: 3.919A pdb=" N THR G 76 " --> pdb=" O MET G 111 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET G 111 " --> pdb=" O THR G 76 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 159 through 163 removed outlier: 4.132A pdb=" N GLY G 159 " --> pdb=" O VAL G 203 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU G 163 " --> pdb=" O GLN G 199 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'J' and resid 5 through 7 Processing sheet with id= K, first strand: chain 'P' and resid 73 through 75 removed outlier: 3.563A pdb=" N LEU P 103 " --> pdb=" O ALA P 115 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA P 115 " --> pdb=" O LEU P 103 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ASP P 105 " --> pdb=" O LEU P 113 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU P 113 " --> pdb=" O ASP P 105 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'P' and resid 124 through 130 removed outlier: 7.008A pdb=" N THR P 151 " --> pdb=" O THR P 125 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N MET P 127 " --> pdb=" O ALA P 149 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ALA P 149 " --> pdb=" O MET P 127 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N SER P 129 " --> pdb=" O PHE P 147 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N PHE P 147 " --> pdb=" O SER P 129 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL P 175 " --> pdb=" O ILE P 159 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLN P 161 " --> pdb=" O THR P 173 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N THR P 173 " --> pdb=" O GLN P 161 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE P 163 " --> pdb=" O LEU P 171 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU P 171 " --> pdb=" O ILE P 163 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N HIS P 165 " --> pdb=" O LEU P 169 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU P 169 " --> pdb=" O HIS P 165 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'P' and resid 192 through 195 removed outlier: 4.113A pdb=" N TYR P 192 " --> pdb=" O SER P 205 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'P' and resid 235 through 238 removed outlier: 4.203A pdb=" N VAL P 266 " --> pdb=" O VAL P 288 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'P' and resid 241 through 243 removed outlier: 4.310A pdb=" N CYS P 251 " --> pdb=" O VAL P 243 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'P' and resid 271 through 274 removed outlier: 3.537A pdb=" N HIS P 279 " --> pdb=" O GLU P 274 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'P' and resid 294 through 298 removed outlier: 4.283A pdb=" N PHE P 326 " --> pdb=" O LEU P 298 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'P' and resid 388 through 391 removed outlier: 3.696A pdb=" N SER P 367 " --> pdb=" O GLN P 382 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'P' and resid 418 through 421 removed outlier: 3.876A pdb=" N ASN P 436 " --> pdb=" O GLN P 481 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER P 479 " --> pdb=" O LEU P 438 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLN P 440 " --> pdb=" O ILE P 477 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE P 477 " --> pdb=" O GLN P 440 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'P' and resid 490 through 493 Processing sheet with id= U, first strand: chain 'P' and resid 519 through 522 removed outlier: 3.685A pdb=" N ILE P 873 " --> pdb=" O LEU P 522 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG P 870 " --> pdb=" O SER P 866 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 534 through 538 Processing sheet with id= W, first strand: chain 'P' and resid 588 through 593 removed outlier: 6.903A pdb=" N VAL P 602 " --> pdb=" O ILE P 589 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N THR P 591 " --> pdb=" O ILE P 600 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE P 600 " --> pdb=" O THR P 591 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU P 622 " --> pdb=" O HIS P 609 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL P 611 " --> pdb=" O ASN P 620 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ASN P 620 " --> pdb=" O VAL P 611 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N THR P 613 " --> pdb=" O TYR P 618 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TYR P 618 " --> pdb=" O THR P 613 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'P' and resid 634 through 637 removed outlier: 3.734A pdb=" N LYS P 655 " --> pdb=" O ILE P 664 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'P' and resid 691 through 694 Processing sheet with id= Z, first strand: chain 'P' and resid 725 through 732 removed outlier: 7.284A pdb=" N GLY P 744 " --> pdb=" O SER P 726 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N MET P 728 " --> pdb=" O HIS P 742 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N HIS P 742 " --> pdb=" O MET P 728 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N MET P 730 " --> pdb=" O ASN P 740 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ASN P 740 " --> pdb=" O MET P 730 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU P 739 " --> pdb=" O ILE P 755 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL P 749 " --> pdb=" O LEU P 745 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS P 754 " --> pdb=" O ASP P 764 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ASP P 764 " --> pdb=" O HIS P 754 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'P' and resid 776 through 782 removed outlier: 6.026A pdb=" N SER P 817 " --> pdb=" O THR P 831 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR P 831 " --> pdb=" O SER P 817 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR P 830 " --> pdb=" O THR P 837 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'P' and resid 972 through 975 removed outlier: 4.936A pdb=" N GLN P 950 " --> pdb=" O HIS P 945 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG P 952 " --> pdb=" O ASP P 943 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ASN P 944 " --> pdb=" O PRO P 926 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'P' and resid 981 through 985 removed outlier: 3.812A pdb=" N SER P 981 " --> pdb=" O CYS P 997 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG P1002 " --> pdb=" O ALA P 998 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'P' and resid 1033 through 1037 removed outlier: 4.454A pdb=" N ALA P1033 " --> pdb=" O ALA P1044 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N GLY P1053 " --> pdb=" O ARG P1061 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ARG P1061 " --> pdb=" O GLY P1053 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'P' and resid 1077 through 1080 removed outlier: 3.554A pdb=" N LEU P1096 " --> pdb=" O VAL P1110 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL P1110 " --> pdb=" O LEU P1096 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE P1098 " --> pdb=" O PRO P1108 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP P1100 " --> pdb=" O PHE P1106 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N PHE P1106 " --> pdb=" O ASP P1100 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'P' and resid 1128 through 1132 removed outlier: 6.355A pdb=" N ARG P1142 " --> pdb=" O LEU P1189 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LEU P1189 " --> pdb=" O ARG P1142 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'P' and resid 60 through 66 removed outlier: 6.604A pdb=" N VAL P1225 " --> pdb=" O LEU P 65 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'Q' and resid 328 through 330 Processing sheet with id= AI, first strand: chain 'R' and resid 82 through 85 Processing sheet with id= AJ, first strand: chain 'R' and resid 179 through 182 Processing sheet with id= AK, first strand: chain 'R' and resid 171 through 173 Processing sheet with id= AL, first strand: chain 'T' and resid 421 through 423 Processing sheet with id= AM, first strand: chain 'U' and resid 58 through 60 removed outlier: 3.599A pdb=" N THR U 73 " --> pdb=" O CYS U 68 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'U' and resid 155 through 158 Processing sheet with id= AO, first strand: chain 'U' and resid 179 through 184 Processing sheet with id= AP, first strand: chain 'W' and resid 56 through 58 removed outlier: 6.881A pdb=" N THR W 78 " --> pdb=" O LEU W 57 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASN W 100 " --> pdb=" O LEU W 79 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASN W 126 " --> pdb=" O LEU W 101 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain 'Y' and resid 72 through 75 Processing sheet with id= AR, first strand: chain 'b' and resid 78 through 83 removed outlier: 5.016A pdb=" N CYS b 48 " --> pdb=" O LEU b 82 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ARG b 21 " --> pdb=" O VAL b 97 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N VAL b 97 " --> pdb=" O ARG b 21 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU b 23 " --> pdb=" O THR b 95 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N THR b 95 " --> pdb=" O LEU b 23 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'd' and resid 69 through 73 removed outlier: 6.700A pdb=" N GLU d 22 " --> pdb=" O LYS d 70 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE d 72 " --> pdb=" O SER d 20 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N SER d 20 " --> pdb=" O ILE d 72 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLN d 43 " --> pdb=" O VAL d 34 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'd' and resid 47 through 50 Processing sheet with id= AU, first strand: chain 'e' and resid 90 through 92 Processing sheet with id= AV, first strand: chain 'e' and resid 42 through 45 removed outlier: 6.617A pdb=" N VAL e 53 " --> pdb=" O VAL e 44 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLY e 78 " --> pdb=" O GLU e 56 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'f' and resid 71 through 73 removed outlier: 6.213A pdb=" N ASN f 54 " --> pdb=" O LEU f 42 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU f 42 " --> pdb=" O ASN f 54 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'f' and resid 27 through 31 Processing sheet with id= AY, first strand: chain 'g' and resid 68 through 73 removed outlier: 6.742A pdb=" N ASN g 18 " --> pdb=" O ILE g 69 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU g 71 " --> pdb=" O LEU g 16 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU g 16 " --> pdb=" O LEU g 71 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ALA g 73 " --> pdb=" O LYS g 14 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LYS g 14 " --> pdb=" O ALA g 73 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL g 39 " --> pdb=" O ARG g 30 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'h' and resid 80 through 82 removed outlier: 4.491A pdb=" N THR h 23 " --> pdb=" O LEU h 19 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL h 15 " --> pdb=" O GLY h 27 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU h 13 " --> pdb=" O LEU h 29 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'h' and resid 38 through 41 Processing sheet with id= BB, first strand: chain 'i' and resid 85 through 91 Processing sheet with id= BC, first strand: chain 'i' and resid 67 through 70 Processing sheet with id= BD, first strand: chain 's' and resid 94 through 96 removed outlier: 3.642A pdb=" N SER s 94 " --> pdb=" O LEU s 23 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLU s 50 " --> pdb=" O VAL s 81 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N VAL s 81 " --> pdb=" O GLU s 50 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 's' and resid 85 through 87 removed outlier: 3.882A pdb=" N ALA s 36 " --> pdb=" O VAL s 44 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASN s 46 " --> pdb=" O LEU s 34 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU s 34 " --> pdb=" O ASN s 46 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 't' and resid 80 through 82 removed outlier: 3.844A pdb=" N GLU t 13 " --> pdb=" O LEU t 29 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 't' and resid 84 through 87 removed outlier: 6.134A pdb=" N THR t 41 " --> pdb=" O LEU t 29 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU t 29 " --> pdb=" O THR t 41 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'u' and resid 85 through 91 Processing sheet with id= BI, first strand: chain 'u' and resid 93 through 96 removed outlier: 6.550A pdb=" N GLU u 70 " --> pdb=" O VAL u 58 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N VAL u 58 " --> pdb=" O GLU u 70 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'v' and resid 56 through 59 Processing sheet with id= BK, first strand: chain 'v' and resid 61 through 64 removed outlier: 6.411A pdb=" N ARG v 45 " --> pdb=" O LEU v 33 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU v 33 " --> pdb=" O ARG v 45 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'w' and resid 89 through 92 removed outlier: 3.576A pdb=" N GLY w 78 " --> pdb=" O ALA w 57 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLU w 59 " --> pdb=" O PRO w 76 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'w' and resid 80 through 82 removed outlier: 3.599A pdb=" N GLY w 45 " --> pdb=" O VAL w 53 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP w 55 " --> pdb=" O ILE w 43 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ILE w 43 " --> pdb=" O ASP w 55 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'x' and resid 66 through 69 removed outlier: 3.725A pdb=" N GLY x 66 " --> pdb=" O GLU x 58 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ALA x 56 " --> pdb=" O LEU x 68 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'x' and resid 71 through 73 removed outlier: 3.615A pdb=" N SER x 44 " --> pdb=" O GLN x 52 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN x 54 " --> pdb=" O LEU x 42 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU x 42 " --> pdb=" O ASN x 54 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'y' and resid 23 through 28 Processing sheet with id= BQ, first strand: chain 'y' and resid 38 through 40 Processing sheet with id= BR, first strand: chain 'y' and resid 43 through 46 removed outlier: 6.771A pdb=" N GLU y 45 " --> pdb=" O ASN y 54 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ASN y 54 " --> pdb=" O GLU y 45 " (cutoff:3.500A) 2295 hydrogen bonds defined for protein. 6291 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 333 hydrogen bonds 638 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 266 stacking parallelities Total time for adding SS restraints: 34.12 Time building geometry restraints manager: 26.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 18639 1.34 - 1.48: 19840 1.48 - 1.62: 28241 1.62 - 1.76: 53 1.76 - 1.90: 404 Bond restraints: 67177 Sorted by residual: bond pdb=" O3' G 21149 " pdb=" P U 21150 " ideal model delta sigma weight residual 1.607 1.900 -0.293 1.50e-02 4.44e+03 3.80e+02 bond pdb=" O3' G 2 143 " pdb=" P G 2 144 " ideal model delta sigma weight residual 1.607 1.833 -0.226 1.50e-02 4.44e+03 2.27e+02 bond pdb=" C3' G 2 143 " pdb=" O3' G 2 143 " ideal model delta sigma weight residual 1.417 1.631 -0.214 1.50e-02 4.44e+03 2.04e+02 bond pdb=" O3' U 21161 " pdb=" P U 21162 " ideal model delta sigma weight residual 1.607 1.420 0.187 1.50e-02 4.44e+03 1.55e+02 bond pdb=" O3' A 21092 " pdb=" P C 21093 " ideal model delta sigma weight residual 1.607 1.429 0.178 1.50e-02 4.44e+03 1.40e+02 ... (remaining 67172 not shown) Histogram of bond angle deviations from ideal: 74.71 - 88.68: 2 88.68 - 102.66: 1141 102.66 - 116.63: 49203 116.63 - 130.61: 42341 130.61 - 144.59: 417 Bond angle restraints: 93104 Sorted by residual: angle pdb=" C4' G 2 144 " pdb=" C3' G 2 144 " pdb=" O3' G 2 144 " ideal model delta sigma weight residual 113.00 74.71 38.29 1.50e+00 4.44e-01 6.52e+02 angle pdb=" C4' U 21151 " pdb=" C3' U 21151 " pdb=" O3' U 21151 " ideal model delta sigma weight residual 113.00 83.00 30.00 1.50e+00 4.44e-01 4.00e+02 angle pdb=" C4' G 2 143 " pdb=" C3' G 2 143 " pdb=" O3' G 2 143 " ideal model delta sigma weight residual 113.00 140.24 -27.24 1.50e+00 4.44e-01 3.30e+02 angle pdb=" O3' A 21092 " pdb=" C3' A 21092 " pdb=" C2' A 21092 " ideal model delta sigma weight residual 113.70 140.56 -26.86 1.50e+00 4.44e-01 3.21e+02 angle pdb=" C3' G 21097 " pdb=" C2' G 21097 " pdb=" O2' G 21097 " ideal model delta sigma weight residual 110.70 135.40 -24.70 1.50e+00 4.44e-01 2.71e+02 ... (remaining 93099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 39534 35.47 - 70.93: 1070 70.93 - 106.40: 151 106.40 - 141.86: 16 141.86 - 177.33: 10 Dihedral angle restraints: 40781 sinusoidal: 20285 harmonic: 20496 Sorted by residual: dihedral pdb=" CA SER F 385 " pdb=" C SER F 385 " pdb=" N ALA F 386 " pdb=" CA ALA F 386 " ideal model delta harmonic sigma weight residual -180.00 -118.24 -61.76 0 5.00e+00 4.00e-02 1.53e+02 dihedral pdb=" CA SER E 410 " pdb=" C SER E 410 " pdb=" N GLN E 411 " pdb=" CA GLN E 411 " ideal model delta harmonic sigma weight residual -180.00 -122.22 -57.78 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA PRO H 69 " pdb=" C PRO H 69 " pdb=" N GLN H 70 " pdb=" CA GLN H 70 " ideal model delta harmonic sigma weight residual -180.00 -122.77 -57.23 0 5.00e+00 4.00e-02 1.31e+02 ... (remaining 40778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.286: 10962 0.286 - 0.572: 52 0.572 - 0.859: 4 0.859 - 1.145: 1 1.145 - 1.431: 3 Chirality restraints: 11022 Sorted by residual: chirality pdb=" C4' U 21150 " pdb=" C5' U 21150 " pdb=" O4' U 21150 " pdb=" C3' U 21150 " both_signs ideal model delta sigma weight residual False -2.50 -1.07 -1.43 2.00e-01 2.50e+01 5.12e+01 chirality pdb=" C3' A 21147 " pdb=" C4' A 21147 " pdb=" O3' A 21147 " pdb=" C2' A 21147 " both_signs ideal model delta sigma weight residual False -2.48 -1.17 -1.31 2.00e-01 2.50e+01 4.28e+01 chirality pdb=" C2' G 21097 " pdb=" C3' G 21097 " pdb=" O2' G 21097 " pdb=" C1' G 21097 " both_signs ideal model delta sigma weight residual False -2.75 -1.59 -1.17 2.00e-01 2.50e+01 3.41e+01 ... (remaining 11019 not shown) Planarity restraints: 10054 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' N 1 428 " 0.440 2.00e-02 2.50e+03 4.35e-01 3.79e+03 pdb=" C2' N 1 428 " 0.414 2.00e-02 2.50e+03 pdb=" C3' N 1 428 " 0.503 2.00e-02 2.50e+03 pdb=" C4' N 1 428 " -0.389 2.00e-02 2.50e+03 pdb=" C5' N 1 428 " -0.126 2.00e-02 2.50e+03 pdb=" O2' N 1 428 " -0.837 2.00e-02 2.50e+03 pdb=" O3' N 1 428 " 0.119 2.00e-02 2.50e+03 pdb=" O4' N 1 428 " -0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' N 1 429 " 0.441 2.00e-02 2.50e+03 4.34e-01 3.77e+03 pdb=" C2' N 1 429 " 0.423 2.00e-02 2.50e+03 pdb=" C3' N 1 429 " 0.499 2.00e-02 2.50e+03 pdb=" C4' N 1 429 " -0.394 2.00e-02 2.50e+03 pdb=" C5' N 1 429 " -0.112 2.00e-02 2.50e+03 pdb=" O2' N 1 429 " -0.829 2.00e-02 2.50e+03 pdb=" O3' N 1 429 " 0.109 2.00e-02 2.50e+03 pdb=" O4' N 1 429 " -0.136 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' N 1 439 " 0.424 2.00e-02 2.50e+03 4.34e-01 3.77e+03 pdb=" C2' N 1 439 " 0.410 2.00e-02 2.50e+03 pdb=" C3' N 1 439 " 0.512 2.00e-02 2.50e+03 pdb=" C4' N 1 439 " -0.377 2.00e-02 2.50e+03 pdb=" C5' N 1 439 " -0.142 2.00e-02 2.50e+03 pdb=" O2' N 1 439 " -0.842 2.00e-02 2.50e+03 pdb=" O3' N 1 439 " 0.124 2.00e-02 2.50e+03 pdb=" O4' N 1 439 " -0.109 2.00e-02 2.50e+03 ... (remaining 10051 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 156 2.33 - 2.97: 32133 2.97 - 3.61: 102017 3.61 - 4.26: 158954 4.26 - 4.90: 243801 Nonbonded interactions: 537061 Sorted by model distance: nonbonded pdb=" O3' C 21098 " pdb=" ND2 ASN W 158 " model vdw 1.687 2.520 nonbonded pdb=" OP1 G 21099 " pdb=" OD1 ASN W 158 " model vdw 1.874 3.040 nonbonded pdb=" OP1 C 21098 " pdb=" NE ARG Y 43 " model vdw 1.878 2.520 nonbonded pdb=" OP1 G 21099 " pdb=" CG ASN W 158 " model vdw 1.910 3.270 nonbonded pdb=" NZ LYS w 83 " pdb=" O CYS x 75 " model vdw 1.946 2.520 ... (remaining 537056 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'd' and resid 4 through 85) selection = chain 'v' } ncs_group { reference = (chain 'e' and resid 10 through 93) selection = (chain 'w' and (resid 10 through 63 or resid 73 through 93)) } ncs_group { reference = chain 'f' selection = chain 'x' } ncs_group { reference = (chain 'g' and resid 2 through 76) selection = (chain 'y' and (resid 2 through 48 or resid 53 through 76)) } ncs_group { reference = (chain 'i' and resid 17 through 108) selection = (chain 'u' and (resid 17 through 80 or resid 83 through 108)) } 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=0.50 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: 6.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.290 Construct map_model_manager: 0.070 Extract box with map and model: 35.800 Check model and map are aligned: 0.720 Set scattering table: 0.440 Process input model: 174.730 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 223.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4156 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 : 0.009 0.293 67177 Z= 0.588 Angle : 1.302 38.294 93104 Z= 0.757 Chirality : 0.070 1.431 11022 Planarity : 0.025 0.435 10054 Dihedral : 15.399 177.330 27402 Min Nonbonded Distance : 1.687 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.80 % Favored : 91.41 % Rotamer: Outliers : 0.57 % Allowed : 3.11 % Favored : 96.32 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.76 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.59 % 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: -3.55 (0.08), residues: 6604 helix: -2.47 (0.07), residues: 2649 sheet: -1.71 (0.14), residues: 1024 loop : -2.35 (0.10), residues: 2931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP D 362 HIS 0.031 0.003 HIS d 17 PHE 0.049 0.003 PHE x 49 TYR 0.062 0.004 TYR s 18 ARG 0.039 0.001 ARG E 157 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13208 Ramachandran restraints generated. 6604 Oldfield, 0 Emsley, 6604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13208 Ramachandran restraints generated. 6604 Oldfield, 0 Emsley, 6604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1103 residues out of total 6237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1070 time to evaluate : 5.160 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 outliers start: 33 outliers final: 4 residues processed: 1097 average time/residue: 0.6991 time to fit residues: 1261.9710 Evaluate side-chains 447 residues out of total 6237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 443 time to evaluate : 5.160 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4737 time to fit residues: 10.6447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 597 optimal weight: 0.6980 chunk 536 optimal weight: 10.0000 chunk 297 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 361 optimal weight: 0.7980 chunk 286 optimal weight: 0.9980 chunk 554 optimal weight: 6.9990 chunk 214 optimal weight: 0.5980 chunk 337 optimal weight: 20.0000 chunk 413 optimal weight: 10.0000 chunk 642 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN C 182 GLN ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 488 ASN ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN E 35 ASN E 72 ASN E 125 GLN E 177 HIS ** E 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 381 ASN ** E 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 GLN ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 445 ASN ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 207 HIS G 217 ASN G 240 ASN G 292 ASN ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 HIS ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 175 ASN O 376 HIS ** O 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 644 ASN O 695 ASN O 769 ASN O 776 GLN ** O 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 887 ASN O 908 GLN O 939 ASN ** P 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 375 ASN ** P 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 385 HIS P 436 ASN ** P 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 491 GLN ** P 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 546 ASN P 590 HIS P 609 HIS ** P 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 738 GLN P 740 ASN P 754 HIS ** P 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 920 GLN ** P 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 945 HIS P1023 HIS ** P1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1117 HIS P1174 GLN P1359 ASN Q 145 GLN ** Q 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 288 HIS R 50 GLN R 170 ASN S 14 GLN T 34 HIS T 167 ASN T 415 HIS ** T 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 55 HIS W 133 GLN W 143 HIS ** W 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 28 ASN ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 90 ASN Z 7 GLN Z 11 GLN Z 41 ASN b 5 GLN d 12 ASN d 68 GLN e 86 ASN ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 12 ASN ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 78 ASN ** i 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 86 ASN ** t 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 4 ASN x 77 ASN y 20 ASN y 56 GLN Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4295 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 67177 Z= 0.221 Angle : 0.921 14.112 93104 Z= 0.523 Chirality : 0.044 0.363 11022 Planarity : 0.008 0.110 10054 Dihedral : 17.488 176.424 14361 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.51 % Favored : 93.10 % Rotamer: Outliers : 2.37 % Allowed : 9.22 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.23 % 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: -2.01 (0.09), residues: 6604 helix: -0.65 (0.09), residues: 2671 sheet: -1.30 (0.15), residues: 994 loop : -1.94 (0.11), residues: 2939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 506 HIS 0.014 0.002 HIS G 207 PHE 0.036 0.002 PHE E 447 TYR 0.040 0.002 TYR D 410 ARG 0.007 0.001 ARG s 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13208 Ramachandran restraints generated. 6604 Oldfield, 0 Emsley, 6604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13208 Ramachandran restraints generated. 6604 Oldfield, 0 Emsley, 6604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 6237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 512 time to evaluate : 5.166 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 outliers start: 138 outliers final: 60 residues processed: 612 average time/residue: 0.6158 time to fit residues: 645.2217 Evaluate side-chains 448 residues out of total 6237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 388 time to evaluate : 5.121 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.4679 time to fit residues: 59.6625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 357 optimal weight: 4.9990 chunk 199 optimal weight: 0.0470 chunk 535 optimal weight: 40.0000 chunk 437 optimal weight: 3.9990 chunk 177 optimal weight: 0.7980 chunk 644 optimal weight: 4.9990 chunk 695 optimal weight: 10.0000 chunk 573 optimal weight: 10.0000 chunk 638 optimal weight: 0.6980 chunk 219 optimal weight: 2.9990 chunk 516 optimal weight: 6.9990 overall best weight: 1.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 HIS D 412 ASN ** D 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN ** D 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 ASN E 91 HIS E 166 ASN ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN ** E 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 446 GLN ** F 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 GLN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 292 ASN ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 882 ASN O 894 HIS ** P 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 641 GLN ** P 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 920 GLN ** P 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 950 GLN ** P1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 303 ASN ** R 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 77 HIS T 307 ASN ** T 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 39 ASN ** W 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 28 ASN ** Z 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 43 GLN ** e 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 24 ASN ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 33 GLN t 14 GLN ** t 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4391 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 67177 Z= 0.240 Angle : 0.856 13.460 93104 Z= 0.494 Chirality : 0.043 0.283 11022 Planarity : 0.008 0.109 10054 Dihedral : 17.098 179.662 14361 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.98 % Favored : 92.64 % Rotamer: Outliers : 1.73 % Allowed : 11.75 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.16 % 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: -1.21 (0.10), residues: 6604 helix: 0.28 (0.10), residues: 2669 sheet: -1.02 (0.15), residues: 996 loop : -1.71 (0.11), residues: 2939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 506 HIS 0.011 0.001 HIS D 563 PHE 0.025 0.002 PHE i 26 TYR 0.024 0.002 TYR E 263 ARG 0.007 0.000 ARG B 198 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13208 Ramachandran restraints generated. 6604 Oldfield, 0 Emsley, 6604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13208 Ramachandran restraints generated. 6604 Oldfield, 0 Emsley, 6604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 6237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 445 time to evaluate : 6.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 37 residues processed: 521 average time/residue: 0.5964 time to fit residues: 543.2758 Evaluate side-chains 405 residues out of total 6237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 368 time to evaluate : 5.123 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 37 outliers final: 1 residues processed: 37 average time/residue: 0.4701 time to fit residues: 39.9095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 636 optimal weight: 0.9980 chunk 484 optimal weight: 2.9990 chunk 334 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 307 optimal weight: 20.0000 chunk 432 optimal weight: 20.0000 chunk 646 optimal weight: 2.9990 chunk 684 optimal weight: 4.9990 chunk 337 optimal weight: 9.9990 chunk 612 optimal weight: 3.9990 chunk 184 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 ASN ** D 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 ASN E 19 ASN E 125 GLN ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 399 GLN ** E 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 ASN ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 ASN G 202 GLN ** G 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 216 GLN O 311 ASN ** O 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 695 ASN ** O 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 696 ASN ** P 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 993 HIS ** P1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1236 ASN ** P1325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 168 ASN R 59 ASN T 28 ASN T 90 GLN ** T 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 77 HIS W 85 ASN Z 37 ASN b 5 GLN ** d 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 28 HIS t 35 GLN ** v 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4546 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 67177 Z= 0.340 Angle : 0.912 13.468 93104 Z= 0.520 Chirality : 0.045 0.323 11022 Planarity : 0.008 0.109 10054 Dihedral : 17.102 174.350 14361 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 20.29 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.43 % Favored : 92.16 % Rotamer: Outliers : 2.95 % Allowed : 12.73 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.14 % 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: -1.08 (0.10), residues: 6604 helix: 0.41 (0.10), residues: 2674 sheet: -0.88 (0.16), residues: 930 loop : -1.68 (0.11), residues: 3000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP P 535 HIS 0.014 0.002 HIS D 563 PHE 0.039 0.002 PHE E 299 TYR 0.052 0.002 TYR T 60 ARG 0.008 0.001 ARG F 377 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13208 Ramachandran restraints generated. 6604 Oldfield, 0 Emsley, 6604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13208 Ramachandran restraints generated. 6604 Oldfield, 0 Emsley, 6604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 6237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 374 time to evaluate : 5.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 172 outliers final: 88 residues processed: 514 average time/residue: 0.5775 time to fit residues: 528.4918 Evaluate side-chains 425 residues out of total 6237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 337 time to evaluate : 5.203 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 0 residues processed: 88 average time/residue: 0.4806 time to fit residues: 87.4975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 569 optimal weight: 2.9990 chunk 388 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 509 optimal weight: 0.6980 chunk 282 optimal weight: 10.0000 chunk 583 optimal weight: 7.9990 chunk 473 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 349 optimal weight: 30.0000 chunk 614 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 GLN F 375 ASN G 245 GLN G 292 ASN ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 311 ASN ** O 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 570 GLN ** O 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 887 ASN ** O 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 382 GLN ** P 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 547 ASN ** P 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 68 GLN e 86 ASN v 15 GLN ** x 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4544 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 67177 Z= 0.286 Angle : 0.858 13.437 93104 Z= 0.495 Chirality : 0.043 0.380 11022 Planarity : 0.008 0.109 10054 Dihedral : 17.029 175.737 14361 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.30 % Favored : 92.34 % Rotamer: Outliers : 1.79 % Allowed : 14.36 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.12 % 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: -0.94 (0.10), residues: 6604 helix: 0.60 (0.10), residues: 2687 sheet: -0.92 (0.16), residues: 954 loop : -1.67 (0.11), residues: 2963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 506 HIS 0.012 0.001 HIS D 563 PHE 0.047 0.002 PHE i 26 TYR 0.025 0.002 TYR W 140 ARG 0.008 0.001 ARG D 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13208 Ramachandran restraints generated. 6604 Oldfield, 0 Emsley, 6604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13208 Ramachandran restraints generated. 6604 Oldfield, 0 Emsley, 6604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 6237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 355 time to evaluate : 5.146 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 outliers start: 104 outliers final: 40 residues processed: 439 average time/residue: 0.5856 time to fit residues: 455.2799 Evaluate side-chains 361 residues out of total 6237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 321 time to evaluate : 5.106 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.4890 time to fit residues: 44.0165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 230 optimal weight: 0.7980 chunk 616 optimal weight: 5.9990 chunk 135 optimal weight: 0.7980 chunk 401 optimal weight: 8.9990 chunk 168 optimal weight: 0.8980 chunk 685 optimal weight: 30.0000 chunk 568 optimal weight: 10.0000 chunk 317 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 226 optimal weight: 40.0000 chunk 359 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 GLN ** D 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 ASN ** D 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 597 GLN ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 311 ASN O 633 ASN O 853 HIS O 917 ASN O 940 ASN ** P 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 740 ASN ** P 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 168 ASN T 90 GLN ** T 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 54 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4449 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 67177 Z= 0.166 Angle : 0.808 13.305 93104 Z= 0.471 Chirality : 0.041 0.339 11022 Planarity : 0.007 0.108 10054 Dihedral : 16.851 178.003 14361 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.90 % Favored : 92.76 % Rotamer: Outliers : 1.43 % Allowed : 15.18 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.11 % 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: -0.66 (0.10), residues: 6604 helix: 0.91 (0.10), residues: 2703 sheet: -0.76 (0.16), residues: 997 loop : -1.63 (0.11), residues: 2904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 506 HIS 0.008 0.001 HIS P1078 PHE 0.035 0.002 PHE E 94 TYR 0.040 0.001 TYR E 60 ARG 0.005 0.000 ARG d 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13208 Ramachandran restraints generated. 6604 Oldfield, 0 Emsley, 6604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13208 Ramachandran restraints generated. 6604 Oldfield, 0 Emsley, 6604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 6237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 395 time to evaluate : 5.205 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 outliers start: 83 outliers final: 36 residues processed: 461 average time/residue: 0.6169 time to fit residues: 506.3363 Evaluate side-chains 373 residues out of total 6237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 337 time to evaluate : 5.469 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.5150 time to fit residues: 42.6827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 660 optimal weight: 5.9990 chunk 77 optimal weight: 0.0670 chunk 390 optimal weight: 7.9990 chunk 500 optimal weight: 9.9990 chunk 387 optimal weight: 0.3980 chunk 576 optimal weight: 20.0000 chunk 382 optimal weight: 6.9990 chunk 682 optimal weight: 3.9990 chunk 427 optimal weight: 30.0000 chunk 416 optimal weight: 7.9990 chunk 315 optimal weight: 8.9990 overall best weight: 3.4924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 GLN ** D 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 ASN ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 381 ASN ** E 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 508 GLN ** F 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 207 HIS ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 311 ASN ** O 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 14 ASN h 83 GLN i 51 ASN v 15 GLN ** x 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4600 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 67177 Z= 0.361 Angle : 0.891 13.476 93104 Z= 0.508 Chirality : 0.044 0.370 11022 Planarity : 0.008 0.110 10054 Dihedral : 16.944 179.831 14361 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.84 % Favored : 91.82 % Rotamer: Outliers : 1.22 % Allowed : 16.23 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.12 % 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: -0.84 (0.10), residues: 6604 helix: 0.71 (0.10), residues: 2708 sheet: -0.93 (0.16), residues: 965 loop : -1.63 (0.11), residues: 2931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP P1139 HIS 0.017 0.001 HIS D 563 PHE 0.054 0.002 PHE E 94 TYR 0.036 0.002 TYR E 112 ARG 0.006 0.001 ARG E 57 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13208 Ramachandran restraints generated. 6604 Oldfield, 0 Emsley, 6604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13208 Ramachandran restraints generated. 6604 Oldfield, 0 Emsley, 6604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 6237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 329 time to evaluate : 5.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 38 residues processed: 383 average time/residue: 0.5828 time to fit residues: 399.9048 Evaluate side-chains 351 residues out of total 6237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 313 time to evaluate : 5.160 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.4780 time to fit residues: 41.4615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 422 optimal weight: 5.9990 chunk 272 optimal weight: 0.9980 chunk 407 optimal weight: 5.9990 chunk 205 optimal weight: 0.8980 chunk 134 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 433 optimal weight: 7.9990 chunk 464 optimal weight: 0.0070 chunk 337 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 536 optimal weight: 0.6980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 412 ASN ** D 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 375 ASN ** F 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 644 ASN O 917 ASN ** P 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 145 GLN Q 168 ASN ** T 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 85 ASN ** v 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4481 moved from start: 0.5255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 67177 Z= 0.169 Angle : 0.810 14.487 93104 Z= 0.471 Chirality : 0.040 0.385 11022 Planarity : 0.007 0.108 10054 Dihedral : 16.814 173.839 14361 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.77 % Favored : 92.91 % Rotamer: Outliers : 0.48 % Allowed : 16.92 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.08 % 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: -0.62 (0.10), residues: 6604 helix: 0.96 (0.10), residues: 2711 sheet: -0.85 (0.16), residues: 1001 loop : -1.59 (0.11), residues: 2892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP E 506 HIS 0.008 0.001 HIS E 140 PHE 0.025 0.001 PHE E 94 TYR 0.029 0.001 TYR E 60 ARG 0.007 0.000 ARG O 440 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13208 Ramachandran restraints generated. 6604 Oldfield, 0 Emsley, 6604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13208 Ramachandran restraints generated. 6604 Oldfield, 0 Emsley, 6604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 6237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 356 time to evaluate : 5.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 13 residues processed: 375 average time/residue: 0.6049 time to fit residues: 405.8446 Evaluate side-chains 343 residues out of total 6237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 330 time to evaluate : 5.202 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.5172 time to fit residues: 19.4706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 620 optimal weight: 1.9990 chunk 653 optimal weight: 2.9990 chunk 596 optimal weight: 4.9990 chunk 635 optimal weight: 0.0670 chunk 382 optimal weight: 6.9990 chunk 277 optimal weight: 10.0000 chunk 499 optimal weight: 20.0000 chunk 195 optimal weight: 3.9990 chunk 574 optimal weight: 1.9990 chunk 601 optimal weight: 0.9980 chunk 633 optimal weight: 0.9980 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN ** F 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 311 ASN ** O 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1236 ASN ** P1325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4506 moved from start: 0.5397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 67177 Z= 0.193 Angle : 0.821 15.985 93104 Z= 0.474 Chirality : 0.040 0.298 11022 Planarity : 0.007 0.109 10054 Dihedral : 16.737 175.470 14361 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.19 % Favored : 92.49 % Rotamer: Outliers : 0.34 % Allowed : 17.52 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.06 % 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: -0.53 (0.10), residues: 6604 helix: 1.04 (0.10), residues: 2716 sheet: -0.75 (0.16), residues: 975 loop : -1.56 (0.11), residues: 2913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP E 506 HIS 0.009 0.001 HIS D 563 PHE 0.027 0.001 PHE Q 194 TYR 0.026 0.001 TYR E 487 ARG 0.008 0.000 ARG O 443 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13208 Ramachandran restraints generated. 6604 Oldfield, 0 Emsley, 6604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13208 Ramachandran restraints generated. 6604 Oldfield, 0 Emsley, 6604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 6237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 342 time to evaluate : 5.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 353 average time/residue: 0.6012 time to fit residues: 376.8382 Evaluate side-chains 330 residues out of total 6237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 322 time to evaluate : 5.136 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.5437 time to fit residues: 14.9993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 417 optimal weight: 9.9990 chunk 672 optimal weight: 8.9990 chunk 410 optimal weight: 5.9990 chunk 318 optimal weight: 20.0000 chunk 467 optimal weight: 5.9990 chunk 705 optimal weight: 30.0000 chunk 649 optimal weight: 0.9990 chunk 561 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 433 optimal weight: 20.0000 chunk 344 optimal weight: 50.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 GLN ** G 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 311 ASN O 407 HIS ** O 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 882 ASN ** P 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 601 GLN P 742 HIS ** P 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1236 ASN ** P1325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 62 ASN T 90 GLN ** T 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 85 ASN d 12 ASN ** d 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 43 GLN d 58 HIS f 14 ASN ** f 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 90 ASN u 64 HIS ** x 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4700 moved from start: 0.5987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.113 67177 Z= 0.491 Angle : 0.996 15.652 93104 Z= 0.557 Chirality : 0.048 0.532 11022 Planarity : 0.009 0.111 10054 Dihedral : 17.119 173.323 14361 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 23.20 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.51 % Favored : 91.14 % Rotamer: Outliers : 0.45 % Allowed : 17.54 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.16 % 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: -1.16 (0.10), residues: 6604 helix: 0.38 (0.10), residues: 2675 sheet: -0.99 (0.16), residues: 968 loop : -1.77 (0.11), residues: 2961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP E 506 HIS 0.027 0.002 HIS D 563 PHE 0.049 0.003 PHE E 447 TYR 0.039 0.003 TYR E 112 ARG 0.009 0.001 ARG i 97 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13208 Ramachandran restraints generated. 6604 Oldfield, 0 Emsley, 6604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13208 Ramachandran restraints generated. 6604 Oldfield, 0 Emsley, 6604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 6237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 316 time to evaluate : 5.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 15 residues processed: 336 average time/residue: 0.6012 time to fit residues: 356.4595 Evaluate side-chains 313 residues out of total 6237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 298 time to evaluate : 5.118 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.4711 time to fit residues: 20.3626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 446 optimal weight: 7.9990 chunk 598 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 517 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 562 optimal weight: 3.9990 chunk 235 optimal weight: 6.9990 chunk 577 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 563 HIS ** D 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 311 ASN ** O 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 601 GLN ** P 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 33 ASN S 62 ASN ** T 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 476 ASN W 97 ASN d 43 GLN ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN v 15 GLN ** x 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.148293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.134568 restraints weight = 287971.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.131727 restraints weight = 459665.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.128825 restraints weight = 474124.617| |-----------------------------------------------------------------------------| r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4221 r_free = 0.4221 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4221 r_free = 0.4221 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5706 moved from start: 0.6135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 67177 Z= 0.306 Angle : 0.881 15.806 93104 Z= 0.504 Chirality : 0.043 0.355 11022 Planarity : 0.008 0.109 10054 Dihedral : 17.045 178.490 14361 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.84 % Favored : 91.84 % Rotamer: Outliers : 0.50 % Allowed : 17.31 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.12 % 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: -1.01 (0.10), residues: 6604 helix: 0.58 (0.10), residues: 2688 sheet: -0.97 (0.16), residues: 952 loop : -1.74 (0.11), residues: 2964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP E 506 HIS 0.015 0.001 HIS W 77 PHE 0.030 0.002 PHE Q 194 TYR 0.027 0.002 TYR E 112 ARG 0.007 0.001 ARG D 378 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10946.13 seconds wall clock time: 196 minutes 42.70 seconds (11802.70 seconds total)