Starting phenix.real_space_refine on Sun Mar 17 05:34:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mq0_3541/03_2024/5mq0_3541_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mq0_3541/03_2024/5mq0_3541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mq0_3541/03_2024/5mq0_3541.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mq0_3541/03_2024/5mq0_3541.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mq0_3541/03_2024/5mq0_3541_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mq0_3541/03_2024/5mq0_3541_neut_updated.pdb" } resolution = 4.17 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 2 8.98 5 Zn 6 6.06 5 P 457 5.49 5 Mg 3 5.21 5 S 209 5.16 5 C 47117 2.51 5 N 13955 2.21 5 O 15692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 284": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A GLU 624": "OE1" <-> "OE2" Residue "A ARG 668": "NH1" <-> "NH2" Residue "A ARG 749": "NH1" <-> "NH2" Residue "A ARG 775": "NH1" <-> "NH2" Residue "A ARG 780": "NH1" <-> "NH2" Residue "A ARG 1163": "NH1" <-> "NH2" Residue "A ARG 1442": "NH1" <-> "NH2" Residue "A ARG 1650": "NH1" <-> "NH2" Residue "A ARG 1962": "NH1" <-> "NH2" Residue "C ARG 120": "NH1" <-> "NH2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 401": "NH1" <-> "NH2" Residue "C ARG 430": "NH1" <-> "NH2" Residue "C ARG 500": "NH1" <-> "NH2" Residue "C TYR 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 938": "NH1" <-> "NH2" Residue "H PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 349": "NH1" <-> "NH2" Residue "H ARG 382": "NH1" <-> "NH2" Residue "H ARG 439": "NH1" <-> "NH2" Residue "J ARG 143": "NH1" <-> "NH2" Residue "J ARG 186": "NH1" <-> "NH2" Residue "J TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 47": "NH1" <-> "NH2" Residue "K ARG 88": "NH1" <-> "NH2" Residue "K ARG 184": "NH1" <-> "NH2" Residue "K ARG 185": "NH1" <-> "NH2" Residue "K ARG 220": "NH1" <-> "NH2" Residue "L ARG 3": "NH1" <-> "NH2" Residue "L ARG 7": "NH1" <-> "NH2" Residue "L ARG 61": "NH1" <-> "NH2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 63": "NH1" <-> "NH2" Residue "M ARG 121": "NH1" <-> "NH2" Residue "M ARG 131": "NH1" <-> "NH2" Residue "M ARG 161": "NH1" <-> "NH2" Residue "M ARG 166": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 79": "NH1" <-> "NH2" Residue "N ARG 111": "NH1" <-> "NH2" Residue "N ARG 252": "NH1" <-> "NH2" Residue "N ARG 261": "NH1" <-> "NH2" Residue "O ARG 104": "NH1" <-> "NH2" Residue "O ARG 158": "NH1" <-> "NH2" Residue "O ARG 169": "NH1" <-> "NH2" Residue "O ARG 189": "NH1" <-> "NH2" Residue "P ARG 6": "NH1" <-> "NH2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "R ARG 22": "NH1" <-> "NH2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "S ARG 82": "NH1" <-> "NH2" Residue "S ARG 219": "NH1" <-> "NH2" Residue "a ARG 80": "NH1" <-> "NH2" Residue "c ARG 170": "NH1" <-> "NH2" Residue "o ARG 60": "NH1" <-> "NH2" Residue "o ARG 63": "NH1" <-> "NH2" Residue "o ARG 278": "NH1" <-> "NH2" Residue "o TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 396": "NH1" <-> "NH2" Residue "y ARG 110": "NH1" <-> "NH2" Residue "b ARG 11": "NH1" <-> "NH2" Residue "f ARG 82": "NH1" <-> "NH2" Residue "g ARG 30": "NH1" <-> "NH2" Residue "h ARG 88": "NH1" <-> "NH2" Residue "j ARG 63": "NH1" <-> "NH2" Residue "j ARG 97": "NH1" <-> "NH2" Residue "k GLU 50": "OE1" <-> "OE2" Residue "k GLU 90": "OE1" <-> "OE2" Residue "l GLU 13": "OE1" <-> "OE2" Residue "l ARG 88": "NH1" <-> "NH2" Residue "m ARG 63": "NH1" <-> "NH2" Residue "m GLU 70": "OE1" <-> "OE2" Residue "m ARG 97": "NH1" <-> "NH2" Residue "r TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 30": "NH1" <-> "NH2" Residue "q ARG 82": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 77441 Number of models: 1 Model: "" Number of chains: 52 Chain: "I" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 714 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 13, 'rna3p_pyr': 18} Link IDs: {'rna2p': 3, 'rna3p': 30} Chain breaks: 1 Chain: "E" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 346 Classifications: {'RNA': 16} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 3} Link IDs: {'rna2p': 5, 'rna3p': 10} Chain: "2" Number of atoms: 3271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 3271 Classifications: {'RNA': 155} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 10, 'rna3p_pur': 64, 'rna3p_pyr': 78} Link IDs: {'rna2p': 13, 'rna3p': 141} Chain breaks: 8 Chain: "6" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 2108 Classifications: {'RNA': 99} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 12, 'rna3p_pur': 45, 'rna3p_pyr': 34} Link IDs: {'rna2p': 20, 'rna3p': 78} Chain breaks: 1 Chain: "5" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2999 Classifications: {'RNA': 141} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 7, 'rna3p_pur': 59, 'rna3p_pyr': 61} Link IDs: {'rna2p': 20, 'rna3p': 120} Chain breaks: 2 Chain: "A" Number of atoms: 15199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1914, 15199 Classifications: {'peptide': 1914} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 162} Link IDs: {'PCIS': 2, 'PTRANS': 98, 'TRANS': 1813} Chain breaks: 3 Unresolved non-hydrogen bonds: 604 Unresolved non-hydrogen angles: 747 Unresolved non-hydrogen dihedrals: 469 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 28, 'PHE:plan': 1, 'GLU:plan': 69, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 459 Chain: "C" Number of atoms: 6562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 874, 6562 Classifications: {'peptide': 874} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PTRANS': 49, 'TRANS': 824} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 439 Unresolved non-hydrogen angles: 529 Unresolved non-hydrogen dihedrals: 369 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 16, 'PHE:plan': 1, 'GLU:plan': 37, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 283 Chain: "H" Number of atoms: 3261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3261 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 394} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "J" Number of atoms: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2690 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 12, 'TRANS': 329} Chain: "K" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1458 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "L" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1162 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 4, 'TRANS': 150} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ARG:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 76 Chain: "M" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2016 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 241} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "N" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1798 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "O" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1755 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 6, 'TRANS': 204} Chain breaks: 1 Chain: "P" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 565 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 614 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 1, 'TRANS': 106} Chain breaks: 1 Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 320 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 14, 'ARG:plan': 9, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 13, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 173 Chain: "S" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3229 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 201} Link IDs: {'PTRANS': 8, 'TRANS': 459} Chain breaks: 14 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 853 Unresolved non-hydrogen angles: 1096 Unresolved non-hydrogen dihedrals: 742 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 17, 'ASN:plan1': 5, 'TRP:plan': 8, 'ASP:plan': 12, 'PHE:plan': 11, 'GLU:plan': 25, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 513 Chain: "T" Number of atoms: 3154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 3154 Classifications: {'peptide': 633} Incomplete info: {'truncation_to_alanine': 585} Link IDs: {'PTRANS': 14, 'TRANS': 618} Chain breaks: 28 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 2259 Unresolved non-hydrogen angles: 2913 Unresolved non-hydrogen dihedrals: 1928 Unresolved non-hydrogen chiralities: 178 Planarities with less than four sites: {'GLN:plan1': 23, 'HIS:plan': 8, 'UNK:plan-1': 18, 'TYR:plan': 33, 'ASN:plan1': 23, 'TRP:plan': 19, 'ASP:plan': 30, 'PHE:plan': 31, 'GLU:plan': 62, 'ARG:plan': 35} Unresolved non-hydrogen planarities: 1320 Chain: "a" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1119 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "c" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 786 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain breaks: 2 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 75 Planarities with less than four sites: {'GLU:plan': 8, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 60 Chain: "o" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2425 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 296} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 58 Chain: "X" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 338 Classifications: {'peptide': 68} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 66} Link IDs: {'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 68} Unresolved non-hydrogen planarities: 68 Chain: "y" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 679 Classifications: {'peptide': 83} Link IDs: {'TRANS': 82} Chain breaks: 2 Chain: "b" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 631 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "d" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 625 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "e" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "f" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 573 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 69} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "g" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 529 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "h" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain breaks: 1 Chain: "j" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 741 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "V" Number of atoms: 3189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 3189 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 569} Link IDs: {'PTRANS': 30, 'TRANS': 614} Chain breaks: 1 Unresolved chain link angles: 30 Unresolved non-hydrogen bonds: 2019 Unresolved non-hydrogen angles: 2575 Unresolved non-hydrogen dihedrals: 1674 Unresolved non-hydrogen chiralities: 189 Planarities with less than four sites: {'GLN:plan1': 30, 'HIS:plan': 15, 'TYR:plan': 29, 'ASN:plan1': 25, 'TRP:plan': 2, 'ASP:plan': 35, 'PHE:plan': 25, 'GLU:plan': 40, 'ARG:plan': 30} Unresolved non-hydrogen planarities: 1056 Chain: "k" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 631 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "l" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 618 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "m" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 89} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "n" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 625 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "r" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 526 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "W" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 816 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 541 Unresolved non-hydrogen angles: 694 Unresolved non-hydrogen dihedrals: 429 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 14, 'TYR:plan': 4, 'ASN:plan1': 14, 'HIS:plan': 7, 'PHE:plan': 4, 'GLU:plan': 8, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 294 Chain: "Y" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 416 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 345 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 1, 'PHE:plan': 8, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 145 Chain: "p" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "q" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 573 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 69} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "3" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'RNA': 3} Modifications used: {'rna3p_pyr': 3} Link IDs: {'rna3p': 2} Chain: "s" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 548 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 401 Unresolved non-hydrogen angles: 514 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 237 Chain: "t" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 2171 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 395} Link IDs: {'PTRANS': 20, 'TRANS': 417} Chain breaks: 5 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1372 Unresolved non-hydrogen angles: 1761 Unresolved non-hydrogen dihedrals: 1142 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 5, 'TYR:plan': 21, 'ASN:plan1': 25, 'TRP:plan': 6, 'ASP:plan': 35, 'PHE:plan': 12, 'GLU:plan': 27, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 708 Chain: "u" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 578 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 444 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 155 Chain: "v" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 588 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 355 Unresolved non-hydrogen angles: 446 Unresolved non-hydrogen dihedrals: 288 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 155 Chain: "w" Number of atoms: 2156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 2156 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 392} Link IDs: {'PTRANS': 20, 'TRANS': 414} Chain breaks: 5 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1365 Unresolved non-hydrogen angles: 1753 Unresolved non-hydrogen dihedrals: 1136 Unresolved non-hydrogen chiralities: 129 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 5, 'TYR:plan': 21, 'ASN:plan1': 25, 'TRP:plan': 6, 'ASP:plan': 35, 'PHE:plan': 12, 'GLU:plan': 27, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 700 Chain: "6" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 2, ' MG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 39416 SG CYS L 104 174.825 184.199 99.661 1.00 75.41 S ATOM 39422 SG CYS L 105 171.484 184.196 102.152 1.00 94.62 S ATOM 39447 SG CYS L 108 174.592 181.531 101.558 1.00 75.02 S ATOM 39727 SG CYS L 148 172.421 182.236 98.785 1.00 84.39 S ATOM 39416 SG CYS L 104 174.825 184.199 99.661 1.00 75.41 S ATOM 39546 SG CYS L 122 177.833 181.020 99.531 1.00 79.14 S ATOM 39737 SG CYS L 150 176.230 182.600 96.606 1.00 83.92 S ATOM 39752 SG CYS L 153 177.808 184.783 98.534 1.00108.43 S ATOM 39447 SG CYS L 108 174.592 181.531 101.558 1.00 75.02 S ATOM 39532 SG CYS L 120 177.038 178.718 101.049 1.00 81.56 S ATOM 39546 SG CYS L 122 177.833 181.020 99.531 1.00 79.14 S ATOM 39704 SG CYS L 145 174.170 178.576 99.287 1.00 99.48 S ATOM 40337 SG CYS M 73 167.095 160.151 87.995 1.00 81.57 S ATOM 40399 SG CYS M 81 165.790 163.175 86.354 1.00 83.60 S ATOM 40439 SG CYS M 87 169.068 163.374 88.583 1.00106.84 S ATOM 42021 SG CYS N 34 170.190 146.082 113.528 1.00 79.22 S ATOM 42044 SG CYS N 37 170.308 144.168 116.076 1.00 94.61 S ATOM 42243 SG CYS N 61 173.325 145.867 116.331 1.00 90.51 S ATOM 42267 SG CYS N 64 173.135 143.053 114.643 1.00101.83 S ATOM 41863 SG CYS N 13 186.031 148.469 105.552 1.00136.95 S ATOM 41887 SG CYS N 16 183.206 150.992 104.415 1.00150.78 S ATOM 42321 SG CYS N 71 182.398 148.333 107.330 1.00119.28 S ATOM 42342 SG CYS N 74 183.285 148.546 103.872 1.00120.09 S Time building chain proxies: 31.41, per 1000 atoms: 0.41 Number of scatterers: 77441 At special positions: 0 Unit cell: (290.29, 286, 247.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 6 29.99 K 2 19.00 S 209 16.00 P 457 15.00 Mg 3 11.99 O 15692 8.00 N 13955 7.00 C 47117 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 3992 O4' G 21149 .*. O " rejected from bonding due to valence issues. Atom "ATOM 3992 O4' G 21149 .*. O " rejected from bonding due to valence issues. Atom "ATOM 3992 O4' G 21149 .*. O " rejected from bonding due to valence issues. Atom "ATOM 3992 O4' G 21149 .*. O " rejected from bonding due to valence issues. Atom "ATOM 3989 O5' G 21149 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 28.76 Conformation dependent library (CDL) restraints added in 10.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L1000 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 104 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 148 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 108 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 105 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 104 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 150 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 122 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 153 " pdb=" ZN L1002 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 108 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 122 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 120 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 145 " pdb=" ZN M1000 " pdb="ZN ZN M1000 " - pdb=" NE2 HIS M 91 " pdb="ZN ZN M1000 " - pdb=" SG CYS M 73 " pdb="ZN ZN M1000 " - pdb=" SG CYS M 87 " pdb="ZN ZN M1000 " - pdb=" SG CYS M 81 " pdb=" ZN N 401 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 34 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 64 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 37 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 61 " pdb=" ZN N 402 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 71 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 16 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 74 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 13 " Number of angles added : 33 18814 Ramachandran restraints generated. 9407 Oldfield, 0 Emsley, 9407 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18678 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 333 helices and 93 sheets defined 41.7% alpha, 10.6% beta 140 base pairs and 235 stacking pairs defined. Time for finding SS restraints: 32.59 Creating SS restraints... Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 156 through 177 removed outlier: 4.397A pdb=" N LYS A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TYR A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 210 through 230 Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 305 through 317 Proline residue: A 317 - end of helix Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 333 through 342 Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 388 through 391 No H-bonds generated for 'chain 'A' and resid 388 through 391' Processing helix chain 'A' and resid 473 through 481 removed outlier: 3.882A pdb=" N SER A 478 " --> pdb=" O LYS A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 507 Processing helix chain 'A' and resid 516 through 534 Processing helix chain 'A' and resid 547 through 553 Processing helix chain 'A' and resid 564 through 586 Processing helix chain 'A' and resid 607 through 613 Processing helix chain 'A' and resid 619 through 640 Processing helix chain 'A' and resid 646 through 658 Processing helix chain 'A' and resid 660 through 663 No H-bonds generated for 'chain 'A' and resid 660 through 663' Processing helix chain 'A' and resid 666 through 669 No H-bonds generated for 'chain 'A' and resid 666 through 669' Processing helix chain 'A' and resid 671 through 691 removed outlier: 4.011A pdb=" N TYR A 688 " --> pdb=" O HIS A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 734 Proline residue: A 720 - end of helix Processing helix chain 'A' and resid 750 through 769 Processing helix chain 'A' and resid 776 through 795 removed outlier: 3.705A pdb=" N THR A 781 " --> pdb=" O LYS A 777 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 782 " --> pdb=" O LYS A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 836 Processing helix chain 'A' and resid 842 through 869 Processing helix chain 'A' and resid 876 through 893 Processing helix chain 'A' and resid 908 through 925 removed outlier: 3.717A pdb=" N VAL A 922 " --> pdb=" O ASP A 918 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N SER A 925 " --> pdb=" O ASP A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 945 Processing helix chain 'A' and resid 947 through 960 Processing helix chain 'A' and resid 986 through 1006 removed outlier: 3.714A pdb=" N THR A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1034 Processing helix chain 'A' and resid 1063 through 1073 Processing helix chain 'A' and resid 1076 through 1086 Processing helix chain 'A' and resid 1109 through 1135 removed outlier: 3.940A pdb=" N GLY A1127 " --> pdb=" O LEU A1124 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLN A1128 " --> pdb=" O LEU A1125 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU A1129 " --> pdb=" O LEU A1126 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG A1130 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA A1131 " --> pdb=" O GLN A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1155 Processing helix chain 'A' and resid 1176 through 1189 Processing helix chain 'A' and resid 1217 through 1233 Processing helix chain 'A' and resid 1243 through 1245 No H-bonds generated for 'chain 'A' and resid 1243 through 1245' Processing helix chain 'A' and resid 1306 through 1320 Processing helix chain 'A' and resid 1328 through 1345 Processing helix chain 'A' and resid 1348 through 1350 No H-bonds generated for 'chain 'A' and resid 1348 through 1350' Processing helix chain 'A' and resid 1354 through 1374 Processing helix chain 'A' and resid 1386 through 1389 No H-bonds generated for 'chain 'A' and resid 1386 through 1389' Processing helix chain 'A' and resid 1392 through 1394 No H-bonds generated for 'chain 'A' and resid 1392 through 1394' Processing helix chain 'A' and resid 1412 through 1415 No H-bonds generated for 'chain 'A' and resid 1412 through 1415' Processing helix chain 'A' and resid 1441 through 1443 No H-bonds generated for 'chain 'A' and resid 1441 through 1443' Processing helix chain 'A' and resid 1447 through 1471 Processing helix chain 'A' and resid 1483 through 1485 No H-bonds generated for 'chain 'A' and resid 1483 through 1485' Processing helix chain 'A' and resid 1491 through 1494 Processing helix chain 'A' and resid 1499 through 1504 removed outlier: 5.396A pdb=" N TYR A1504 " --> pdb=" O HIS A1500 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1515 Processing helix chain 'A' and resid 1530 through 1533 No H-bonds generated for 'chain 'A' and resid 1530 through 1533' Processing helix chain 'A' and resid 1540 through 1549 Processing helix chain 'A' and resid 1552 through 1559 removed outlier: 4.180A pdb=" N GLU A1558 " --> pdb=" O GLU A1554 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HIS A1559 " --> pdb=" O THR A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1562 through 1565 No H-bonds generated for 'chain 'A' and resid 1562 through 1565' Processing helix chain 'A' and resid 1571 through 1573 No H-bonds generated for 'chain 'A' and resid 1571 through 1573' Processing helix chain 'A' and resid 1602 through 1609 removed outlier: 3.857A pdb=" N PHE A1606 " --> pdb=" O PRO A1602 " (cutoff:3.500A) Processing helix chain 'A' and resid 1611 through 1614 No H-bonds generated for 'chain 'A' and resid 1611 through 1614' Processing helix chain 'A' and resid 1639 through 1648 Processing helix chain 'A' and resid 1653 through 1671 Processing helix chain 'A' and resid 1688 through 1691 Processing helix chain 'A' and resid 1749 through 1759 Processing helix chain 'A' and resid 1795 through 1808 Processing helix chain 'A' and resid 1810 through 1822 Processing helix chain 'A' and resid 1841 through 1843 No H-bonds generated for 'chain 'A' and resid 1841 through 1843' Processing helix chain 'A' and resid 1896 through 1900 Processing helix chain 'A' and resid 1905 through 1923 removed outlier: 3.668A pdb=" N LYS A1910 " --> pdb=" O SER A1906 " (cutoff:3.500A) Processing helix chain 'A' and resid 1941 through 1950 removed outlier: 3.806A pdb=" N VAL A1946 " --> pdb=" O ASP A1942 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASP A1950 " --> pdb=" O VAL A1946 " (cutoff:3.500A) Processing helix chain 'A' and resid 1967 through 1970 Processing helix chain 'A' and resid 1972 through 1980 Processing helix chain 'A' and resid 1994 through 1998 Processing helix chain 'A' and resid 2001 through 2017 Processing helix chain 'A' and resid 2019 through 2026 Processing helix chain 'A' and resid 2045 through 2066 Processing helix chain 'A' and resid 2075 through 2083 Processing helix chain 'A' and resid 2091 through 2099 Processing helix chain 'C' and resid 120 through 128 Processing helix chain 'C' and resid 146 through 157 Processing helix chain 'C' and resid 166 through 170 Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 221 through 231 Processing helix chain 'C' and resid 247 through 259 Processing helix chain 'C' and resid 270 through 275 Processing helix chain 'C' and resid 281 through 298 Processing helix chain 'C' and resid 324 through 331 Processing helix chain 'C' and resid 339 through 348 removed outlier: 3.878A pdb=" N ASP C 342 " --> pdb=" O SER C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 376 Processing helix chain 'C' and resid 378 through 390 Processing helix chain 'C' and resid 393 through 402 Processing helix chain 'C' and resid 410 through 414 removed outlier: 3.860A pdb=" N GLN C 414 " --> pdb=" O GLN C 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 410 through 414' Processing helix chain 'C' and resid 417 through 428 Processing helix chain 'C' and resid 434 through 444 Processing helix chain 'C' and resid 447 through 456 removed outlier: 3.548A pdb=" N ASP C 450 " --> pdb=" O GLU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 465 No H-bonds generated for 'chain 'C' and resid 463 through 465' Processing helix chain 'C' and resid 508 through 514 Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing helix chain 'C' and resid 583 through 588 Processing helix chain 'C' and resid 612 through 628 Proline residue: C 616 - end of helix Processing helix chain 'C' and resid 649 through 662 Processing helix chain 'C' and resid 717 through 724 removed outlier: 3.600A pdb=" N GLN C 721 " --> pdb=" O SER C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 755 Processing helix chain 'C' and resid 760 through 764 Processing helix chain 'C' and resid 782 through 785 No H-bonds generated for 'chain 'C' and resid 782 through 785' Processing helix chain 'C' and resid 793 through 804 Processing helix chain 'C' and resid 831 through 852 Proline residue: C 840 - end of helix Processing helix chain 'C' and resid 870 through 882 Proline residue: C 874 - end of helix Processing helix chain 'C' and resid 914 through 921 Processing helix chain 'C' and resid 962 through 974 Processing helix chain 'C' and resid 991 through 996 Processing helix chain 'H' and resid 12 through 31 Proline residue: H 27 - end of helix removed outlier: 3.826A pdb=" N SER H 30 " --> pdb=" O SER H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 removed outlier: 4.092A pdb=" N LEU H 37 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLN H 38 " --> pdb=" O ASP H 35 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLU H 39 " --> pdb=" O ASN H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 65 Processing helix chain 'H' and resid 72 through 86 Processing helix chain 'H' and resid 88 through 107 Processing helix chain 'H' and resid 111 through 126 Processing helix chain 'H' and resid 134 through 144 Processing helix chain 'H' and resid 152 through 164 removed outlier: 5.808A pdb=" N TRP H 160 " --> pdb=" O LYS H 156 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LYS H 161 " --> pdb=" O ILE H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 182 Processing helix chain 'H' and resid 188 through 203 removed outlier: 3.681A pdb=" N LYS H 203 " --> pdb=" O GLU H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 261 removed outlier: 3.810A pdb=" N THR H 252 " --> pdb=" O PHE H 248 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA H 254 " --> pdb=" O GLU H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 290 through 301 Processing helix chain 'H' and resid 305 through 314 Processing helix chain 'H' and resid 322 through 335 Processing helix chain 'H' and resid 341 through 353 Processing helix chain 'H' and resid 355 through 370 Processing helix chain 'H' and resid 372 through 375 Processing helix chain 'H' and resid 378 through 392 Processing helix chain 'H' and resid 416 through 430 Processing helix chain 'H' and resid 433 through 442 Processing helix chain 'H' and resid 458 through 467 Processing helix chain 'H' and resid 473 through 480 Processing helix chain 'J' and resid 111 through 120 Processing helix chain 'K' and resid 40 through 42 No H-bonds generated for 'chain 'K' and resid 40 through 42' Processing helix chain 'K' and resid 60 through 84 Processing helix chain 'K' and resid 88 through 91 Processing helix chain 'K' and resid 154 through 163 Proline residue: K 160 - end of helix Processing helix chain 'K' and resid 182 through 185 No H-bonds generated for 'chain 'K' and resid 182 through 185' Processing helix chain 'K' and resid 201 through 224 Processing helix chain 'L' and resid 14 through 33 removed outlier: 3.716A pdb=" N GLU L 17 " --> pdb=" O ASP L 14 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS L 18 " --> pdb=" O GLY L 15 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS L 20 " --> pdb=" O GLU L 17 " (cutoff:3.500A) Proline residue: L 21 - end of helix removed outlier: 3.690A pdb=" N THR L 24 " --> pdb=" O PRO L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 67 Processing helix chain 'L' and resid 75 through 84 Processing helix chain 'L' and resid 89 through 96 Processing helix chain 'L' and resid 106 through 109 Processing helix chain 'L' and resid 121 through 123 No H-bonds generated for 'chain 'L' and resid 121 through 123' Processing helix chain 'L' and resid 126 through 136 Processing helix chain 'M' and resid 55 through 58 No H-bonds generated for 'chain 'M' and resid 55 through 58' Processing helix chain 'M' and resid 63 through 67 Processing helix chain 'M' and resid 74 through 78 Processing helix chain 'M' and resid 84 through 86 No H-bonds generated for 'chain 'M' and resid 84 through 86' Processing helix chain 'M' and resid 96 through 102 Processing helix chain 'M' and resid 105 through 107 No H-bonds generated for 'chain 'M' and resid 105 through 107' Processing helix chain 'M' and resid 142 through 145 No H-bonds generated for 'chain 'M' and resid 142 through 145' Processing helix chain 'M' and resid 153 through 167 removed outlier: 3.655A pdb=" N ARG M 166 " --> pdb=" O PHE M 162 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU M 167 " --> pdb=" O VAL M 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 198 Processing helix chain 'M' and resid 232 through 253 removed outlier: 4.182A pdb=" N ARG M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 68 Processing helix chain 'N' and resid 84 through 93 Processing helix chain 'N' and resid 107 through 115 removed outlier: 4.013A pdb=" N ARG N 111 " --> pdb=" O ASP N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 127 removed outlier: 4.288A pdb=" N ILE N 125 " --> pdb=" O GLY N 121 " (cutoff:3.500A) Processing helix chain 'N' and resid 129 through 143 Processing helix chain 'N' and resid 216 through 225 Processing helix chain 'N' and resid 256 through 265 Processing helix chain 'N' and resid 307 through 323 Processing helix chain 'O' and resid 15 through 28 Processing helix chain 'O' and resid 33 through 39 Processing helix chain 'O' and resid 45 through 54 Processing helix chain 'O' and resid 67 through 79 Processing helix chain 'O' and resid 84 through 91 Processing helix chain 'O' and resid 95 through 106 Processing helix chain 'O' and resid 145 through 159 Processing helix chain 'O' and resid 165 through 194 Processing helix chain 'O' and resid 231 through 250 Processing helix chain 'P' and resid 15 through 19 Processing helix chain 'P' and resid 164 through 172 Processing helix chain 'R' and resid 11 through 14 No H-bonds generated for 'chain 'R' and resid 11 through 14' Processing helix chain 'R' and resid 26 through 30 Processing helix chain 'R' and resid 37 through 46 removed outlier: 3.588A pdb=" N GLN R 43 " --> pdb=" O ARG R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 86 Processing helix chain 'R' and resid 92 through 115 Processing helix chain 'S' and resid 40 through 60 Processing helix chain 'S' and resid 65 through 78 Processing helix chain 'S' and resid 81 through 94 Processing helix chain 'S' and resid 99 through 111 Processing helix chain 'S' and resid 115 through 128 Processing helix chain 'S' and resid 133 through 146 Processing helix chain 'S' and resid 149 through 162 Processing helix chain 'S' and resid 166 through 178 Processing helix chain 'S' and resid 185 through 195 Processing helix chain 'S' and resid 199 through 211 Processing helix chain 'S' and resid 215 through 231 Processing helix chain 'S' and resid 240 through 256 Processing helix chain 'S' and resid 260 through 273 Processing helix chain 'S' and resid 278 through 290 Processing helix chain 'S' and resid 296 through 314 Processing helix chain 'S' and resid 321 through 331 Processing helix chain 'S' and resid 335 through 348 Processing helix chain 'S' and resid 357 through 376 Processing helix chain 'S' and resid 382 through 394 Processing helix chain 'S' and resid 404 through 415 Processing helix chain 'S' and resid 420 through 431 removed outlier: 3.562A pdb=" N LYS S 425 " --> pdb=" O PRO S 421 " (cutoff:3.500A) Processing helix chain 'S' and resid 440 through 449 Processing helix chain 'S' and resid 453 through 466 Processing helix chain 'S' and resid 471 through 482 Processing helix chain 'S' and resid 486 through 499 Processing helix chain 'S' and resid 508 through 520 Processing helix chain 'S' and resid 531 through 540 Processing helix chain 'S' and resid 546 through 555 Processing helix chain 'T' and resid 22 through 32 Processing helix chain 'T' and resid 38 through 47 removed outlier: 3.727A pdb=" N TYR T 46 " --> pdb=" O ARG T 42 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TRP T 47 " --> pdb=" O TYR T 43 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 67 Processing helix chain 'T' and resid 72 through 82 Processing helix chain 'T' and resid 90 through 101 Processing helix chain 'T' and resid 108 through 120 Processing helix chain 'T' and resid 128 through 138 Processing helix chain 'T' and resid 145 through 158 Proline residue: T 150 - end of helix Processing helix chain 'T' and resid 175 through 190 Processing helix chain 'T' and resid 210 through 217 Processing helix chain 'T' and resid 225 through 237 Processing helix chain 'T' and resid 241 through 250 Processing helix chain 'T' and resid 271 through 281 Processing helix chain 'T' and resid 285 through 295 Processing helix chain 'T' and resid 301 through 313 Processing helix chain 'T' and resid 318 through 331 Processing helix chain 'T' and resid 340 through 364 removed outlier: 3.565A pdb=" N LYS T 362 " --> pdb=" O LEU T 358 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU T 363 " --> pdb=" O GLY T 359 " (cutoff:3.500A) Processing helix chain 'T' and resid 374 through 402 removed outlier: 3.855A pdb=" N TYR T 392 " --> pdb=" O LEU T 388 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ASP T 393 " --> pdb=" O ILE T 389 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ILE T 394 " --> pdb=" O ASN T 390 " (cutoff:3.500A) Processing helix chain 'T' and resid 408 through 419 removed outlier: 3.878A pdb=" N LYS T 419 " --> pdb=" O VAL T 415 " (cutoff:3.500A) Processing helix chain 'T' and resid 425 through 434 Processing helix chain 'T' and resid 436 through 439 No H-bonds generated for 'chain 'T' and resid 436 through 439' Processing helix chain 'T' and resid 450 through 460 Processing helix chain 'T' and resid 463 through 474 Processing helix chain 'T' and resid 484 through 496 removed outlier: 3.518A pdb=" N ARG T 494 " --> pdb=" O ASN T 490 " (cutoff:3.500A) Processing helix chain 'T' and resid 503 through 522 Proline residue: T 515 - end of helix Proline residue: T 518 - end of helix Processing helix chain 'T' and resid 542 through 554 Processing helix chain 'T' and resid 567 through 580 Processing helix chain 'T' and resid 586 through 596 Processing helix chain 'T' and resid 602 through 613 Proline residue: T 613 - end of helix Processing helix chain 'T' and resid 619 through 633 Processing helix chain 'T' and resid 642 through 654 Processing helix chain 'T' and resid 662 through 676 Processing helix chain 'T' and resid 681 through 692 Processing helix chain 'T' and resid 703 through 718 Processing helix chain 'T' and resid 724 through 734 Processing helix chain 'T' and resid 740 through 754 Processing helix chain 'T' and resid 759 through 770 Processing helix chain 'T' and resid 778 through 789 Processing helix chain 'T' and resid 1001 through 1016 Processing helix chain 'a' and resid 77 through 88 Processing helix chain 'a' and resid 107 through 126 Processing helix chain 'a' and resid 134 through 152 removed outlier: 4.052A pdb=" N ASP a 138 " --> pdb=" O GLU a 134 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS a 141 " --> pdb=" O LEU a 137 " (cutoff:3.500A) Proline residue: a 145 - end of helix removed outlier: 3.746A pdb=" N ARG a 152 " --> pdb=" O LEU a 148 " (cutoff:3.500A) Processing helix chain 'a' and resid 157 through 171 removed outlier: 3.559A pdb=" N SER a 162 " --> pdb=" O ASP a 158 " (cutoff:3.500A) Processing helix chain 'a' and resid 176 through 187 Processing helix chain 'a' and resid 226 through 245 Processing helix chain 'c' and resid 167 through 171 Processing helix chain 'c' and resid 180 through 195 removed outlier: 3.588A pdb=" N ASP c 192 " --> pdb=" O LYS c 188 " (cutoff:3.500A) Processing helix chain 'c' and resid 218 through 223 Processing helix chain 'c' and resid 295 through 312 Processing helix chain 'c' and resid 325 through 328 No H-bonds generated for 'chain 'c' and resid 325 through 328' Processing helix chain 'c' and resid 334 through 347 removed outlier: 3.711A pdb=" N LEU c 339 " --> pdb=" O TYR c 336 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS c 342 " --> pdb=" O LEU c 339 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN c 345 " --> pdb=" O LYS c 342 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU c 346 " --> pdb=" O ARG c 343 " (cutoff:3.500A) Processing helix chain 'o' and resid 53 through 59 Processing helix chain 'o' and resid 277 through 282 Processing helix chain 'X' and resid 7 through 14 Processing helix chain 'X' and resid 17 through 25 Processing helix chain 'X' and resid 93 through 128 removed outlier: 4.649A pdb=" N UNK X 107 " --> pdb=" O UNK X 103 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N UNK X 108 " --> pdb=" O UNK X 104 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N UNK X 117 " --> pdb=" O UNK X 113 " (cutoff:3.500A) Processing helix chain 'y' and resid 97 through 113 Processing helix chain 'y' and resid 158 through 183 Processing helix chain 'y' and resid 198 through 208 removed outlier: 3.509A pdb=" N GLN y 202 " --> pdb=" O ASP y 198 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 15 No H-bonds generated for 'chain 'b' and resid 13 through 15' Processing helix chain 'd' and resid 6 through 13 Processing helix chain 'd' and resid 66 through 68 No H-bonds generated for 'chain 'd' and resid 66 through 68' Processing helix chain 'e' and resid 13 through 23 Processing helix chain 'e' and resid 84 through 86 No H-bonds generated for 'chain 'e' and resid 84 through 86' Processing helix chain 'f' and resid 15 through 22 Processing helix chain 'h' and resid 3 through 9 Processing helix chain 'h' and resid 103 through 107 Processing helix chain 'j' and resid 16 through 28 Processing helix chain 'j' and resid 30 through 40 removed outlier: 3.993A pdb=" N ILE j 34 " --> pdb=" O MET j 31 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA j 37 " --> pdb=" O ILE j 34 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR j 40 " --> pdb=" O ALA j 37 " (cutoff:3.500A) Processing helix chain 'V' and resid 477 through 482 removed outlier: 3.912A pdb=" N THR V 482 " --> pdb=" O ALA V 478 " (cutoff:3.500A) Processing helix chain 'V' and resid 484 through 498 removed outlier: 5.436A pdb=" N SER V 490 " --> pdb=" O ALA V 487 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP V 498 " --> pdb=" O ALA V 495 " (cutoff:3.500A) Processing helix chain 'V' and resid 512 through 524 removed outlier: 4.541A pdb=" N THR V 517 " --> pdb=" O THR V 513 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN V 518 " --> pdb=" O THR V 514 " (cutoff:3.500A) Processing helix chain 'V' and resid 538 through 552 Processing helix chain 'V' and resid 581 through 590 removed outlier: 3.571A pdb=" N LEU V 590 " --> pdb=" O ARG V 586 " (cutoff:3.500A) Processing helix chain 'V' and resid 605 through 607 No H-bonds generated for 'chain 'V' and resid 605 through 607' Processing helix chain 'V' and resid 610 through 625 removed outlier: 3.601A pdb=" N LYS V 621 " --> pdb=" O ALA V 617 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ILE V 624 " --> pdb=" O LYS V 620 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS V 625 " --> pdb=" O LYS V 621 " (cutoff:3.500A) Processing helix chain 'V' and resid 641 through 646 Processing helix chain 'V' and resid 674 through 688 Processing helix chain 'V' and resid 701 through 717 Processing helix chain 'V' and resid 736 through 743 removed outlier: 3.933A pdb=" N LYS V 741 " --> pdb=" O GLU V 737 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE V 742 " --> pdb=" O ILE V 738 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N PHE V 743 " --> pdb=" O GLN V 739 " (cutoff:3.500A) Processing helix chain 'V' and resid 758 through 762 removed outlier: 3.973A pdb=" N THR V 762 " --> pdb=" O ILE V 759 " (cutoff:3.500A) Processing helix chain 'V' and resid 799 through 810 removed outlier: 4.239A pdb=" N ALA V 809 " --> pdb=" O ARG V 805 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY V 810 " --> pdb=" O LYS V 806 " (cutoff:3.500A) Processing helix chain 'V' and resid 823 through 828 Processing helix chain 'V' and resid 837 through 840 Processing helix chain 'V' and resid 844 through 852 Processing helix chain 'V' and resid 869 through 882 Processing helix chain 'V' and resid 893 through 900 removed outlier: 3.622A pdb=" N LEU V 900 " --> pdb=" O LYS V 896 " (cutoff:3.500A) Processing helix chain 'V' and resid 905 through 915 removed outlier: 4.931A pdb=" N VAL V 915 " --> pdb=" O LEU V 911 " (cutoff:3.500A) Processing helix chain 'V' and resid 920 through 931 Processing helix chain 'V' and resid 943 through 952 removed outlier: 3.523A pdb=" N LYS V 952 " --> pdb=" O SER V 948 " (cutoff:3.500A) Processing helix chain 'V' and resid 959 through 970 Processing helix chain 'V' and resid 979 through 983 Processing helix chain 'V' and resid 987 through 1007 Processing helix chain 'V' and resid 1018 through 1029 Processing helix chain 'V' and resid 1088 through 1094 Processing helix chain 'V' and resid 1101 through 1103 No H-bonds generated for 'chain 'V' and resid 1101 through 1103' Processing helix chain 'V' and resid 1109 through 1119 Proline residue: V1116 - end of helix Processing helix chain 'l' and resid 4 through 9 Processing helix chain 'm' and resid 17 through 20 No H-bonds generated for 'chain 'm' and resid 17 through 20' Processing helix chain 'm' and resid 25 through 28 No H-bonds generated for 'chain 'm' and resid 25 through 28' Processing helix chain 'm' and resid 32 through 39 Processing helix chain 'n' and resid 6 through 13 Processing helix chain 'W' and resid 5 through 10 Processing helix chain 'W' and resid 43 through 45 No H-bonds generated for 'chain 'W' and resid 43 through 45' Processing helix chain 'W' and resid 112 through 115 Processing helix chain 'W' and resid 140 through 147 Processing helix chain 'W' and resid 161 through 166 Processing helix chain 'Y' and resid 41 through 52 Processing helix chain 'Y' and resid 79 through 88 Processing helix chain 'p' and resid 13 through 23 removed outlier: 3.586A pdb=" N ILE p 17 " --> pdb=" O PRO p 13 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE p 18 " --> pdb=" O ILE p 14 " (cutoff:3.500A) Processing helix chain 'q' and resid 15 through 21 Processing helix chain 's' and resid 16 through 30 Processing helix chain 's' and resid 86 through 93 removed outlier: 4.092A pdb=" N ARG s 93 " --> pdb=" O GLU s 89 " (cutoff:3.500A) Processing helix chain 's' and resid 114 through 117 No H-bonds generated for 'chain 's' and resid 114 through 117' Processing helix chain 's' and resid 121 through 130 Processing helix chain 's' and resid 138 through 173 removed outlier: 3.690A pdb=" N ASN s 143 " --> pdb=" O GLN s 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR s 146 " --> pdb=" O ILE s 142 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE s 153 " --> pdb=" O GLN s 149 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL s 154 " --> pdb=" O THR s 150 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU s 155 " --> pdb=" O CYS s 151 " (cutoff:3.500A) Processing helix chain 't' and resid 25 through 34 Processing helix chain 't' and resid 79 through 142 removed outlier: 3.563A pdb=" N ALA t 90 " --> pdb=" O ASN t 86 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS t 108 " --> pdb=" O SER t 104 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL t 122 " --> pdb=" O ALA t 118 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA t 123 " --> pdb=" O ALA t 119 " (cutoff:3.500A) Proline residue: t 138 - end of helix Processing helix chain 'u' and resid 25 through 34 Processing helix chain 'u' and resid 77 through 138 removed outlier: 3.711A pdb=" N THR u 82 " --> pdb=" O PRO u 78 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU u 93 " --> pdb=" O ASP u 89 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU u 98 " --> pdb=" O GLU u 94 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR u 101 " --> pdb=" O LYS u 97 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU u 102 " --> pdb=" O LEU u 98 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR u 106 " --> pdb=" O LEU u 102 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS u 107 " --> pdb=" O ASP u 103 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL u 112 " --> pdb=" O LYS u 108 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU u 121 " --> pdb=" O ASP u 117 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA u 124 " --> pdb=" O LYS u 120 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN u 125 " --> pdb=" O LEU u 121 " (cutoff:3.500A) Proline residue: u 138 - end of helix Processing helix chain 'v' and resid 25 through 34 removed outlier: 3.578A pdb=" N LYS v 33 " --> pdb=" O GLU v 29 " (cutoff:3.500A) Processing helix chain 'v' and resid 77 through 80 No H-bonds generated for 'chain 'v' and resid 77 through 80' Processing helix chain 'v' and resid 82 through 140 removed outlier: 3.502A pdb=" N LEU v 105 " --> pdb=" O THR v 101 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER v 110 " --> pdb=" O THR v 106 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N THR v 111 " --> pdb=" O LYS v 107 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN v 131 " --> pdb=" O LEU v 127 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU v 132 " --> pdb=" O MET v 128 " (cutoff:3.500A) Proline residue: v 138 - end of helix Processing helix chain 'w' and resid 25 through 34 removed outlier: 3.562A pdb=" N GLN w 30 " --> pdb=" O SER w 26 " (cutoff:3.500A) Processing helix chain 'w' and resid 78 through 105 removed outlier: 3.815A pdb=" N LEU w 93 " --> pdb=" O ASP w 89 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU w 98 " --> pdb=" O GLU w 94 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR w 101 " --> pdb=" O LYS w 97 " (cutoff:3.500A) Processing helix chain 'w' and resid 107 through 136 removed outlier: 3.780A pdb=" N THR w 111 " --> pdb=" O LYS w 107 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL w 112 " --> pdb=" O LYS w 108 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU w 121 " --> pdb=" O ASP w 117 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL w 122 " --> pdb=" O ALA w 118 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN w 131 " --> pdb=" O LEU w 127 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 188 through 194 Processing sheet with id= B, first strand: chain 'A' and resid 591 through 593 Processing sheet with id= C, first strand: chain 'A' and resid 968 through 972 Processing sheet with id= D, first strand: chain 'A' and resid 1167 through 1174 Processing sheet with id= E, first strand: chain 'A' and resid 1257 through 1262 removed outlier: 6.935A pdb=" N LEU A1288 " --> pdb=" O THR A1297 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS A1299 " --> pdb=" O TRP A1286 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N TRP A1286 " --> pdb=" O LYS A1299 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1406 through 1408 Processing sheet with id= G, first strand: chain 'A' and resid 1624 through 1626 Processing sheet with id= H, first strand: chain 'A' and resid 1731 through 1734 Processing sheet with id= I, first strand: chain 'A' and resid 1773 through 1778 Processing sheet with id= J, first strand: chain 'A' and resid 1880 through 1882 removed outlier: 6.166A pdb=" N GLN A1932 " --> pdb=" O LEU A1850 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL A1852 " --> pdb=" O GLN A1932 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE A1934 " --> pdb=" O VAL A1852 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA A1955 " --> pdb=" O ILE A1933 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N VAL A1935 " --> pdb=" O ALA A1955 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ARG A1957 " --> pdb=" O VAL A1935 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1859 through 1864 removed outlier: 4.561A pdb=" N ARG A1859 " --> pdb=" O ILE A1875 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 133 through 135 removed outlier: 8.931A pdb=" N ILE C 134 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N MET C 209 " --> pdb=" O ILE C 134 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 238 through 240 removed outlier: 6.327A pdb=" N VAL C 266 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ILE C 312 " --> pdb=" O ILE C 267 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 500 through 503 removed outlier: 4.356A pdb=" N LEU C 468 " --> pdb=" O SER C 579 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP C 469 " --> pdb=" O SER C 490 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER C 490 " --> pdb=" O TRP C 469 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N HIS C 471 " --> pdb=" O ILE C 488 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ILE C 488 " --> pdb=" O HIS C 471 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 474 through 476 Processing sheet with id= P, first strand: chain 'C' and resid 492 through 494 Processing sheet with id= Q, first strand: chain 'C' and resid 543 through 545 Processing sheet with id= R, first strand: chain 'C' and resid 642 through 646 Processing sheet with id= S, first strand: chain 'C' and resid 678 through 681 Processing sheet with id= T, first strand: chain 'C' and resid 775 through 777 removed outlier: 6.395A pdb=" N SER C 709 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 928 through 931 removed outlier: 4.035A pdb=" N LYS C 890 " --> pdb=" O ARG C 903 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN C 905 " --> pdb=" O ILE C 888 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ILE C 888 " --> pdb=" O GLN C 905 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 144 through 147 removed outlier: 6.461A pdb=" N ASP J 168 " --> pdb=" O LEU J 174 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU J 174 " --> pdb=" O ASP J 168 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 185 through 190 removed outlier: 6.952A pdb=" N VAL J 200 " --> pdb=" O ARG J 186 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL J 188 " --> pdb=" O PHE J 198 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE J 198 " --> pdb=" O VAL J 188 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL J 190 " --> pdb=" O TYR J 196 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TYR J 196 " --> pdb=" O VAL J 190 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ASP J 210 " --> pdb=" O ILE J 216 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ILE J 216 " --> pdb=" O ASP J 210 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 227 through 232 removed outlier: 6.902A pdb=" N ALA J 242 " --> pdb=" O ARG J 228 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL J 230 " --> pdb=" O ALA J 240 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA J 240 " --> pdb=" O VAL J 230 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE J 232 " --> pdb=" O LEU J 238 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU J 238 " --> pdb=" O ILE J 232 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY J 243 " --> pdb=" O VAL J 247 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL J 247 " --> pdb=" O GLY J 243 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE J 248 " --> pdb=" O LEU J 262 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ASP J 252 " --> pdb=" O PRO J 258 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'J' and resid 271 through 274 removed outlier: 4.668A pdb=" N VAL J 281 " --> pdb=" O TRP J 293 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ASP J 294 " --> pdb=" O THR J 300 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N THR J 300 " --> pdb=" O ASP J 294 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'J' and resid 314 through 316 Processing sheet with id= AA, first strand: chain 'J' and resid 363 through 367 removed outlier: 3.959A pdb=" N ALA J 366 " --> pdb=" O SER J 374 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ASP J 377 " --> pdb=" O LYS J 383 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS J 383 " --> pdb=" O ASP J 377 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 129 through 133 removed outlier: 6.641A pdb=" N ILE J 425 " --> pdb=" O SER J 132 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'J' and resid 333 through 335 removed outlier: 4.791A pdb=" N GLY J 335 " --> pdb=" O LEU J 341 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N LEU J 341 " --> pdb=" O GLY J 335 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'M' and resid 222 through 225 removed outlier: 3.777A pdb=" N LEU M 137 " --> pdb=" O VAL M 184 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'N' and resid 26 through 28 Processing sheet with id= AF, first strand: chain 'N' and resid 206 through 208 removed outlier: 4.138A pdb=" N PHE N 206 " --> pdb=" O PRO N 292 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE N 290 " --> pdb=" O TYR N 208 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'o' and resid 156 through 158 removed outlier: 4.242A pdb=" N LYS o 450 " --> pdb=" O GLY o 446 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'o' and resid 177 through 179 Processing sheet with id= AI, first strand: chain 'o' and resid 230 through 234 removed outlier: 3.692A pdb=" N ALA o 211 " --> pdb=" O SER o 224 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'o' and resid 252 through 255 removed outlier: 3.638A pdb=" N ASP o 252 " --> pdb=" O GLY o 266 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'o' and resid 339 through 342 removed outlier: 3.503A pdb=" N MET o 339 " --> pdb=" O GLN o 354 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'o' and resid 385 through 388 removed outlier: 4.341A pdb=" N TYR o 385 " --> pdb=" O GLY o 401 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'y' and resid 144 through 146 Processing sheet with id= AN, first strand: chain 'b' and resid 80 through 83 removed outlier: 6.183A pdb=" N CYS b 48 " --> pdb=" O LEU b 82 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ARG b 21 " --> pdb=" O VAL b 97 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N VAL b 97 " --> pdb=" O ARG b 21 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU b 23 " --> pdb=" O THR b 95 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N THR b 95 " --> pdb=" O LEU b 23 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'b' and resid 43 through 45 Processing sheet with id= AP, first strand: chain 'd' and resid 69 through 73 removed outlier: 7.060A pdb=" N GLU d 22 " --> pdb=" O LYS d 70 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILE d 72 " --> pdb=" O SER d 20 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N SER d 20 " --> pdb=" O ILE d 72 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN d 43 " --> pdb=" O VAL d 34 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'd' and resid 48 through 50 Processing sheet with id= AR, first strand: chain 'e' and resid 26 through 30 Processing sheet with id= AS, first strand: chain 'e' and resid 52 through 54 removed outlier: 4.090A pdb=" N VAL e 52 " --> pdb=" O LEU e 82 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU e 82 " --> pdb=" O VAL e 52 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'f' and resid 71 through 73 removed outlier: 3.866A pdb=" N GLN f 52 " --> pdb=" O SER f 44 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER f 44 " --> pdb=" O GLN f 52 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ASN f 54 " --> pdb=" O LEU f 42 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU f 42 " --> pdb=" O ASN f 54 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'f' and resid 28 through 31 Processing sheet with id= AV, first strand: chain 'g' and resid 23 through 25 Processing sheet with id= AW, first strand: chain 'g' and resid 38 through 41 Processing sheet with id= AX, first strand: chain 'h' and resid 24 through 26 Processing sheet with id= AY, first strand: chain 'h' and resid 84 through 87 removed outlier: 6.636A pdb=" N THR h 41 " --> pdb=" O LEU h 29 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LEU h 29 " --> pdb=" O THR h 41 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'h' and resid 16 through 19 Processing sheet with id= BA, first strand: chain 'j' and resid 67 through 70 Processing sheet with id= BB, first strand: chain 'j' and resid 72 through 77 Processing sheet with id= BC, first strand: chain 'j' and resid 44 through 48 removed outlier: 3.907A pdb=" N VAL j 103 " --> pdb=" O SER j 47 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'V' and resid 651 through 655 removed outlier: 6.626A pdb=" N VAL V 631 " --> pdb=" O LEU V 502 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE V 504 " --> pdb=" O VAL V 631 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL V 633 " --> pdb=" O ILE V 504 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N GLY V 506 " --> pdb=" O VAL V 633 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N SER V 635 " --> pdb=" O GLY V 506 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N MET V 530 " --> pdb=" O SER V 598 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE V 600 " --> pdb=" O MET V 530 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY V 532 " --> pdb=" O ILE V 600 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU V 602 " --> pdb=" O GLY V 532 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR V 534 " --> pdb=" O LEU V 602 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'V' and resid 662 through 666 removed outlier: 6.802A pdb=" N GLY V 815 " --> pdb=" O GLU V 663 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N LEU V 665 " --> pdb=" O GLY V 815 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N CYS V 817 " --> pdb=" O LEU V 665 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASP V 693 " --> pdb=" O TYR V 770 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N VAL V 772 " --> pdb=" O ASP V 693 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU V 695 " --> pdb=" O VAL V 772 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ASP V 774 " --> pdb=" O LEU V 695 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE V 697 " --> pdb=" O ASP V 774 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'V' and resid 777 through 784 Processing sheet with id= BG, first strand: chain 'V' and resid 1041 through 1044 Processing sheet with id= BH, first strand: chain 'V' and resid 1071 through 1074 Processing sheet with id= BI, first strand: chain 'k' and resid 29 through 33 removed outlier: 3.807A pdb=" N LYS k 19 " --> pdb=" O ASP k 99 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP k 99 " --> pdb=" O LYS k 19 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ARG k 21 " --> pdb=" O VAL k 97 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N VAL k 97 " --> pdb=" O ARG k 21 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'm' and resid 43 through 47 removed outlier: 3.824A pdb=" N GLU m 74 " --> pdb=" O ARG m 89 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG m 89 " --> pdb=" O GLU m 74 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TRP m 76 " --> pdb=" O ARG m 87 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG m 87 " --> pdb=" O TRP m 76 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'm' and resid 57 through 60 removed outlier: 6.851A pdb=" N VAL m 68 " --> pdb=" O LYS m 59 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'n' and resid 18 through 20 removed outlier: 3.502A pdb=" N GLY n 31 " --> pdb=" O VAL n 19 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR n 28 " --> pdb=" O THR n 50 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG n 30 " --> pdb=" O ILE n 48 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'n' and resid 42 through 45 removed outlier: 3.508A pdb=" N VAL n 42 " --> pdb=" O VAL n 64 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'n' and resid 21 through 23 Processing sheet with id= BO, first strand: chain 'r' and resid 26 through 28 removed outlier: 3.529A pdb=" N SER r 70 " --> pdb=" O ASN r 18 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'Y' and resid 30 through 32 removed outlier: 3.846A pdb=" N ALA Y 72 " --> pdb=" O VAL Y 32 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'Y' and resid 92 through 94 removed outlier: 3.921A pdb=" N GLU Y 92 " --> pdb=" O LEU Y 99 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS Y 97 " --> pdb=" O PHE Y 94 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'p' and resid 37 through 40 Processing sheet with id= BS, first strand: chain 'p' and resid 52 through 54 removed outlier: 3.973A pdb=" N VAL p 52 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU p 82 " --> pdb=" O VAL p 52 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'q' and resid 57 through 59 removed outlier: 4.073A pdb=" N LYS q 30 " --> pdb=" O TYR q 80 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR q 80 " --> pdb=" O LYS q 30 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'q' and resid 51 through 53 Processing sheet with id= BV, first strand: chain 't' and resid 13 through 15 Processing sheet with id= BW, first strand: chain 't' and resid 197 through 200 Processing sheet with id= BX, first strand: chain 't' and resid 210 through 216 Processing sheet with id= BY, first strand: chain 't' and resid 248 through 251 removed outlier: 3.513A pdb=" N ILE t 248 " --> pdb=" O LEU t 260 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASP t 270 " --> pdb=" O VAL t 276 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL t 276 " --> pdb=" O ASP t 270 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 't' and resid 288 through 292 removed outlier: 6.514A pdb=" N ALA t 305 " --> pdb=" O ILE t 289 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N MET t 291 " --> pdb=" O ILE t 303 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE t 303 " --> pdb=" O MET t 291 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N PHE t 313 " --> pdb=" O ILE t 323 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE t 323 " --> pdb=" O PHE t 313 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N SER t 315 " --> pdb=" O GLN t 321 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLN t 321 " --> pdb=" O SER t 315 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 't' and resid 335 through 338 Processing sheet with id= CB, first strand: chain 't' and resid 397 through 401 Processing sheet with id= CC, first strand: chain 't' and resid 424 through 428 removed outlier: 6.236A pdb=" N LYS t 449 " --> pdb=" O LYS t 459 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LYS t 459 " --> pdb=" O LYS t 449 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 't' and resid 476 through 482 removed outlier: 3.801A pdb=" N GLY t 482 " --> pdb=" O GLY t 485 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE t 486 " --> pdb=" O LEU t 501 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA t 500 " --> pdb=" O LEU t 182 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU t 182 " --> pdb=" O ALA t 500 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR t 502 " --> pdb=" O LEU t 180 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LEU t 180 " --> pdb=" O THR t 502 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'u' and resid 13 through 16 removed outlier: 4.064A pdb=" N THR u 21 " --> pdb=" O SER u 16 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'v' and resid 13 through 15 Processing sheet with id= CG, first strand: chain 'w' and resid 13 through 15 Processing sheet with id= CH, first strand: chain 'w' and resid 197 through 200 Processing sheet with id= CI, first strand: chain 'w' and resid 210 through 216 Processing sheet with id= CJ, first strand: chain 'w' and resid 248 through 251 removed outlier: 3.515A pdb=" N ILE w 248 " --> pdb=" O LEU w 260 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASP w 270 " --> pdb=" O VAL w 276 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL w 276 " --> pdb=" O ASP w 270 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain 'w' and resid 288 through 292 removed outlier: 6.515A pdb=" N ALA w 305 " --> pdb=" O ILE w 289 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N MET w 291 " --> pdb=" O ILE w 303 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE w 303 " --> pdb=" O MET w 291 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N PHE w 313 " --> pdb=" O ILE w 323 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ILE w 323 " --> pdb=" O PHE w 313 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N SER w 315 " --> pdb=" O GLN w 321 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLN w 321 " --> pdb=" O SER w 315 " (cutoff:3.500A) Processing sheet with id= CL, first strand: chain 'w' and resid 335 through 338 Processing sheet with id= CM, first strand: chain 'w' and resid 397 through 401 Processing sheet with id= CN, first strand: chain 'w' and resid 424 through 428 removed outlier: 6.236A pdb=" N LYS w 449 " --> pdb=" O LYS w 459 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LYS w 459 " --> pdb=" O LYS w 449 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain 'w' and resid 476 through 482 removed outlier: 3.801A pdb=" N GLY w 482 " --> pdb=" O GLY w 485 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE w 486 " --> pdb=" O LEU w 501 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA w 500 " --> pdb=" O LEU w 182 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LEU w 182 " --> pdb=" O ALA w 500 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR w 502 " --> pdb=" O LEU w 180 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LEU w 180 " --> pdb=" O THR w 502 " (cutoff:3.500A) 3197 hydrogen bonds defined for protein. 8961 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 339 hydrogen bonds 606 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 235 stacking parallelities Total time for adding SS restraints: 49.80 Time building geometry restraints manager: 31.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.40: 31466 1.40 - 1.64: 47730 1.64 - 1.88: 345 1.88 - 2.12: 0 2.12 - 2.35: 2 Bond restraints: 79543 Sorted by residual: bond pdb=" C MET V 903 " pdb=" N ASP V 904 " ideal model delta sigma weight residual 1.328 2.352 -1.024 1.44e-02 4.82e+03 5.06e+03 bond pdb=" C ASP T 300 " pdb=" N LYS T 301 " ideal model delta sigma weight residual 1.332 2.163 -0.830 1.40e-02 5.10e+03 3.52e+03 bond pdb=" C LEU V1009 " pdb=" N LYS V1010 " ideal model delta sigma weight residual 1.331 1.503 -0.172 1.37e-02 5.33e+03 1.58e+02 bond pdb=" C THR V 834 " pdb=" N VAL V 835 " ideal model delta sigma weight residual 1.329 1.215 0.115 1.13e-02 7.83e+03 1.03e+02 bond pdb=" C LEU v 109 " pdb=" N SER v 110 " ideal model delta sigma weight residual 1.335 1.440 -0.105 1.31e-02 5.83e+03 6.46e+01 ... (remaining 79538 not shown) Histogram of bond angle deviations from ideal: 5.11 - 37.39: 2 37.39 - 69.67: 1 69.67 - 101.95: 717 101.95 - 134.23: 109662 134.23 - 166.52: 4 Bond angle restraints: 110386 Sorted by residual: angle pdb=" C THR V 834 " pdb=" N VAL V 835 " pdb=" CA VAL V 835 " ideal model delta sigma weight residual 122.13 5.11 117.02 1.85e+00 2.92e-01 4.00e+03 angle pdb=" CA THR V 834 " pdb=" C THR V 834 " pdb=" N VAL V 835 " ideal model delta sigma weight residual 116.84 31.91 84.93 1.71e+00 3.42e-01 2.47e+03 angle pdb=" CA LEU V1009 " pdb=" C LEU V1009 " pdb=" N LYS V1010 " ideal model delta sigma weight residual 116.39 67.67 48.72 1.26e+00 6.30e-01 1.49e+03 angle pdb=" O LEU V1009 " pdb=" C LEU V1009 " pdb=" N LYS V1010 " ideal model delta sigma weight residual 123.13 166.52 -43.39 1.15e+00 7.56e-01 1.42e+03 angle pdb=" C LEU V1009 " pdb=" N LYS V1010 " pdb=" CA LYS V1010 " ideal model delta sigma weight residual 120.95 74.32 46.63 1.40e+00 5.10e-01 1.11e+03 ... (remaining 110381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 46414 35.47 - 70.94: 1704 70.94 - 106.40: 162 106.40 - 141.87: 13 141.87 - 177.34: 7 Dihedral angle restraints: 48300 sinusoidal: 19775 harmonic: 28525 Sorted by residual: dihedral pdb=" CA LEU s 132 " pdb=" C LEU s 132 " pdb=" N PRO s 133 " pdb=" CA PRO s 133 " ideal model delta harmonic sigma weight residual 180.00 -129.71 -50.29 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA THR V 834 " pdb=" C THR V 834 " pdb=" N VAL V 835 " pdb=" CA VAL V 835 " ideal model delta harmonic sigma weight residual -180.00 -134.69 -45.31 0 5.00e+00 4.00e-02 8.21e+01 dihedral pdb=" O4' C 5 79 " pdb=" C1' C 5 79 " pdb=" N1 C 5 79 " pdb=" C2 C 5 79 " ideal model delta sinusoidal sigma weight residual 200.00 68.39 131.61 1 1.50e+01 4.44e-03 7.10e+01 ... (remaining 48297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.990: 13540 0.990 - 1.980: 0 1.980 - 2.970: 0 2.970 - 3.960: 0 3.960 - 4.950: 2 Chirality restraints: 13542 Sorted by residual: chirality pdb=" C2 IHP A3001 " pdb=" C1 IHP A3001 " pdb=" C3 IHP A3001 " pdb=" O12 IHP A3001 " both_signs ideal model delta sigma weight residual False -2.52 2.43 -4.95 2.00e-01 2.50e+01 6.12e+02 chirality pdb=" C3 IHP A3001 " pdb=" C2 IHP A3001 " pdb=" C4 IHP A3001 " pdb=" O13 IHP A3001 " both_signs ideal model delta sigma weight residual False -2.34 2.45 -4.79 2.00e-01 2.50e+01 5.74e+02 chirality pdb=" C3' C 6 92 " pdb=" C4' C 6 92 " pdb=" O3' C 6 92 " pdb=" C2' C 6 92 " both_signs ideal model delta sigma weight residual False -2.74 -2.01 -0.73 2.00e-01 2.50e+01 1.34e+01 ... (remaining 13539 not shown) Planarity restraints: 12622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR V 659 " -0.141 2.00e-02 2.50e+03 2.46e-01 6.07e+02 pdb=" C THR V 659 " 0.421 2.00e-02 2.50e+03 pdb=" O THR V 659 " -0.198 2.00e-02 2.50e+03 pdb=" N PHE V 660 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP T 300 " -0.129 2.00e-02 2.50e+03 1.94e-01 3.75e+02 pdb=" C ASP T 300 " 0.332 2.00e-02 2.50e+03 pdb=" O ASP T 300 " -0.139 2.00e-02 2.50e+03 pdb=" N LYS T 301 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR V 834 " -0.219 2.00e-02 2.50e+03 1.78e-01 3.17e+02 pdb=" C THR V 834 " 0.129 2.00e-02 2.50e+03 pdb=" O THR V 834 " -0.125 2.00e-02 2.50e+03 pdb=" N VAL V 835 " 0.215 2.00e-02 2.50e+03 ... (remaining 12619 not shown) Histogram of nonbonded interaction distances: 0.68 - 1.57: 34 1.57 - 2.46: 212 2.46 - 3.36: 101315 3.36 - 4.25: 230265 4.25 - 5.14: 409645 Warning: very small nonbonded interaction distances. Nonbonded interactions: 741471 Sorted by model distance: nonbonded pdb=" C4' G 21149 " pdb=" NH1 ARG k 52 " model vdw 0.679 3.550 nonbonded pdb=" CB TYR T 274 " pdb=" CB MET T 294 " model vdw 0.680 3.840 nonbonded pdb=" O4' G 21149 " pdb=" CZ ARG k 52 " model vdw 0.683 3.270 nonbonded pdb=" O2' C 21093 " pdb=" C GLY n 54 " model vdw 0.834 3.270 nonbonded pdb=" C LEU k 102 " pdb=" C TYR W 14 " model vdw 0.937 3.500 ... (remaining 741466 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'b' selection = chain 'k' } ncs_group { reference = chain 'd' selection = chain 'n' } ncs_group { reference = chain 'e' selection = chain 'p' } ncs_group { reference = chain 'f' selection = chain 'q' } ncs_group { reference = (chain 'g' and (resid 2 through 40 or (resid 41 through 43 and (name N or name C \ A or name C or name O or name CB )) or resid 44 through 76)) selection = chain 'r' } ncs_group { reference = (chain 'h' and (resid 1 through 98 or (resid 99 and (name N or name CA or name C \ or name O or name CB )) or resid 100 through 106)) selection = chain 'l' } ncs_group { reference = (chain 'j' and (resid 16 through 78 or (resid 79 and (name N or name CA or name \ C or name O or name CB )) or resid 80 through 108)) selection = chain 'm' } ncs_group { reference = (chain 't' and (resid 1 through 139 or resid 171 through 503)) selection = (chain 'w' and (resid 1 through 51 or resid 78 through 503)) } ncs_group { reference = (chain 'u' and (resid 1 through 51 or resid 76 through 139)) selection = (chain 'v' and resid 1 through 139) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 17.340 Check model and map are aligned: 0.870 Set scattering table: 0.560 Process input model: 222.110 Find NCS groups from input model: 2.660 Set up NCS constraints: 0.560 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 250.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5646 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 : 0.010 1.024 79543 Z= 0.648 Angle : 1.544 117.021 110386 Z= 1.081 Chirality : 0.107 4.950 13542 Planarity : 0.008 0.246 12622 Dihedral : 17.517 177.338 29622 Min Nonbonded Distance : 0.679 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.89 % Allowed : 7.71 % Favored : 91.40 % Rotamer: Outliers : 2.73 % Allowed : 7.86 % Favored : 89.41 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.08), residues: 9407 helix: 0.16 (0.07), residues: 4061 sheet: -2.22 (0.13), residues: 1232 loop : -2.62 (0.09), residues: 4114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 711 HIS 0.014 0.002 HIS A 138 PHE 0.039 0.003 PHE J 198 TYR 0.030 0.003 TYR J 378 ARG 0.010 0.001 ARG C 973 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18814 Ramachandran restraints generated. 9407 Oldfield, 0 Emsley, 9407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18814 Ramachandran restraints generated. 9407 Oldfield, 0 Emsley, 9407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1131 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 978 time to evaluate : 6.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 GLU cc_start: 0.8697 (tt0) cc_final: 0.8488 (tt0) REVERT: A 777 LYS cc_start: 0.7806 (mppt) cc_final: 0.7475 (pttt) REVERT: A 788 GLU cc_start: 0.9244 (tt0) cc_final: 0.8808 (tp30) REVERT: A 841 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8204 (mm-30) REVERT: A 842 LYS cc_start: 0.9146 (ttpt) cc_final: 0.8744 (mttm) REVERT: A 958 LEU cc_start: 0.9153 (mt) cc_final: 0.8884 (tt) REVERT: A 1007 LYS cc_start: 0.8937 (mmtm) cc_final: 0.8574 (ttpt) REVERT: A 1049 LEU cc_start: 0.8445 (tp) cc_final: 0.8109 (tt) REVERT: A 1086 ASN cc_start: 0.9133 (m-40) cc_final: 0.8921 (t0) REVERT: A 1103 LEU cc_start: 0.8903 (tt) cc_final: 0.8684 (tt) REVERT: A 1171 LEU cc_start: 0.8673 (tp) cc_final: 0.8425 (tp) REVERT: A 1212 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7878 (ptt180) REVERT: A 1304 VAL cc_start: 0.9019 (t) cc_final: 0.8509 (p) REVERT: A 1308 GLU cc_start: 0.9345 (mm-30) cc_final: 0.8845 (mm-30) REVERT: A 1309 ILE cc_start: 0.9699 (mt) cc_final: 0.9481 (tt) REVERT: A 1321 MET cc_start: 0.8074 (ptp) cc_final: 0.7865 (ppp) REVERT: A 1414 TRP cc_start: 0.9113 (m-90) cc_final: 0.8877 (m-90) REVERT: A 1627 LEU cc_start: 0.8626 (mt) cc_final: 0.8332 (mt) REVERT: A 1783 MET cc_start: 0.8162 (mtt) cc_final: 0.7903 (tpt) REVERT: A 2005 PHE cc_start: 0.9312 (t80) cc_final: 0.9100 (t80) REVERT: C 123 MET cc_start: 0.9144 (ttp) cc_final: 0.8918 (mtp) REVERT: C 163 ASP cc_start: 0.8486 (m-30) cc_final: 0.8017 (t0) REVERT: C 209 MET cc_start: 0.8556 (ppp) cc_final: 0.8219 (ppp) REVERT: C 658 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.7979 (t70) REVERT: C 774 LEU cc_start: 0.5129 (OUTLIER) cc_final: 0.2517 (mm) REVERT: C 920 LEU cc_start: 0.9052 (mt) cc_final: 0.8807 (mt) REVERT: C 968 MET cc_start: 0.8800 (mmm) cc_final: 0.8310 (mmm) REVERT: H 20 MET cc_start: 0.6402 (ptm) cc_final: 0.6180 (ppp) REVERT: H 169 THR cc_start: 0.8976 (m) cc_final: 0.8390 (t) REVERT: J 399 GLU cc_start: 0.8982 (tt0) cc_final: 0.8445 (tt0) REVERT: K 37 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8125 (t0) REVERT: L 55 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8337 (tt) REVERT: M 31 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.8059 (t0) REVERT: M 98 ASP cc_start: 0.8776 (m-30) cc_final: 0.8536 (m-30) REVERT: N 106 ASN cc_start: 0.7397 (OUTLIER) cc_final: 0.7072 (t0) REVERT: N 130 SER cc_start: 0.9508 (m) cc_final: 0.9243 (p) REVERT: N 207 LEU cc_start: 0.8308 (mp) cc_final: 0.8044 (tp) REVERT: O 204 LYS cc_start: 0.6836 (mttt) cc_final: 0.6073 (tppt) REVERT: O 234 ASP cc_start: 0.8616 (m-30) cc_final: 0.8326 (m-30) REVERT: P 161 THR cc_start: 0.8304 (p) cc_final: 0.7814 (m) REVERT: P 162 LYS cc_start: 0.9206 (mttt) cc_final: 0.8979 (mmtt) REVERT: P 164 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7783 (tp30) REVERT: P 167 GLN cc_start: 0.9019 (mt0) cc_final: 0.8434 (mm-40) REVERT: R 17 SER cc_start: 0.9387 (OUTLIER) cc_final: 0.9098 (t) REVERT: S 128 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8402 (p) REVERT: S 141 ILE cc_start: 0.9548 (pt) cc_final: 0.9242 (mm) REVERT: S 163 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7141 (tm-30) REVERT: S 180 LYS cc_start: 0.9254 (mtmm) cc_final: 0.9047 (mmmt) REVERT: S 199 MET cc_start: 0.9024 (tpp) cc_final: 0.7688 (mmm) REVERT: a 177 ASN cc_start: 0.9042 (t0) cc_final: 0.8798 (m-40) REVERT: a 183 TYR cc_start: 0.8908 (t80) cc_final: 0.8684 (t80) REVERT: b 5 GLN cc_start: 0.8620 (mt0) cc_final: 0.8230 (pp30) REVERT: d 60 ASP cc_start: 0.9200 (m-30) cc_final: 0.8856 (p0) REVERT: d 76 ASP cc_start: 0.8555 (m-30) cc_final: 0.8090 (p0) REVERT: f 55 GLU cc_start: 0.9608 (mt-10) cc_final: 0.9244 (tm-30) REVERT: f 57 GLU cc_start: 0.9428 (mt-10) cc_final: 0.8929 (mm-30) REVERT: g 8 LYS cc_start: 0.7918 (mtpt) cc_final: 0.7605 (tptp) REVERT: g 17 LEU cc_start: 0.8213 (mp) cc_final: 0.7951 (tp) REVERT: j 31 MET cc_start: 0.8542 (mmm) cc_final: 0.8086 (mpp) REVERT: l 30 GLN cc_start: 0.6119 (mt0) cc_final: 0.5909 (mt0) REVERT: l 31 SER cc_start: 0.3134 (p) cc_final: 0.2906 (t) REVERT: l 36 MET cc_start: 0.6122 (ttm) cc_final: 0.5610 (mpp) REVERT: l 43 VAL cc_start: 0.0103 (OUTLIER) cc_final: -0.0171 (p) REVERT: l 92 ILE cc_start: 0.4570 (mm) cc_final: 0.4224 (pt) REVERT: m 41 ARG cc_start: 0.5533 (OUTLIER) cc_final: 0.5245 (ptp-170) REVERT: m 84 VAL cc_start: 0.2930 (t) cc_final: 0.2699 (m) REVERT: n 18 ILE cc_start: 0.4076 (mm) cc_final: 0.3819 (tt) REVERT: n 20 SER cc_start: 0.5311 (OUTLIER) cc_final: 0.4771 (m) REVERT: p 42 LYS cc_start: 0.7966 (mttt) cc_final: 0.7685 (ttpp) outliers start: 153 outliers final: 29 residues processed: 1109 average time/residue: 0.7956 time to fit residues: 1518.1454 Evaluate side-chains 545 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 504 time to evaluate : 6.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 844 optimal weight: 40.0000 chunk 757 optimal weight: 20.0000 chunk 420 optimal weight: 3.9990 chunk 258 optimal weight: 3.9990 chunk 511 optimal weight: 0.8980 chunk 404 optimal weight: 0.9990 chunk 783 optimal weight: 5.9990 chunk 303 optimal weight: 10.0000 chunk 476 optimal weight: 0.8980 chunk 583 optimal weight: 40.0000 chunk 908 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN A 542 HIS A 558 GLN A 760 ASN A 848 ASN A 868 GLN A1190 ASN A1368 GLN A1369 ASN ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1532 HIS A1856 ASN A2018 ASN A2047 GLN C 143 HIS C 158 HIS C 194 ASN C 211 ASN C 289 ASN C 358 ASN C 403 ASN C 423 HIS C 431 GLN C 557 HIS C 683 ASN C 764 ASN C 776 ASN ** C 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN ** H 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 367 GLN J 136 ASN J 271 GLN ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 306 HIS ** J 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 ASN ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 HIS R 21 GLN S 73 GLN S 117 HIS S 248 ASN a 246 ASN ** c 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 332 ASN o 261 HIS o 348 GLN y 144 GLN ** y 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 15 ASN g 66 ASN l 21 ASN l 30 GLN ** l 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 43 GLN r 18 ASN r 53 ASN q 24 ASN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5720 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 79543 Z= 0.239 Angle : 0.696 20.821 110386 Z= 0.359 Chirality : 0.044 0.506 13542 Planarity : 0.005 0.114 12622 Dihedral : 17.651 175.996 17101 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.90 % Favored : 94.97 % Rotamer: Outliers : 0.27 % Allowed : 3.62 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.09), residues: 9411 helix: 1.71 (0.08), residues: 4081 sheet: -1.79 (0.13), residues: 1341 loop : -2.13 (0.09), residues: 3989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1012 HIS 0.010 0.001 HIS A 785 PHE 0.033 0.002 PHE e 18 TYR 0.024 0.002 TYR S 156 ARG 0.035 0.001 ARG R 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 627 time to evaluate : 6.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ILE cc_start: 0.9648 (mt) cc_final: 0.9395 (mm) REVERT: A 224 MET cc_start: 0.9220 (mtp) cc_final: 0.8980 (mtp) REVERT: A 578 MET cc_start: 0.8555 (mtp) cc_final: 0.8350 (mtp) REVERT: A 912 LEU cc_start: 0.9478 (tt) cc_final: 0.9188 (tt) REVERT: A 914 LEU cc_start: 0.8930 (mp) cc_final: 0.8474 (tp) REVERT: A 958 LEU cc_start: 0.9168 (mt) cc_final: 0.8916 (tt) REVERT: A 1049 LEU cc_start: 0.8317 (tp) cc_final: 0.8007 (tt) REVERT: A 1057 MET cc_start: 0.8366 (tmm) cc_final: 0.8157 (tmm) REVERT: A 1171 LEU cc_start: 0.8662 (tp) cc_final: 0.8301 (tp) REVERT: A 1262 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8201 (mtm) REVERT: A 1627 LEU cc_start: 0.8664 (mt) cc_final: 0.8223 (mt) REVERT: A 1783 MET cc_start: 0.8281 (mtt) cc_final: 0.8002 (tpt) REVERT: A 1806 MET cc_start: 0.8464 (mmp) cc_final: 0.8233 (ttt) REVERT: A 1819 ILE cc_start: 0.9542 (OUTLIER) cc_final: 0.9331 (pt) REVERT: A 1969 MET cc_start: 0.8370 (tpp) cc_final: 0.7890 (tpp) REVERT: A 1974 LEU cc_start: 0.9317 (mt) cc_final: 0.9086 (tp) REVERT: C 123 MET cc_start: 0.9118 (ttp) cc_final: 0.8909 (ttp) REVERT: C 163 ASP cc_start: 0.8612 (m-30) cc_final: 0.8396 (t0) REVERT: C 209 MET cc_start: 0.8187 (ppp) cc_final: 0.7952 (ppp) REVERT: C 658 ASP cc_start: 0.8632 (m-30) cc_final: 0.8294 (t70) REVERT: C 968 MET cc_start: 0.8876 (mmm) cc_final: 0.8317 (mmm) REVERT: H 155 MET cc_start: 0.8526 (mpp) cc_final: 0.8053 (mpp) REVERT: J 399 GLU cc_start: 0.9065 (tt0) cc_final: 0.8482 (tt0) REVERT: K 107 ASN cc_start: 0.9185 (p0) cc_final: 0.8788 (m-40) REVERT: K 149 MET cc_start: 0.8256 (tmm) cc_final: 0.7453 (ppp) REVERT: N 75 MET cc_start: 0.6567 (mmp) cc_final: 0.6333 (mmp) REVERT: O 204 LYS cc_start: 0.7145 (mttt) cc_final: 0.6436 (tppt) REVERT: O 234 ASP cc_start: 0.8691 (m-30) cc_final: 0.8376 (m-30) REVERT: P 161 THR cc_start: 0.8403 (p) cc_final: 0.6889 (m) REVERT: P 162 LYS cc_start: 0.9110 (mttt) cc_final: 0.8593 (mmtt) REVERT: P 167 GLN cc_start: 0.8923 (mt0) cc_final: 0.8674 (tp40) REVERT: S 117 HIS cc_start: 0.8863 (OUTLIER) cc_final: 0.8547 (m90) REVERT: S 129 LEU cc_start: 0.9210 (mp) cc_final: 0.8986 (mm) REVERT: S 163 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7511 (tm-30) REVERT: b 5 GLN cc_start: 0.8687 (mt0) cc_final: 0.8334 (pp30) REVERT: b 46 ASN cc_start: 0.8724 (t0) cc_final: 0.8339 (p0) REVERT: d 76 ASP cc_start: 0.8593 (m-30) cc_final: 0.8171 (p0) REVERT: e 18 PHE cc_start: 0.8968 (m-80) cc_final: 0.8743 (m-10) REVERT: g 8 LYS cc_start: 0.8329 (mtpt) cc_final: 0.8022 (tptp) REVERT: g 11 MET cc_start: 0.6254 (mmm) cc_final: 0.6045 (mmm) REVERT: j 31 MET cc_start: 0.8457 (mmm) cc_final: 0.8213 (mpp) REVERT: l 31 SER cc_start: 0.3539 (p) cc_final: 0.2409 (m) REVERT: l 36 MET cc_start: 0.6177 (ttm) cc_final: 0.5883 (mpp) REVERT: l 92 ILE cc_start: 0.4807 (mm) cc_final: 0.4527 (pt) REVERT: m 31 MET cc_start: 0.2179 (mtt) cc_final: 0.1299 (mpp) REVERT: m 38 MET cc_start: -0.0047 (ttt) cc_final: -0.0384 (ttt) REVERT: m 58 VAL cc_start: 0.4291 (t) cc_final: 0.3875 (m) REVERT: p 42 LYS cc_start: 0.7916 (mttt) cc_final: 0.7704 (ttpp) outliers start: 15 outliers final: 4 residues processed: 639 average time/residue: 0.7171 time to fit residues: 802.3887 Evaluate side-chains 430 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 423 time to evaluate : 6.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 504 optimal weight: 8.9990 chunk 281 optimal weight: 9.9990 chunk 755 optimal weight: 10.0000 chunk 618 optimal weight: 20.0000 chunk 250 optimal weight: 4.9990 chunk 909 optimal weight: 40.0000 chunk 982 optimal weight: 50.0000 chunk 810 optimal weight: 30.0000 chunk 902 optimal weight: 10.0000 chunk 310 optimal weight: 9.9990 chunk 729 optimal weight: 3.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN A 254 HIS A 392 ASN ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 ASN ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 ASN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 ASN A1030 GLN A1091 ASN A1115 GLN ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1449 ASN ** A1471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1559 HIS ** A2018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2047 GLN ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 ASN C 511 GLN C 817 GLN ** C 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 934 HIS H 66 ASN ** H 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 335 GLN ** H 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 429 ASN H 437 GLN ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 306 HIS J 354 ASN K 50 ASN ** K 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 195 ASN ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 HIS ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 252 HIS N 98 ASN ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 134 ASN ** N 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 210 ASN ** S 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 268 GLN S 277 ASN ** a 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 247 HIS ** o 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 354 GLN ** o 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 14 ASN ** b 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 80 ASN ** e 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 50 ASN ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6004 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.174 79543 Z= 0.520 Angle : 0.927 22.480 110386 Z= 0.474 Chirality : 0.049 0.397 13542 Planarity : 0.007 0.158 12622 Dihedral : 17.965 176.322 17101 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 25.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.80 % Favored : 92.14 % Rotamer: Outliers : 0.46 % Allowed : 7.34 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.26 % Twisted General : 0.04 % 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: -1.10 (0.08), residues: 9411 helix: 0.84 (0.08), residues: 4072 sheet: -1.66 (0.13), residues: 1339 loop : -2.06 (0.09), residues: 4000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP H 357 HIS 0.024 0.003 HIS J 382 PHE 0.078 0.003 PHE O 241 TYR 0.112 0.004 TYR A 154 ARG 0.055 0.002 ARG c 194 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 463 time to evaluate : 6.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.7950 (mtt) cc_final: 0.7669 (mtt) REVERT: A 172 ILE cc_start: 0.9720 (mt) cc_final: 0.9486 (mm) REVERT: A 224 MET cc_start: 0.9405 (mtp) cc_final: 0.9138 (mtp) REVERT: A 387 PHE cc_start: 0.8892 (m-80) cc_final: 0.8571 (m-10) REVERT: A 493 MET cc_start: 0.8898 (mmp) cc_final: 0.8378 (mmt) REVERT: A 763 MET cc_start: 0.9210 (ttp) cc_final: 0.8983 (tmm) REVERT: A 775 ARG cc_start: 0.8718 (mmp-170) cc_final: 0.8064 (tpp80) REVERT: A 914 LEU cc_start: 0.9188 (mp) cc_final: 0.8932 (tp) REVERT: A 1057 MET cc_start: 0.8950 (tmm) cc_final: 0.8563 (tmm) REVERT: A 1213 MET cc_start: 0.8779 (mmm) cc_final: 0.7887 (tpp) REVERT: A 1379 MET cc_start: 0.8124 (ttt) cc_final: 0.7846 (tpp) REVERT: A 1519 LEU cc_start: 0.9371 (tp) cc_final: 0.8930 (tp) REVERT: A 1806 MET cc_start: 0.8765 (mmp) cc_final: 0.8383 (ttt) REVERT: A 1986 MET cc_start: 0.8668 (tpt) cc_final: 0.8251 (tpt) REVERT: C 209 MET cc_start: 0.8783 (ppp) cc_final: 0.8479 (ppp) REVERT: H 155 MET cc_start: 0.8537 (mpp) cc_final: 0.8222 (mpp) REVERT: J 183 MET cc_start: 0.7878 (mtp) cc_final: 0.7674 (mtp) REVERT: J 311 VAL cc_start: 0.9248 (t) cc_final: 0.9024 (t) REVERT: J 399 GLU cc_start: 0.9149 (tt0) cc_final: 0.8811 (tt0) REVERT: K 123 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9190 (mt) REVERT: L 86 TYR cc_start: 0.7512 (m-80) cc_final: 0.7280 (m-10) REVERT: N 68 ARG cc_start: 0.9336 (OUTLIER) cc_final: 0.8236 (ttm-80) REVERT: N 107 ASP cc_start: 0.9048 (m-30) cc_final: 0.8556 (t0) REVERT: O 204 LYS cc_start: 0.7370 (mttt) cc_final: 0.6812 (tppt) REVERT: O 234 ASP cc_start: 0.8967 (m-30) cc_final: 0.8604 (m-30) REVERT: P 161 THR cc_start: 0.8207 (p) cc_final: 0.7657 (p) REVERT: P 162 LYS cc_start: 0.9213 (mttt) cc_final: 0.9009 (mmtt) REVERT: S 65 MET cc_start: 0.9230 (mmm) cc_final: 0.8988 (mmm) REVERT: S 81 MET cc_start: 0.7646 (mmp) cc_final: 0.7365 (mmp) REVERT: S 98 PHE cc_start: 0.8950 (t80) cc_final: 0.8744 (t80) REVERT: S 121 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9025 (tp) REVERT: S 122 MET cc_start: 0.8942 (ttt) cc_final: 0.8420 (tmm) REVERT: S 163 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8254 (tm-30) REVERT: a 138 ASP cc_start: 0.9120 (m-30) cc_final: 0.8597 (p0) REVERT: b 5 GLN cc_start: 0.8757 (mt0) cc_final: 0.8295 (pp30) REVERT: b 48 CYS cc_start: 0.8214 (t) cc_final: 0.7850 (t) REVERT: d 38 ASP cc_start: 0.9347 (t0) cc_final: 0.9141 (t0) REVERT: d 76 ASP cc_start: 0.8875 (OUTLIER) cc_final: 0.8522 (p0) REVERT: e 18 PHE cc_start: 0.8754 (m-80) cc_final: 0.8503 (m-10) REVERT: l 92 ILE cc_start: 0.5155 (mm) cc_final: 0.4771 (pt) REVERT: l 104 ASP cc_start: 0.3309 (p0) cc_final: 0.2841 (t0) REVERT: m 31 MET cc_start: 0.1019 (mtt) cc_final: 0.0297 (mpp) REVERT: p 42 LYS cc_start: 0.7386 (mttt) cc_final: 0.7128 (ttpp) outliers start: 26 outliers final: 6 residues processed: 485 average time/residue: 0.6778 time to fit residues: 588.4559 Evaluate side-chains 368 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 358 time to evaluate : 6.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 898 optimal weight: 30.0000 chunk 683 optimal weight: 5.9990 chunk 472 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 434 optimal weight: 0.8980 chunk 610 optimal weight: 0.9980 chunk 913 optimal weight: 50.0000 chunk 966 optimal weight: 30.0000 chunk 477 optimal weight: 6.9990 chunk 865 optimal weight: 20.0000 chunk 260 optimal weight: 1.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 HIS ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1471 GLN A1737 GLN A2047 GLN ** C 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 ASN C 398 ASN ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 869 HIS C 905 GLN C 934 HIS H 17 ASN ** H 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 194 HIS ** J 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 354 ASN L 29 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 ASN ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 170 ASN S 214 ASN ** a 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 171 GLN ** a 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 157 ASN o 247 ASN o 283 GLN ** y 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5916 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 79543 Z= 0.248 Angle : 0.646 20.379 110386 Z= 0.330 Chirality : 0.042 0.380 13542 Planarity : 0.005 0.070 12622 Dihedral : 17.680 176.668 17101 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.21 % Favored : 94.72 % Rotamer: Outliers : 0.02 % Allowed : 3.48 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.09), residues: 9411 helix: 1.52 (0.08), residues: 4081 sheet: -1.41 (0.14), residues: 1334 loop : -1.82 (0.10), residues: 3996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP l 26 HIS 0.008 0.001 HIS o 292 PHE 0.033 0.002 PHE A 239 TYR 0.028 0.002 TYR C 382 ARG 0.009 0.001 ARG l 93 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 476 time to evaluate : 6.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 PHE cc_start: 0.8889 (m-80) cc_final: 0.8622 (m-10) REVERT: A 578 MET cc_start: 0.8663 (mtp) cc_final: 0.8393 (mtp) REVERT: A 763 MET cc_start: 0.9240 (ttp) cc_final: 0.9009 (tmm) REVERT: A 775 ARG cc_start: 0.8761 (mmp-170) cc_final: 0.8247 (tpp-160) REVERT: A 914 LEU cc_start: 0.9080 (mp) cc_final: 0.8771 (tp) REVERT: A 1057 MET cc_start: 0.8825 (tmm) cc_final: 0.8485 (tmm) REVERT: A 1519 LEU cc_start: 0.9331 (tp) cc_final: 0.8878 (tp) REVERT: A 1766 MET cc_start: 0.9303 (ppp) cc_final: 0.9094 (ppp) REVERT: A 1986 MET cc_start: 0.8689 (tpt) cc_final: 0.8416 (tpt) REVERT: C 126 MET cc_start: 0.9022 (tpp) cc_final: 0.8621 (tpp) REVERT: C 209 MET cc_start: 0.8593 (ppp) cc_final: 0.8313 (ppp) REVERT: C 263 MET cc_start: 0.8822 (ptt) cc_final: 0.8587 (ptt) REVERT: C 391 MET cc_start: 0.8003 (ttp) cc_final: 0.7798 (ptm) REVERT: H 155 MET cc_start: 0.8466 (mpp) cc_final: 0.8142 (mpp) REVERT: J 183 MET cc_start: 0.7990 (mtp) cc_final: 0.7706 (mtm) REVERT: J 399 GLU cc_start: 0.9106 (tt0) cc_final: 0.8735 (tt0) REVERT: N 107 ASP cc_start: 0.8988 (m-30) cc_final: 0.8455 (t70) REVERT: O 204 LYS cc_start: 0.7452 (mttt) cc_final: 0.6955 (tppt) REVERT: O 234 ASP cc_start: 0.8867 (m-30) cc_final: 0.8539 (m-30) REVERT: P 161 THR cc_start: 0.7894 (p) cc_final: 0.7221 (p) REVERT: P 162 LYS cc_start: 0.9123 (mttt) cc_final: 0.8913 (mmtt) REVERT: S 163 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8264 (tm-30) REVERT: c 181 GLU cc_start: 0.9195 (tm-30) cc_final: 0.8842 (pm20) REVERT: o 69 TRP cc_start: 0.7226 (t-100) cc_final: 0.5932 (t-100) REVERT: b 5 GLN cc_start: 0.8778 (mt0) cc_final: 0.8194 (pp30) REVERT: d 59 MET cc_start: 0.8425 (ppp) cc_final: 0.7983 (ppp) REVERT: d 76 ASP cc_start: 0.9012 (m-30) cc_final: 0.8515 (p0) REVERT: j 31 MET cc_start: 0.8617 (mpp) cc_final: 0.8323 (mpp) REVERT: l 104 ASP cc_start: 0.2638 (p0) cc_final: 0.2027 (t0) REVERT: m 31 MET cc_start: 0.1027 (mtt) cc_final: 0.0349 (mpp) REVERT: n 17 HIS cc_start: 0.3555 (m90) cc_final: 0.3347 (m90) REVERT: r 68 ILE cc_start: 0.3415 (mm) cc_final: 0.3170 (mm) REVERT: p 42 LYS cc_start: 0.7631 (mttt) cc_final: 0.7328 (ttpp) outliers start: 1 outliers final: 0 residues processed: 477 average time/residue: 0.6702 time to fit residues: 572.7839 Evaluate side-chains 367 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 6.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 805 optimal weight: 30.0000 chunk 548 optimal weight: 2.9990 chunk 14 optimal weight: 50.0000 chunk 719 optimal weight: 7.9990 chunk 398 optimal weight: 2.9990 chunk 824 optimal weight: 30.0000 chunk 668 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 493 optimal weight: 3.9990 chunk 867 optimal weight: 20.0000 chunk 243 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 HIS ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2047 GLN ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 837 GLN ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN ** H 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN ** K 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 248 ASN M 252 HIS ** N 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 303 ASN o 247 ASN o 282 ASN ** o 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 91 GLN ** e 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5956 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 79543 Z= 0.291 Angle : 0.657 19.237 110386 Z= 0.336 Chirality : 0.042 0.289 13542 Planarity : 0.005 0.071 12622 Dihedral : 17.599 174.427 17101 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.74 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.09), residues: 9411 helix: 1.53 (0.08), residues: 4105 sheet: -1.24 (0.14), residues: 1352 loop : -1.78 (0.10), residues: 3954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1012 HIS 0.009 0.001 HIS M 252 PHE 0.041 0.002 PHE e 18 TYR 0.030 0.002 TYR A1620 ARG 0.005 0.001 ARG c 191 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 431 time to evaluate : 6.570 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: A 387 PHE cc_start: 0.8919 (m-80) cc_final: 0.8657 (m-10) REVERT: A 914 LEU cc_start: 0.9074 (mp) cc_final: 0.8741 (tp) REVERT: A 1519 LEU cc_start: 0.9311 (tp) cc_final: 0.8901 (tp) REVERT: A 1783 MET cc_start: 0.8699 (mtt) cc_final: 0.8372 (mtp) REVERT: A 1840 TYR cc_start: 0.8786 (t80) cc_final: 0.8071 (t80) REVERT: A 1986 MET cc_start: 0.8605 (tpt) cc_final: 0.8288 (tpt) REVERT: A 2005 PHE cc_start: 0.8880 (t80) cc_final: 0.8513 (t80) REVERT: C 209 MET cc_start: 0.8682 (ppp) cc_final: 0.8353 (ppp) REVERT: C 880 MET cc_start: 0.9496 (tpp) cc_final: 0.9157 (tpt) REVERT: H 155 MET cc_start: 0.8494 (mpp) cc_final: 0.8195 (mpp) REVERT: H 172 MET cc_start: 0.9384 (mmp) cc_final: 0.9161 (mmp) REVERT: H 350 MET cc_start: 0.9050 (mmm) cc_final: 0.8433 (mmm) REVERT: J 399 GLU cc_start: 0.9062 (tt0) cc_final: 0.8786 (tt0) REVERT: K 32 ASP cc_start: 0.8705 (t0) cc_final: 0.8503 (m-30) REVERT: N 107 ASP cc_start: 0.8971 (m-30) cc_final: 0.8397 (t70) REVERT: N 221 ASP cc_start: 0.9069 (p0) cc_final: 0.8818 (p0) REVERT: O 204 LYS cc_start: 0.7621 (mttt) cc_final: 0.7241 (tppt) REVERT: P 161 THR cc_start: 0.8091 (p) cc_final: 0.7455 (p) REVERT: P 162 LYS cc_start: 0.9132 (mttt) cc_final: 0.8922 (mmtt) REVERT: S 163 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8306 (tm-30) REVERT: c 181 GLU cc_start: 0.9203 (tm-30) cc_final: 0.8914 (pm20) REVERT: o 69 TRP cc_start: 0.7440 (t-100) cc_final: 0.6232 (t-100) REVERT: o 278 ARG cc_start: 0.8300 (mpp-170) cc_final: 0.7838 (mmm160) REVERT: b 5 GLN cc_start: 0.8795 (mt0) cc_final: 0.8187 (pp30) REVERT: b 48 CYS cc_start: 0.7885 (t) cc_final: 0.7553 (t) REVERT: d 76 ASP cc_start: 0.8968 (m-30) cc_final: 0.8417 (p0) REVERT: j 31 MET cc_start: 0.8702 (mpp) cc_final: 0.8422 (mpp) REVERT: l 104 ASP cc_start: 0.2692 (p0) cc_final: 0.2346 (t0) REVERT: m 31 MET cc_start: 0.1013 (mtt) cc_final: 0.0350 (mpp) REVERT: n 17 HIS cc_start: 0.3659 (m90) cc_final: 0.3432 (m90) REVERT: p 42 LYS cc_start: 0.7510 (mttt) cc_final: 0.7241 (ttpp) outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 0.7020 time to fit residues: 541.3585 Evaluate side-chains 349 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 7.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 325 optimal weight: 20.0000 chunk 870 optimal weight: 9.9990 chunk 191 optimal weight: 20.0000 chunk 567 optimal weight: 0.1980 chunk 238 optimal weight: 3.9990 chunk 967 optimal weight: 10.0000 chunk 803 optimal weight: 2.9990 chunk 447 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 320 optimal weight: 9.9990 chunk 507 optimal weight: 30.0000 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 ASN A 636 HIS ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 ASN A1202 ASN ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1947 HIS A2047 GLN ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 ASN ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 837 GLN ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 934 HIS ** H 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 306 HIS L 29 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 247 ASN ** o 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 8 HIS ** e 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 35 ASN ** m 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5940 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 79543 Z= 0.240 Angle : 0.627 24.711 110386 Z= 0.318 Chirality : 0.042 0.270 13542 Planarity : 0.004 0.068 12622 Dihedral : 17.496 173.245 17101 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.53 % Favored : 94.40 % Rotamer: Outliers : 0.02 % Allowed : 2.68 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.09), residues: 9411 helix: 1.71 (0.08), residues: 4101 sheet: -1.10 (0.14), residues: 1335 loop : -1.66 (0.10), residues: 3975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP J 209 HIS 0.007 0.001 HIS C 218 PHE 0.022 0.002 PHE S 88 TYR 0.055 0.002 TYR S 105 ARG 0.018 0.001 ARG A1442 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 441 time to evaluate : 6.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 PHE cc_start: 0.8857 (m-80) cc_final: 0.8625 (m-10) REVERT: A 578 MET cc_start: 0.8645 (mtp) cc_final: 0.8355 (mtp) REVERT: A 763 MET cc_start: 0.9333 (tmm) cc_final: 0.9104 (tmm) REVERT: A 914 LEU cc_start: 0.9026 (mp) cc_final: 0.8683 (tp) REVERT: A 1057 MET cc_start: 0.8756 (tmm) cc_final: 0.8421 (tmm) REVERT: A 1213 MET cc_start: 0.8462 (tpt) cc_final: 0.8226 (tpt) REVERT: A 1519 LEU cc_start: 0.9398 (tp) cc_final: 0.9122 (tp) REVERT: A 1703 MET cc_start: 0.7640 (mmm) cc_final: 0.7116 (mmm) REVERT: A 1732 MET cc_start: 0.8262 (tpp) cc_final: 0.7960 (tpp) REVERT: A 1783 MET cc_start: 0.8655 (mtt) cc_final: 0.8199 (mtp) REVERT: A 1840 TYR cc_start: 0.8782 (t80) cc_final: 0.8556 (t80) REVERT: C 126 MET cc_start: 0.8937 (tpp) cc_final: 0.8421 (tpp) REVERT: C 263 MET cc_start: 0.8824 (ptt) cc_final: 0.8445 (ptt) REVERT: C 391 MET cc_start: 0.8287 (ptm) cc_final: 0.7916 (ptm) REVERT: C 968 MET cc_start: 0.8840 (mmm) cc_final: 0.8526 (mmm) REVERT: H 147 SER cc_start: 0.8560 (t) cc_final: 0.8244 (m) REVERT: H 155 MET cc_start: 0.8570 (mpp) cc_final: 0.8268 (mpp) REVERT: J 399 GLU cc_start: 0.9017 (tt0) cc_final: 0.8721 (tt0) REVERT: N 107 ASP cc_start: 0.8978 (m-30) cc_final: 0.8303 (t70) REVERT: N 221 ASP cc_start: 0.9122 (p0) cc_final: 0.8909 (p0) REVERT: O 204 LYS cc_start: 0.7645 (mttt) cc_final: 0.7344 (tppt) REVERT: P 161 THR cc_start: 0.7988 (p) cc_final: 0.7724 (m) REVERT: S 122 MET cc_start: 0.8924 (ttt) cc_final: 0.8406 (tpt) REVERT: S 163 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8248 (tm-30) REVERT: S 174 ASP cc_start: 0.9040 (m-30) cc_final: 0.8670 (t70) REVERT: c 181 GLU cc_start: 0.9177 (tm-30) cc_final: 0.8932 (pm20) REVERT: o 69 TRP cc_start: 0.7327 (t-100) cc_final: 0.6133 (t-100) REVERT: o 278 ARG cc_start: 0.8264 (mpp-170) cc_final: 0.7839 (mmm160) REVERT: b 5 GLN cc_start: 0.8795 (mt0) cc_final: 0.8174 (pp30) REVERT: b 48 CYS cc_start: 0.7929 (t) cc_final: 0.7621 (t) REVERT: d 76 ASP cc_start: 0.8856 (m-30) cc_final: 0.8506 (p0) REVERT: j 31 MET cc_start: 0.8684 (mpp) cc_final: 0.8379 (mpp) REVERT: l 104 ASP cc_start: 0.2846 (p0) cc_final: 0.2485 (t0) REVERT: m 31 MET cc_start: 0.1412 (mtt) cc_final: 0.0895 (mpp) REVERT: p 42 LYS cc_start: 0.7395 (mttt) cc_final: 0.7121 (ttpp) outliers start: 1 outliers final: 0 residues processed: 442 average time/residue: 0.6915 time to fit residues: 547.8828 Evaluate side-chains 350 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 6.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 932 optimal weight: 30.0000 chunk 109 optimal weight: 0.5980 chunk 551 optimal weight: 8.9990 chunk 706 optimal weight: 2.9990 chunk 547 optimal weight: 5.9990 chunk 814 optimal weight: 5.9990 chunk 540 optimal weight: 0.0170 chunk 963 optimal weight: 20.0000 chunk 603 optimal weight: 0.0870 chunk 587 optimal weight: 30.0000 chunk 444 optimal weight: 9.9990 overall best weight: 1.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS A 558 GLN A 636 HIS ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 ASN ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1548 GLN A2047 GLN ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 ASN ** H 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 252 HIS ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 117 ASN ** N 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 193 GLN ** O 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 247 ASN o 282 ASN o 354 GLN ** o 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 184 GLN ** y 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 61 GLN ** e 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 94 GLN ** m 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 43 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5916 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 79543 Z= 0.193 Angle : 0.596 18.854 110386 Z= 0.302 Chirality : 0.041 0.371 13542 Planarity : 0.004 0.067 12622 Dihedral : 17.369 173.671 17101 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.67 % Favored : 94.27 % Rotamer: Outliers : 0.02 % Allowed : 1.71 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.09), residues: 9411 helix: 1.85 (0.08), residues: 4097 sheet: -0.99 (0.14), residues: 1315 loop : -1.56 (0.10), residues: 3999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP H 174 HIS 0.009 0.001 HIS M 252 PHE 0.045 0.002 PHE e 18 TYR 0.039 0.002 TYR S 105 ARG 0.011 0.000 ARG A1521 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 444 time to evaluate : 6.471 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: A 387 PHE cc_start: 0.8864 (m-80) cc_final: 0.8661 (m-10) REVERT: A 914 LEU cc_start: 0.8979 (mp) cc_final: 0.8638 (tp) REVERT: A 1057 MET cc_start: 0.8727 (tmm) cc_final: 0.8423 (tmm) REVERT: A 1213 MET cc_start: 0.8443 (tpt) cc_final: 0.8241 (tpt) REVERT: A 1519 LEU cc_start: 0.9382 (tp) cc_final: 0.9159 (tp) REVERT: A 1703 MET cc_start: 0.7897 (mmm) cc_final: 0.7523 (mmm) REVERT: A 1783 MET cc_start: 0.8467 (mtt) cc_final: 0.7964 (mtp) REVERT: A 1840 TYR cc_start: 0.8875 (t80) cc_final: 0.8637 (t80) REVERT: C 126 MET cc_start: 0.8867 (tpp) cc_final: 0.8422 (tpp) REVERT: C 391 MET cc_start: 0.8280 (ptm) cc_final: 0.7920 (ptm) REVERT: C 968 MET cc_start: 0.8872 (mmm) cc_final: 0.8539 (mmm) REVERT: H 147 SER cc_start: 0.8781 (t) cc_final: 0.8539 (p) REVERT: H 155 MET cc_start: 0.8571 (mpp) cc_final: 0.8277 (mpp) REVERT: H 172 MET cc_start: 0.9383 (mmp) cc_final: 0.9150 (mmp) REVERT: J 399 GLU cc_start: 0.8910 (tt0) cc_final: 0.8659 (tt0) REVERT: N 107 ASP cc_start: 0.8954 (m-30) cc_final: 0.8245 (t0) REVERT: N 221 ASP cc_start: 0.9102 (p0) cc_final: 0.8870 (p0) REVERT: O 204 LYS cc_start: 0.7595 (mttt) cc_final: 0.7336 (tppt) REVERT: S 98 PHE cc_start: 0.8933 (t80) cc_final: 0.8722 (t80) REVERT: S 163 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8221 (tm-30) REVERT: S 174 ASP cc_start: 0.9016 (m-30) cc_final: 0.8653 (t70) REVERT: a 138 ASP cc_start: 0.9174 (m-30) cc_final: 0.8494 (p0) REVERT: o 69 TRP cc_start: 0.7317 (t-100) cc_final: 0.6110 (t-100) REVERT: o 278 ARG cc_start: 0.8256 (mpp-170) cc_final: 0.7870 (mmm160) REVERT: b 5 GLN cc_start: 0.8824 (mt0) cc_final: 0.8204 (pp30) REVERT: d 76 ASP cc_start: 0.8802 (m-30) cc_final: 0.8429 (p0) REVERT: g 44 MET cc_start: 0.6213 (tpt) cc_final: 0.5875 (tpp) REVERT: j 31 MET cc_start: 0.8702 (mpp) cc_final: 0.8402 (mpp) REVERT: l 104 ASP cc_start: 0.2794 (p0) cc_final: 0.2415 (t0) REVERT: m 31 MET cc_start: 0.2397 (mtt) cc_final: 0.1925 (mpp) REVERT: n 58 HIS cc_start: 0.5382 (m-70) cc_final: 0.5009 (t70) REVERT: p 42 LYS cc_start: 0.7362 (mttt) cc_final: 0.7063 (ttpp) outliers start: 1 outliers final: 0 residues processed: 445 average time/residue: 0.6736 time to fit residues: 542.2802 Evaluate side-chains 349 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 6.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 596 optimal weight: 10.0000 chunk 384 optimal weight: 0.9990 chunk 575 optimal weight: 40.0000 chunk 290 optimal weight: 8.9990 chunk 189 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 612 optimal weight: 3.9990 chunk 656 optimal weight: 9.9990 chunk 476 optimal weight: 1.9990 chunk 89 optimal weight: 0.2980 chunk 757 optimal weight: 30.0000 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 HIS ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2047 GLN ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 371 GLN ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 ASN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 303 ASN o 247 ASN ** o 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 52 HIS ** l 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5904 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 79543 Z= 0.183 Angle : 0.580 17.888 110386 Z= 0.294 Chirality : 0.040 0.350 13542 Planarity : 0.004 0.065 12622 Dihedral : 17.261 173.941 17101 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.10 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.09), residues: 9411 helix: 1.97 (0.08), residues: 4083 sheet: -0.92 (0.14), residues: 1335 loop : -1.49 (0.10), residues: 3993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP J 209 HIS 0.009 0.001 HIS J 382 PHE 0.032 0.001 PHE e 18 TYR 0.037 0.002 TYR A 655 ARG 0.008 0.000 ARG A1442 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 449 time to evaluate : 6.468 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: A 134 MET cc_start: 0.7356 (ptp) cc_final: 0.6284 (pmm) REVERT: A 139 LEU cc_start: 0.9134 (tt) cc_final: 0.8910 (tt) REVERT: A 578 MET cc_start: 0.8508 (mtp) cc_final: 0.8151 (mtp) REVERT: A 763 MET cc_start: 0.9289 (tmm) cc_final: 0.8904 (tmm) REVERT: A 914 LEU cc_start: 0.8968 (mp) cc_final: 0.8611 (tp) REVERT: A 1057 MET cc_start: 0.8710 (tmm) cc_final: 0.8409 (tmm) REVERT: A 1213 MET cc_start: 0.8474 (tpt) cc_final: 0.8274 (tpt) REVERT: A 1379 MET cc_start: 0.8095 (tpp) cc_final: 0.7750 (tpp) REVERT: A 1519 LEU cc_start: 0.9394 (tp) cc_final: 0.9172 (tp) REVERT: A 1703 MET cc_start: 0.7769 (mmm) cc_final: 0.7365 (mmm) REVERT: A 1732 MET cc_start: 0.8185 (tpp) cc_final: 0.7879 (tpp) REVERT: A 1783 MET cc_start: 0.8453 (mtt) cc_final: 0.7946 (mtp) REVERT: A 1840 TYR cc_start: 0.8965 (t80) cc_final: 0.8453 (t80) REVERT: A 1945 GLU cc_start: 0.9570 (mt-10) cc_final: 0.9315 (mt-10) REVERT: A 2005 PHE cc_start: 0.9207 (t80) cc_final: 0.8731 (t80) REVERT: C 126 MET cc_start: 0.8802 (tpp) cc_final: 0.8425 (tpp) REVERT: C 348 LEU cc_start: 0.9255 (mt) cc_final: 0.9018 (mt) REVERT: H 20 MET cc_start: 0.6041 (ppp) cc_final: 0.5552 (ptm) REVERT: H 147 SER cc_start: 0.8810 (t) cc_final: 0.8560 (p) REVERT: H 155 MET cc_start: 0.8532 (mpp) cc_final: 0.8179 (mpp) REVERT: H 172 MET cc_start: 0.9348 (mmp) cc_final: 0.9110 (mmp) REVERT: J 183 MET cc_start: 0.8157 (mtt) cc_final: 0.7819 (mtp) REVERT: J 399 GLU cc_start: 0.8854 (tt0) cc_final: 0.8584 (tt0) REVERT: N 107 ASP cc_start: 0.8949 (m-30) cc_final: 0.8263 (t70) REVERT: N 221 ASP cc_start: 0.8912 (p0) cc_final: 0.8628 (p0) REVERT: O 204 LYS cc_start: 0.7676 (mttt) cc_final: 0.7346 (tppt) REVERT: S 98 PHE cc_start: 0.8936 (t80) cc_final: 0.8693 (t80) REVERT: S 163 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8228 (tm-30) REVERT: S 174 ASP cc_start: 0.8989 (m-30) cc_final: 0.8651 (t70) REVERT: a 138 ASP cc_start: 0.9181 (m-30) cc_final: 0.8531 (p0) REVERT: o 69 TRP cc_start: 0.7279 (t-100) cc_final: 0.6077 (t-100) REVERT: o 239 LYS cc_start: 0.8594 (mtmt) cc_final: 0.8275 (pttm) REVERT: o 278 ARG cc_start: 0.8418 (mpp-170) cc_final: 0.7877 (mmm160) REVERT: b 5 GLN cc_start: 0.8933 (mt0) cc_final: 0.8236 (pp30) REVERT: d 76 ASP cc_start: 0.8819 (m-30) cc_final: 0.8464 (p0) REVERT: g 44 MET cc_start: 0.5909 (tpt) cc_final: 0.5574 (tpp) REVERT: j 31 MET cc_start: 0.8721 (mpp) cc_final: 0.8421 (mpp) REVERT: l 104 ASP cc_start: 0.2934 (p0) cc_final: 0.2535 (t0) REVERT: m 31 MET cc_start: 0.1671 (mtt) cc_final: 0.1173 (mpp) REVERT: m 38 MET cc_start: 0.0299 (ttt) cc_final: -0.0087 (tpp) REVERT: m 61 PHE cc_start: -0.0050 (t80) cc_final: -0.0309 (t80) REVERT: n 58 HIS cc_start: 0.5444 (m-70) cc_final: 0.5176 (t70) REVERT: p 42 LYS cc_start: 0.7125 (mttt) cc_final: 0.6811 (ttpp) outliers start: 0 outliers final: 0 residues processed: 449 average time/residue: 0.6690 time to fit residues: 538.5718 Evaluate side-chains 353 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 6.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 876 optimal weight: 10.0000 chunk 923 optimal weight: 30.0000 chunk 842 optimal weight: 7.9990 chunk 898 optimal weight: 50.0000 chunk 540 optimal weight: 6.9990 chunk 391 optimal weight: 9.9990 chunk 705 optimal weight: 5.9990 chunk 275 optimal weight: 6.9990 chunk 811 optimal weight: 4.9990 chunk 849 optimal weight: 30.0000 chunk 895 optimal weight: 50.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 HIS A 596 ASN ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 ASN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 ASN ** A1404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2047 GLN ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 ASN ** C 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 457 HIS ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 GLN M 180 ASN ** N 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 GLN ** S 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 247 ASN ** o 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 5 ASN r 66 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6051 moved from start: 0.6216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.124 79543 Z= 0.432 Angle : 0.790 19.544 110386 Z= 0.404 Chirality : 0.045 0.318 13542 Planarity : 0.006 0.144 12622 Dihedral : 17.606 171.556 17101 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 25.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.77 % Favored : 92.18 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.09), residues: 9411 helix: 1.31 (0.08), residues: 4057 sheet: -1.02 (0.14), residues: 1320 loop : -1.67 (0.10), residues: 4034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A1286 HIS 0.012 0.002 HIS S 117 PHE 0.035 0.003 PHE o 226 TYR 0.052 0.003 TYR S 139 ARG 0.011 0.001 ARG C 401 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 6.504 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: A 134 MET cc_start: 0.8128 (ptp) cc_final: 0.7749 (pmm) REVERT: A 387 PHE cc_start: 0.8925 (m-80) cc_final: 0.8603 (m-10) REVERT: A 578 MET cc_start: 0.8553 (mtp) cc_final: 0.8180 (mtp) REVERT: A 634 ASP cc_start: 0.9033 (m-30) cc_final: 0.8430 (t0) REVERT: A 763 MET cc_start: 0.9326 (tmm) cc_final: 0.8607 (tmm) REVERT: A 804 MET cc_start: 0.7577 (mmp) cc_final: 0.7307 (mmp) REVERT: A 914 LEU cc_start: 0.9178 (mp) cc_final: 0.8823 (tp) REVERT: A 1213 MET cc_start: 0.8526 (tpt) cc_final: 0.8326 (tpp) REVERT: A 1379 MET cc_start: 0.8726 (tpp) cc_final: 0.7813 (tpp) REVERT: A 1519 LEU cc_start: 0.9445 (tp) cc_final: 0.9235 (tp) REVERT: A 1703 MET cc_start: 0.7976 (mmm) cc_final: 0.7605 (mmm) REVERT: A 1783 MET cc_start: 0.8075 (mtt) cc_final: 0.7820 (mtp) REVERT: A 1840 TYR cc_start: 0.9007 (t80) cc_final: 0.7942 (t80) REVERT: A 1979 MET cc_start: 0.8771 (tpp) cc_final: 0.8451 (tmm) REVERT: A 1986 MET cc_start: 0.9169 (tpt) cc_final: 0.8184 (tpt) REVERT: A 2005 PHE cc_start: 0.9249 (t80) cc_final: 0.8766 (t80) REVERT: C 126 MET cc_start: 0.8980 (tpp) cc_final: 0.8665 (tpp) REVERT: C 263 MET cc_start: 0.8906 (ptt) cc_final: 0.8583 (ptt) REVERT: C 391 MET cc_start: 0.8327 (ptm) cc_final: 0.7682 (ptm) REVERT: C 968 MET cc_start: 0.8951 (mmm) cc_final: 0.8545 (mmm) REVERT: H 155 MET cc_start: 0.8676 (mpp) cc_final: 0.8300 (mpp) REVERT: J 183 MET cc_start: 0.8284 (mtt) cc_final: 0.7965 (mtp) REVERT: N 107 ASP cc_start: 0.9105 (m-30) cc_final: 0.8622 (t70) REVERT: O 204 LYS cc_start: 0.7772 (mttt) cc_final: 0.7524 (tppt) REVERT: S 163 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8374 (tm-30) REVERT: o 239 LYS cc_start: 0.8665 (mtmt) cc_final: 0.8378 (ptpp) REVERT: o 278 ARG cc_start: 0.8438 (mpp-170) cc_final: 0.7768 (mmm160) REVERT: o 281 GLU cc_start: 0.7261 (pm20) cc_final: 0.7013 (pm20) REVERT: b 5 GLN cc_start: 0.8979 (mt0) cc_final: 0.8296 (pp30) REVERT: b 41 MET cc_start: 0.9564 (tpp) cc_final: 0.9095 (ttp) REVERT: b 48 CYS cc_start: 0.8300 (t) cc_final: 0.8066 (t) REVERT: d 76 ASP cc_start: 0.9209 (m-30) cc_final: 0.8454 (p0) REVERT: g 44 MET cc_start: 0.6511 (tpt) cc_final: 0.6255 (tpp) REVERT: l 104 ASP cc_start: 0.3063 (p0) cc_final: 0.2559 (t0) REVERT: m 31 MET cc_start: 0.1414 (mtt) cc_final: 0.0842 (mpp) REVERT: m 38 MET cc_start: 0.0484 (ttt) cc_final: 0.0044 (tpp) REVERT: n 58 HIS cc_start: 0.4761 (m-70) cc_final: 0.4526 (t70) REVERT: p 42 LYS cc_start: 0.6889 (mttt) cc_final: 0.6557 (ttpp) outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.6962 time to fit residues: 516.2563 Evaluate side-chains 335 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 6.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 589 optimal weight: 50.0000 chunk 949 optimal weight: 20.0000 chunk 579 optimal weight: 0.0370 chunk 450 optimal weight: 10.0000 chunk 660 optimal weight: 2.9990 chunk 996 optimal weight: 0.0670 chunk 916 optimal weight: 50.0000 chunk 793 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 612 optimal weight: 6.9990 chunk 486 optimal weight: 4.9990 overall best weight: 1.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN A 481 HIS ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 ASN A1404 HIS A1424 HIS A2047 GLN ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN C 934 HIS ** H 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 247 ASN o 283 GLN ** o 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 17 HIS n 43 GLN r 55 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5948 moved from start: 0.6240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 79543 Z= 0.195 Angle : 0.613 18.512 110386 Z= 0.309 Chirality : 0.041 0.273 13542 Planarity : 0.004 0.067 12622 Dihedral : 17.397 174.374 17101 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.03 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.09), residues: 9411 helix: 1.72 (0.08), residues: 4086 sheet: -0.92 (0.14), residues: 1325 loop : -1.55 (0.10), residues: 4000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP C 933 HIS 0.009 0.001 HIS J 382 PHE 0.031 0.002 PHE e 18 TYR 0.052 0.002 TYR S 105 ARG 0.008 0.000 ARG A1347 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18822 Ramachandran restraints generated. 9411 Oldfield, 0 Emsley, 9411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 429 time to evaluate : 6.738 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: A 134 MET cc_start: 0.7683 (ptp) cc_final: 0.6535 (pmm) REVERT: A 210 GLU cc_start: 0.8924 (tt0) cc_final: 0.8681 (tm-30) REVERT: A 578 MET cc_start: 0.8557 (mtp) cc_final: 0.8244 (mtp) REVERT: A 763 MET cc_start: 0.9257 (tmm) cc_final: 0.8434 (tmm) REVERT: A 914 LEU cc_start: 0.8915 (mp) cc_final: 0.8607 (tp) REVERT: A 1057 MET cc_start: 0.8861 (tmm) cc_final: 0.8650 (tmm) REVERT: A 1117 TYR cc_start: 0.8788 (t80) cc_final: 0.8510 (t80) REVERT: A 1213 MET cc_start: 0.8425 (tpt) cc_final: 0.8137 (tpt) REVERT: A 1703 MET cc_start: 0.7757 (mmm) cc_final: 0.7458 (mmm) REVERT: A 1732 MET cc_start: 0.8209 (tpp) cc_final: 0.7838 (tpp) REVERT: A 1783 MET cc_start: 0.7998 (mtt) cc_final: 0.7742 (mtp) REVERT: A 1840 TYR cc_start: 0.8902 (t80) cc_final: 0.7766 (t80) REVERT: A 1986 MET cc_start: 0.8894 (tpt) cc_final: 0.8555 (tpt) REVERT: A 2005 PHE cc_start: 0.9256 (t80) cc_final: 0.8632 (t80) REVERT: C 126 MET cc_start: 0.8825 (tpp) cc_final: 0.8435 (tpp) REVERT: C 263 MET cc_start: 0.8852 (ptt) cc_final: 0.8428 (ptt) REVERT: C 968 MET cc_start: 0.8939 (mmm) cc_final: 0.8458 (mmm) REVERT: H 155 MET cc_start: 0.8489 (mpp) cc_final: 0.8136 (mpp) REVERT: J 183 MET cc_start: 0.8130 (mtt) cc_final: 0.7785 (mtp) REVERT: K 149 MET cc_start: 0.8132 (ppp) cc_final: 0.7891 (ppp) REVERT: N 107 ASP cc_start: 0.9064 (m-30) cc_final: 0.8508 (t70) REVERT: S 122 MET cc_start: 0.8883 (ttm) cc_final: 0.8553 (ttm) REVERT: S 163 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8232 (tm-30) REVERT: S 174 ASP cc_start: 0.9091 (m-30) cc_final: 0.8719 (t70) REVERT: a 184 MET cc_start: 0.8621 (ttp) cc_final: 0.8264 (ttp) REVERT: o 69 TRP cc_start: 0.7181 (t-100) cc_final: 0.6088 (t-100) REVERT: o 239 LYS cc_start: 0.8515 (mtmt) cc_final: 0.8294 (pttm) REVERT: b 5 GLN cc_start: 0.8990 (mt0) cc_final: 0.8284 (pp30) REVERT: b 41 MET cc_start: 0.9515 (tpp) cc_final: 0.9028 (ttp) REVERT: d 76 ASP cc_start: 0.9227 (m-30) cc_final: 0.8474 (p0) REVERT: g 44 MET cc_start: 0.6629 (tpt) cc_final: 0.6353 (tpp) REVERT: j 31 MET cc_start: 0.8745 (mpp) cc_final: 0.8438 (mpp) REVERT: l 104 ASP cc_start: 0.3119 (p0) cc_final: 0.2599 (t0) REVERT: m 31 MET cc_start: 0.1389 (mtt) cc_final: 0.0824 (mpp) REVERT: m 38 MET cc_start: 0.0577 (ttt) cc_final: 0.0110 (tpp) REVERT: n 58 HIS cc_start: 0.5051 (m-70) cc_final: 0.4837 (t70) REVERT: p 42 LYS cc_start: 0.6907 (mttt) cc_final: 0.6596 (ttpp) outliers start: 0 outliers final: 0 residues processed: 429 average time/residue: 0.6854 time to fit residues: 535.1071 Evaluate side-chains 343 residues out of total 8767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 343 time to evaluate : 6.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1000 random chunks: chunk 630 optimal weight: 3.9990 chunk 845 optimal weight: 50.0000 chunk 243 optimal weight: 0.0870 chunk 731 optimal weight: 20.0000 chunk 117 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 794 optimal weight: 3.9990 chunk 332 optimal weight: 7.9990 chunk 815 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2047 GLN C 194 ASN ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 444 GLN H 362 ASN ** H 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 247 ASN ** o 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 86 ASN ** m 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 17 HIS n 43 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.080101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.062307 restraints weight = 676003.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.061394 restraints weight = 497047.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.061896 restraints weight = 371832.835| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.6371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 79543 Z= 0.207 Angle : 0.598 18.995 110386 Z= 0.302 Chirality : 0.041 0.307 13542 Planarity : 0.004 0.066 12622 Dihedral : 17.289 175.667 17101 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.99 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.09), residues: 9411 helix: 1.84 (0.08), residues: 4082 sheet: -0.91 (0.14), residues: 1357 loop : -1.49 (0.10), residues: 3972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 933 HIS 0.007 0.001 HIS c 309 PHE 0.034 0.002 PHE J 365 TYR 0.047 0.002 TYR S 105 ARG 0.008 0.000 ARG n 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13390.30 seconds wall clock time: 239 minutes 21.37 seconds (14361.37 seconds total)