Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 02:16:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwn_34317/04_2023/8gwn_34317_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwn_34317/04_2023/8gwn_34317.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwn_34317/04_2023/8gwn_34317.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwn_34317/04_2023/8gwn_34317.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwn_34317/04_2023/8gwn_34317_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwn_34317/04_2023/8gwn_34317_updated.pdb" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.031 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: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 55 5.49 5 S 157 5.16 5 C 13680 2.51 5 N 3680 2.21 5 O 4280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 10": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ASP 36": "OD1" <-> "OD2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A ASP 208": "OD1" <-> "OD2" Residue "A ASP 235": "OD1" <-> "OD2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 350": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A ASP 418": "OD1" <-> "OD2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 608": "OD1" <-> "OD2" Residue "A ASP 618": "OD1" <-> "OD2" Residue "A ASP 623": "OD1" <-> "OD2" Residue "A PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 711": "OD1" <-> "OD2" Residue "A TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 736": "OD1" <-> "OD2" Residue "A ASP 738": "OD1" <-> "OD2" Residue "A TYR 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 761": "OD1" <-> "OD2" Residue "A PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 824": "OD1" <-> "OD2" Residue "A TYR 828": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A ASP 851": "OD1" <-> "OD2" Residue "A GLU 857": "OE1" <-> "OE2" Residue "A PHE 859": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 865": "OD1" <-> "OD2" Residue "B TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 52": "OD1" <-> "OD2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D ASP 50": "OD1" <-> "OD2" Residue "D ASP 52": "OD1" <-> "OD2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D ASP 64": "OD1" <-> "OD2" Residue "D TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 77": "OE1" <-> "OE2" Residue "D ASP 78": "OD1" <-> "OD2" Residue "D TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "F PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 129": "NH1" <-> "NH2" Residue "F PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 136": "OE1" <-> "OE2" Residue "F GLU 142": "OE1" <-> "OE2" Residue "F TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 156": "OE1" <-> "OE2" Residue "F GLU 168": "OE1" <-> "OE2" Residue "F TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 260": "OD1" <-> "OD2" Residue "F GLU 261": "OE1" <-> "OE2" Residue "F PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 319": "OE1" <-> "OE2" Residue "F ASP 328": "OD1" <-> "OD2" Residue "F GLU 341": "OE1" <-> "OE2" Residue "F GLU 353": "OE1" <-> "OE2" Residue "F ASP 369": "OD1" <-> "OD2" Residue "F PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 374": "OD1" <-> "OD2" Residue "F GLU 375": "OE1" <-> "OE2" Residue "F TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 418": "OE1" <-> "OE2" Residue "F TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 435": "OD1" <-> "OD2" Residue "F PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 442": "NH1" <-> "NH2" Residue "F TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 466": "OD1" <-> "OD2" Residue "F PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 483": "OD1" <-> "OD2" Residue "F ARG 507": "NH1" <-> "NH2" Residue "F TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 580": "OD1" <-> "OD2" Residue "F PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 59": "OD1" <-> "OD2" Residue "E TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 113": "OD1" <-> "OD2" Residue "E TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "E TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 168": "OE1" <-> "OE2" Residue "E PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 223": "OD1" <-> "OD2" Residue "E TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 260": "OD1" <-> "OD2" Residue "E TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 315": "OD1" <-> "OD2" Residue "E GLU 319": "OE1" <-> "OE2" Residue "E ASP 328": "OD1" <-> "OD2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 369": "OD1" <-> "OD2" Residue "E ASP 374": "OD1" <-> "OD2" Residue "E TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 418": "OE1" <-> "OE2" Residue "E PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 435": "OD1" <-> "OD2" Residue "E PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 442": "NH1" <-> "NH2" Residue "E ASP 450": "OD1" <-> "OD2" Residue "E ASP 458": "OD1" <-> "OD2" Residue "E PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 507": "NH1" <-> "NH2" Residue "E TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 542": "OD1" <-> "OD2" Residue "E ASP 580": "OD1" <-> "OD2" Residue "G GLU 3": "OE1" <-> "OE2" Residue "G ASP 25": "OD1" <-> "OD2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 47": "OD1" <-> "OD2" Residue "G ASP 60": "OD1" <-> "OD2" Residue "G GLU 68": "OE1" <-> "OE2" Residue "G TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 21860 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 926, 7458 Classifications: {'peptide': 926} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 895} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1396 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 553 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "D" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1414 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 179} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 16, 'rna3p_pyr': 8} Link IDs: {'rna3p': 24} Chain: "J" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 565 Classifications: {'RNA': 27} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 25} Chain: "F" Number of atoms: 4508 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4593 Chain: "E" Number of atoms: 4513 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4598 Chain: "G" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 868 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' ZN': 2, 'GNP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" 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: "E" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2446 SG CYS A 301 74.280 54.942 120.937 1.00 61.03 S ATOM 2487 SG CYS A 306 74.416 55.990 124.470 1.00 52.01 S ATOM 2519 SG CYS A 310 75.733 52.495 123.381 1.00 54.62 S ATOM 3927 SG CYS A 487 76.596 68.467 104.297 1.00 81.63 S ATOM 5180 SG CYS A 645 76.072 70.276 107.632 1.00 97.07 S ATOM 5186 SG CYS A 646 74.444 67.003 107.129 1.00 93.93 S ATOM 12035 SG CYS F 16 102.069 64.263 49.138 1.00184.25 S ATOM 12050 SG CYS F 19 102.611 61.058 47.444 1.00216.23 S ATOM 11953 SG CYS F 5 114.775 65.599 50.631 1.00195.56 S ATOM 11974 SG CYS F 8 115.770 67.865 48.306 1.00207.32 S ATOM 12112 SG CYS F 26 113.677 69.268 51.082 1.00170.90 S ATOM 12129 SG CYS F 29 112.210 67.456 47.985 1.00173.45 S ATOM 12294 SG CYS F 50 91.661 75.350 63.482 1.00170.32 S ATOM 12324 SG CYS F 55 88.824 73.752 61.593 1.00174.05 S ATOM 12457 SG CYS F 72 89.998 77.327 60.561 1.00173.25 S ATOM 16548 SG CYS E 16 59.780 73.270 64.162 1.00158.57 S ATOM 16563 SG CYS E 19 57.247 70.438 63.668 1.00176.05 S ATOM 16466 SG CYS E 5 69.445 69.147 57.445 1.00167.73 S ATOM 16487 SG CYS E 8 68.770 71.370 54.348 1.00188.38 S ATOM 16625 SG CYS E 26 70.633 73.072 57.176 1.00171.23 S ATOM 16642 SG CYS E 29 67.187 72.462 57.046 1.00180.75 S ATOM 16807 SG CYS E 50 65.123 86.919 78.331 1.00196.86 S ATOM 16837 SG CYS E 55 61.510 87.331 79.191 1.00214.41 S ATOM 16970 SG CYS E 72 62.922 88.544 75.859 1.00205.06 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AMET F 474 " occ=0.41 ... (14 atoms not shown) pdb=" CE BMET F 474 " occ=0.59 residue: pdb=" N AMET E 474 " occ=0.41 ... (14 atoms not shown) pdb=" CE BMET E 474 " occ=0.59 Time building chain proxies: 16.03, per 1000 atoms: 0.73 Number of scatterers: 21860 At special positions: 0 Unit cell: (154.16, 135.3, 182.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 157 16.00 P 55 15.00 O 4280 8.00 N 3680 7.00 C 13680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.99 Conformation dependent library (CDL) restraints added in 4.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 16 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 19 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 26 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 5 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" NE2 HIS E 75 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 72 " pdb=" ZN F 701 " pdb="ZN ZN F 701 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F 701 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 19 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 16 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 8 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 26 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 5 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 29 " pdb=" ZN F 703 " pdb="ZN ZN F 703 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 55 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 72 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 50 " Number of angles added : 28 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5068 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 83 helices and 20 sheets defined 32.3% alpha, 5.3% beta 14 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 7.40 Creating SS restraints... Processing helix chain 'A' and resid 6 through 11 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 78 through 90 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 154 through 157 Processing helix chain 'A' and resid 171 through 177 removed outlier: 4.275A pdb=" N ASN A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 199 Processing helix chain 'A' and resid 236 through 247 Proline residue: A 243 - end of helix removed outlier: 4.712A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 305 through 317 removed outlier: 4.727A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 375 Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 449 through 458 removed outlier: 4.914A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 481 removed outlier: 5.683A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 512 through 517 Processing helix chain 'A' and resid 521 through 528 Processing helix chain 'A' and resid 562 through 579 removed outlier: 4.926A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 605 Processing helix chain 'A' and resid 628 through 638 Processing helix chain 'A' and resid 649 through 662 Processing helix chain 'A' and resid 687 through 708 removed outlier: 4.083A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 731 Processing helix chain 'A' and resid 739 through 751 Processing helix chain 'A' and resid 780 through 790 Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 853 through 865 removed outlier: 3.912A pdb=" N ILE A 856 " --> pdb=" O THR A 853 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N GLU A 857 " --> pdb=" O LEU A 854 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE A 859 " --> pdb=" O ILE A 856 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL A 860 " --> pdb=" O GLU A 857 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 862 " --> pdb=" O PHE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 902 removed outlier: 3.671A pdb=" N ASP A 879 " --> pdb=" O GLN A 875 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY A 897 " --> pdb=" O ASP A 893 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N MET A 902 " --> pdb=" O HIS A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 921 No H-bonds generated for 'chain 'A' and resid 918 through 921' Processing helix chain 'A' and resid 923 through 925 No H-bonds generated for 'chain 'A' and resid 923 through 925' Processing helix chain 'B' and resid 12 through 28 Processing helix chain 'B' and resid 33 through 49 removed outlier: 3.564A pdb=" N LEU B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 94 removed outlier: 4.724A pdb=" N ARG B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'C' and resid 3 through 20 removed outlier: 3.801A pdb=" N LEU C 20 " --> pdb=" O VAL C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 39 removed outlier: 3.521A pdb=" N CYS C 32 " --> pdb=" O TRP C 29 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 33 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS C 36 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE C 39 " --> pdb=" O HIS C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 60 removed outlier: 3.508A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 70 No H-bonds generated for 'chain 'C' and resid 67 through 70' Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 32 through 40 Processing helix chain 'D' and resid 43 through 49 Processing helix chain 'D' and resid 52 through 81 removed outlier: 4.594A pdb=" N ARG D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ALA D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 98 removed outlier: 4.494A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 112 Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'F' and resid 27 through 36 removed outlier: 4.304A pdb=" N SER F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 110 Processing helix chain 'F' and resid 117 through 123 Processing helix chain 'F' and resid 128 through 146 Processing helix chain 'F' and resid 266 through 272 removed outlier: 5.289A pdb=" N LYS F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 298 removed outlier: 3.824A pdb=" N LEU F 297 " --> pdb=" O ILE F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 324 removed outlier: 4.234A pdb=" N ALA F 316 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LEU F 317 " --> pdb=" O ALA F 313 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU F 322 " --> pdb=" O CYS F 318 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 390 removed outlier: 3.846A pdb=" N VAL F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN F 388 " --> pdb=" O LEU F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 422 Processing helix chain 'F' and resid 424 through 428 removed outlier: 3.547A pdb=" N LEU F 428 " --> pdb=" O SER F 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 424 through 428' Processing helix chain 'F' and resid 448 through 453 Processing helix chain 'F' and resid 490 through 502 Processing helix chain 'F' and resid 516 through 522 Processing helix chain 'F' and resid 553 through 556 No H-bonds generated for 'chain 'F' and resid 553 through 556' Processing helix chain 'F' and resid 562 through 567 removed outlier: 3.818A pdb=" N THR F 566 " --> pdb=" O ASN F 562 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG F 567 " --> pdb=" O VAL F 563 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 562 through 567' Processing helix chain 'E' and resid 27 through 35 Processing helix chain 'E' and resid 104 through 111 Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'E' and resid 128 through 146 Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 263 through 272 removed outlier: 4.094A pdb=" N ALA E 267 " --> pdb=" O SER E 263 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN E 268 " --> pdb=" O SER E 264 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 298 removed outlier: 5.137A pdb=" N ILE E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU E 297 " --> pdb=" O ILE E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 324 removed outlier: 3.834A pdb=" N ALA E 321 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU E 322 " --> pdb=" O CYS E 318 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS E 323 " --> pdb=" O GLU E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 390 Processing helix chain 'E' and resid 419 through 421 No H-bonds generated for 'chain 'E' and resid 419 through 421' Processing helix chain 'E' and resid 424 through 428 Processing helix chain 'E' and resid 447 through 455 Processing helix chain 'E' and resid 490 through 500 removed outlier: 4.807A pdb=" N VAL E 495 " --> pdb=" O PRO E 491 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG E 497 " --> pdb=" O ILE E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 504 through 506 No H-bonds generated for 'chain 'E' and resid 504 through 506' Processing helix chain 'E' and resid 517 through 525 removed outlier: 4.402A pdb=" N LYS E 524 " --> pdb=" O ALA E 520 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE E 525 " --> pdb=" O VAL E 521 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 109 Processing sheet with id= A, first strand: chain 'A' and resid 202 through 204 removed outlier: 6.228A pdb=" N VAL A 231 " --> pdb=" O GLY A 203 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 331 through 335 removed outlier: 3.511A pdb=" N ARG A 331 " --> pdb=" O VAL A 342 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL A 342 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 345 through 347 Processing sheet with id= D, first strand: chain 'A' and resid 816 through 818 Processing sheet with id= E, first strand: chain 'B' and resid 129 through 131 Processing sheet with id= F, first strand: chain 'B' and resid 146 through 149 removed outlier: 3.659A pdb=" N TYR B 149 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA B 152 " --> pdb=" O TYR B 149 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 153 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 146 through 149 Processing sheet with id= H, first strand: chain 'F' and resid 183 through 185 removed outlier: 3.609A pdb=" N TYR F 224 " --> pdb=" O TYR F 185 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 277 through 279 removed outlier: 7.006A pdb=" N TYR F 396 " --> pdb=" O SER F 278 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'F' and resid 330 through 332 removed outlier: 6.407A pdb=" N TYR F 355 " --> pdb=" O SER F 331 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'F' and resid 545 through 547 removed outlier: 6.725A pdb=" N LEU F 573 " --> pdb=" O PHE F 546 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'F' and resid 154 through 157 removed outlier: 3.639A pdb=" N ARG F 155 " --> pdb=" O HIS F 164 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N HIS F 164 " --> pdb=" O ARG F 155 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 64 through 66 removed outlier: 4.119A pdb=" N GLY E 66 " --> pdb=" O SER E 69 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 192 through 198 removed outlier: 6.424A pdb=" N GLY E 184 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLU E 197 " --> pdb=" O PHE E 182 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE E 182 " --> pdb=" O GLU E 197 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL E 226 " --> pdb=" O THR E 183 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N HIS E 164 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 277 through 279 removed outlier: 5.728A pdb=" N TYR E 396 " --> pdb=" O SER E 278 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'E' and resid 355 through 357 removed outlier: 5.870A pdb=" N ILE E 304 " --> pdb=" O VAL E 356 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE E 370 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N THR E 307 " --> pdb=" O ILE E 370 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL E 372 " --> pdb=" O THR E 307 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'E' and resid 511 through 513 removed outlier: 4.408A pdb=" N GLN E 531 " --> pdb=" O PHE E 511 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER E 513 " --> pdb=" O GLN E 531 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'E' and resid 543 through 546 removed outlier: 6.512A pdb=" N GLY E 571 " --> pdb=" O VAL E 544 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N PHE E 546 " --> pdb=" O GLY E 571 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LEU E 573 " --> pdb=" O PHE E 546 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'G' and resid 74 through 79 removed outlier: 3.616A pdb=" N LYS G 86 " --> pdb=" O PHE G 75 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR G 79 " --> pdb=" O GLY G 82 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N TYR G 31 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 53 through 57 521 hydrogen bonds defined for protein. 1479 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 6.99 Time building geometry restraints manager: 11.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3631 1.31 - 1.44: 6360 1.44 - 1.57: 12114 1.57 - 1.70: 105 1.70 - 1.83: 224 Bond restraints: 22434 Sorted by residual: bond pdb=" CA ALA A 130 " pdb=" C ALA A 130 " ideal model delta sigma weight residual 1.523 1.383 0.140 1.34e-02 5.57e+03 1.09e+02 bond pdb=" CA MET A 899 " pdb=" C MET A 899 " ideal model delta sigma weight residual 1.522 1.407 0.116 1.37e-02 5.33e+03 7.14e+01 bond pdb=" CA GLN A 210 " pdb=" CB GLN A 210 " ideal model delta sigma weight residual 1.530 1.420 0.110 1.69e-02 3.50e+03 4.23e+01 bond pdb=" CA ALA A 176 " pdb=" C ALA A 176 " ideal model delta sigma weight residual 1.523 1.438 0.085 1.34e-02 5.57e+03 4.05e+01 bond pdb=" CA ASN B 100 " pdb=" C ASN B 100 " ideal model delta sigma weight residual 1.530 1.468 0.062 1.14e-02 7.69e+03 2.98e+01 ... (remaining 22429 not shown) Histogram of bond angle deviations from ideal: 97.12 - 105.72: 733 105.72 - 114.31: 13354 114.31 - 122.91: 14864 122.91 - 131.50: 1769 131.50 - 140.10: 34 Bond angle restraints: 30754 Sorted by residual: angle pdb=" N VAL C 22 " pdb=" CA VAL C 22 " pdb=" C VAL C 22 " ideal model delta sigma weight residual 112.83 105.42 7.41 9.90e-01 1.02e+00 5.60e+01 angle pdb=" CA CYS E 72 " pdb=" C CYS E 72 " pdb=" O CYS E 72 " ideal model delta sigma weight residual 117.94 121.40 -3.46 5.80e-01 2.97e+00 3.55e+01 angle pdb=" C ASP B 99 " pdb=" N ASN B 100 " pdb=" CA ASN B 100 " ideal model delta sigma weight residual 122.08 113.25 8.83 1.50e+00 4.44e-01 3.46e+01 angle pdb=" C PRO F 172 " pdb=" N ARG F 173 " pdb=" CA ARG F 173 " ideal model delta sigma weight residual 121.27 140.10 -18.83 3.40e+00 8.65e-02 3.07e+01 angle pdb=" N CYS F 358 " pdb=" CA CYS F 358 " pdb=" C CYS F 358 " ideal model delta sigma weight residual 107.73 114.78 -7.05 1.34e+00 5.57e-01 2.77e+01 ... (remaining 30749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.88: 12027 25.88 - 51.76: 1139 51.76 - 77.64: 120 77.64 - 103.52: 14 103.52 - 129.40: 1 Dihedral angle restraints: 13301 sinusoidal: 5445 harmonic: 7856 Sorted by residual: dihedral pdb=" CA TRP B 182 " pdb=" C TRP B 182 " pdb=" N PRO B 183 " pdb=" CA PRO B 183 " ideal model delta harmonic sigma weight residual 180.00 133.36 46.64 0 5.00e+00 4.00e-02 8.70e+01 dihedral pdb=" CA TYR A 903 " pdb=" C TYR A 903 " pdb=" N SER A 904 " pdb=" CA SER A 904 " ideal model delta harmonic sigma weight residual 180.00 143.29 36.71 0 5.00e+00 4.00e-02 5.39e+01 dihedral pdb=" CA VAL A 848 " pdb=" C VAL A 848 " pdb=" N LYS A 849 " pdb=" CA LYS A 849 " ideal model delta harmonic sigma weight residual 180.00 144.69 35.31 0 5.00e+00 4.00e-02 4.99e+01 ... (remaining 13298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2359 0.055 - 0.109: 974 0.109 - 0.164: 199 0.164 - 0.218: 30 0.218 - 0.273: 3 Chirality restraints: 3565 Sorted by residual: chirality pdb=" CA MET A 899 " pdb=" N MET A 899 " pdb=" C MET A 899 " pdb=" CB MET A 899 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA ALA A 130 " pdb=" N ALA A 130 " pdb=" C ALA A 130 " pdb=" CB ALA A 130 " both_signs ideal model delta sigma weight residual False 2.48 2.22 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA ARG G 10 " pdb=" N ARG G 10 " pdb=" C ARG G 10 " pdb=" CB ARG G 10 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 3562 not shown) Planarity restraints: 3731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP B 182 " 0.094 5.00e-02 4.00e+02 1.39e-01 3.09e+01 pdb=" N PRO B 183 " -0.240 5.00e-02 4.00e+02 pdb=" CA PRO B 183 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO B 183 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 231 " -0.063 5.00e-02 4.00e+02 9.48e-02 1.44e+01 pdb=" N PRO A 232 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO A 232 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 232 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 132 " -0.062 5.00e-02 4.00e+02 9.26e-02 1.37e+01 pdb=" N PRO D 133 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO D 133 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO D 133 " -0.050 5.00e-02 4.00e+02 ... (remaining 3728 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 661 2.56 - 3.15: 21185 3.15 - 3.73: 35321 3.73 - 4.32: 48357 4.32 - 4.90: 76357 Nonbonded interactions: 181881 Sorted by model distance: nonbonded pdb=" O PHE E 145 " pdb=" OG SER E 148 " model vdw 1.979 2.440 nonbonded pdb=" O ARG A 533 " pdb=" ND2 ASN A 534 " model vdw 1.990 2.520 nonbonded pdb=" OH TYR F 269 " pdb=" O PHE F 291 " model vdw 1.996 2.440 nonbonded pdb=" O THR C 45 " pdb=" OG1 THR C 45 " model vdw 2.023 2.440 nonbonded pdb=" O ASN F 107 " pdb=" N THR F 111 " model vdw 2.026 2.520 ... (remaining 181876 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 191)) selection = (chain 'D' and (resid 6 through 21 or (resid 22 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 42 or (resid 43 and (name N or name CA or name C or na \ me O or name CB )) or resid 44 through 46 or (resid 47 and (name N or name CA or \ name C or name O or name CB )) or resid 48 through 191)) } ncs_group { reference = (chain 'E' and (resid 2 through 473 or resid 475 through 593 or resid 701 throug \ h 703)) selection = (chain 'F' and (resid 2 through 473 or resid 475 through 593 or resid 701 throug \ h 703)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.160 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: 0.020 Extract box with map and model: 20.480 Check model and map are aligned: 0.390 Set scattering table: 0.200 Process input model: 72.720 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 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 : 0.015 0.140 22434 Z= 0.971 Angle : 1.230 18.827 30754 Z= 0.692 Chirality : 0.059 0.273 3565 Planarity : 0.007 0.139 3731 Dihedral : 18.405 129.398 8233 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 38.61 Ramachandran Plot: Outliers : 1.52 % Allowed : 23.51 % Favored : 74.97 % Rotamer Outliers : 14.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.20 % 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: -6.16 (0.11), residues: 2639 helix: -3.70 (0.10), residues: 940 sheet: -4.60 (0.26), residues: 214 loop : -4.47 (0.12), residues: 1485 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 317 poor density : 118 time to evaluate : 2.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 317 outliers final: 224 residues processed: 421 average time/residue: 0.3172 time to fit residues: 212.6229 Evaluate side-chains 334 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 110 time to evaluate : 2.390 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 224 outliers final: 1 residues processed: 224 average time/residue: 0.2044 time to fit residues: 87.1078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 20.0000 chunk 201 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 135 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 126 optimal weight: 0.8980 chunk 155 optimal weight: 9.9990 chunk 241 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 GLN ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 22434 Z= 0.228 Angle : 0.790 10.508 30754 Z= 0.405 Chirality : 0.045 0.217 3565 Planarity : 0.006 0.095 3731 Dihedral : 8.832 126.586 3516 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 21.84 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.34 % Favored : 87.28 % Rotamer Outliers : 3.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -4.56 (0.13), residues: 2639 helix: -2.05 (0.15), residues: 923 sheet: -4.06 (0.27), residues: 235 loop : -3.65 (0.13), residues: 1481 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 141 time to evaluate : 2.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 27 residues processed: 206 average time/residue: 0.3841 time to fit residues: 121.3684 Evaluate side-chains 146 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 2.575 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 27 outliers final: 1 residues processed: 27 average time/residue: 0.2449 time to fit residues: 15.0694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 241 optimal weight: 0.5980 chunk 261 optimal weight: 0.9990 chunk 215 optimal weight: 10.0000 chunk 239 optimal weight: 0.0070 chunk 82 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 overall best weight: 0.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 GLN ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 GLN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 22434 Z= 0.200 Angle : 0.696 10.808 30754 Z= 0.354 Chirality : 0.042 0.244 3565 Planarity : 0.005 0.081 3731 Dihedral : 8.134 127.431 3516 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.47 % Favored : 88.30 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -3.70 (0.15), residues: 2639 helix: -1.08 (0.17), residues: 920 sheet: -3.62 (0.27), residues: 254 loop : -3.29 (0.14), residues: 1465 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 138 time to evaluate : 2.804 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 outliers start: 66 outliers final: 25 residues processed: 196 average time/residue: 0.3739 time to fit residues: 113.0669 Evaluate side-chains 143 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 2.603 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 25 outliers final: 1 residues processed: 25 average time/residue: 0.2078 time to fit residues: 12.8502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 0.9990 chunk 181 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 162 optimal weight: 0.8980 chunk 242 optimal weight: 20.0000 chunk 257 optimal weight: 20.0000 chunk 126 optimal weight: 0.9990 chunk 230 optimal weight: 20.0000 chunk 69 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 ASN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 GLN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 22434 Z= 0.188 Angle : 0.663 8.378 30754 Z= 0.336 Chirality : 0.041 0.177 3565 Planarity : 0.004 0.073 3731 Dihedral : 7.834 127.084 3516 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.57 % Favored : 90.20 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -3.22 (0.15), residues: 2639 helix: -0.62 (0.17), residues: 901 sheet: -3.42 (0.28), residues: 252 loop : -3.00 (0.14), residues: 1486 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 129 time to evaluate : 2.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 15 residues processed: 168 average time/residue: 0.3889 time to fit residues: 101.2371 Evaluate side-chains 133 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 2.600 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.2319 time to fit residues: 10.0416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 191 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 chunk 219 optimal weight: 20.0000 chunk 177 optimal weight: 30.0000 chunk 0 optimal weight: 7.9990 chunk 131 optimal weight: 0.6980 chunk 230 optimal weight: 30.0000 chunk 64 optimal weight: 0.7980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 ASN A 600 ASN ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 HIS ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 ASN ** F 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 22434 Z= 0.301 Angle : 0.695 9.823 30754 Z= 0.351 Chirality : 0.043 0.178 3565 Planarity : 0.004 0.060 3731 Dihedral : 7.820 128.271 3516 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.39 % Favored : 88.38 % Rotamer Outliers : 2.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -3.13 (0.15), residues: 2639 helix: -0.60 (0.17), residues: 910 sheet: -3.32 (0.27), residues: 285 loop : -2.91 (0.15), residues: 1444 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 118 time to evaluate : 2.419 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 outliers start: 58 outliers final: 27 residues processed: 168 average time/residue: 0.3846 time to fit residues: 101.0482 Evaluate side-chains 139 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 2.522 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 27 outliers final: 1 residues processed: 27 average time/residue: 0.2376 time to fit residues: 15.2023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 0.8980 chunk 231 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 257 optimal weight: 20.0000 chunk 213 optimal weight: 20.0000 chunk 119 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 135 optimal weight: 10.0000 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 600 ASN ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 22434 Z= 0.292 Angle : 0.695 11.881 30754 Z= 0.350 Chirality : 0.042 0.178 3565 Planarity : 0.004 0.058 3731 Dihedral : 7.782 128.235 3516 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 18.58 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.60 % Favored : 89.18 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -3.06 (0.15), residues: 2639 helix: -0.57 (0.17), residues: 913 sheet: -3.34 (0.26), residues: 295 loop : -2.82 (0.15), residues: 1431 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 118 time to evaluate : 2.604 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 outliers start: 34 outliers final: 15 residues processed: 147 average time/residue: 0.3925 time to fit residues: 88.5187 Evaluate side-chains 129 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 2.555 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.2075 time to fit residues: 9.1645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 187 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 216 optimal weight: 0.8980 chunk 143 optimal weight: 0.6980 chunk 256 optimal weight: 20.0000 chunk 160 optimal weight: 0.9990 chunk 156 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 ASN ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 22434 Z= 0.177 Angle : 0.640 12.071 30754 Z= 0.321 Chirality : 0.040 0.176 3565 Planarity : 0.004 0.056 3731 Dihedral : 7.486 127.145 3516 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.38 % Favored : 90.43 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -2.73 (0.16), residues: 2639 helix: -0.27 (0.18), residues: 906 sheet: -3.10 (0.28), residues: 266 loop : -2.67 (0.15), residues: 1467 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 2.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 150 average time/residue: 0.3880 time to fit residues: 90.9420 Evaluate side-chains 126 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 2.672 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.2173 time to fit residues: 7.9754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/iotbx/cli_parser.py", line 870, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.3466 > 50: distance: 49 - 72: 12.131 distance: 53 - 80: 11.362 distance: 59 - 64: 19.593 distance: 60 - 88: 17.914 distance: 64 - 65: 4.449 distance: 65 - 66: 10.565 distance: 65 - 68: 30.558 distance: 66 - 72: 29.496 distance: 68 - 69: 6.574 distance: 69 - 70: 32.348 distance: 69 - 71: 29.466 distance: 72 - 73: 4.296 distance: 73 - 74: 20.896 distance: 73 - 76: 10.639 distance: 74 - 75: 17.019 distance: 74 - 80: 21.703 distance: 76 - 77: 3.402 distance: 76 - 78: 12.282 distance: 77 - 79: 7.227 distance: 80 - 81: 3.853 distance: 81 - 82: 7.188 distance: 81 - 84: 7.624 distance: 82 - 83: 28.206 distance: 82 - 88: 13.239 distance: 84 - 85: 15.217 distance: 84 - 86: 11.014 distance: 85 - 87: 13.345 distance: 88 - 89: 26.717 distance: 89 - 90: 37.770 distance: 89 - 92: 15.542 distance: 90 - 91: 38.505 distance: 90 - 96: 56.347 distance: 92 - 93: 12.661 distance: 93 - 94: 10.280 distance: 93 - 95: 3.909 distance: 96 - 97: 13.558 distance: 97 - 98: 20.585 distance: 97 - 100: 22.499 distance: 98 - 99: 10.478 distance: 98 - 104: 12.552 distance: 100 - 101: 8.625 distance: 101 - 102: 11.486 distance: 101 - 103: 3.924 distance: 104 - 105: 5.653 distance: 105 - 106: 7.744 distance: 105 - 108: 6.840 distance: 106 - 107: 4.402 distance: 106 - 109: 12.734 distance: 109 - 110: 11.240 distance: 110 - 111: 9.692 distance: 110 - 113: 9.586 distance: 111 - 112: 17.115 distance: 111 - 120: 17.683 distance: 113 - 114: 4.033 distance: 114 - 115: 11.794 distance: 116 - 117: 3.100 distance: 120 - 121: 16.479 distance: 121 - 122: 15.510 distance: 121 - 124: 12.504 distance: 122 - 123: 10.349 distance: 122 - 128: 11.276 distance: 124 - 125: 16.699 distance: 125 - 126: 15.434 distance: 125 - 127: 11.748 distance: 128 - 129: 10.585 distance: 129 - 130: 17.084 distance: 130 - 131: 5.358 distance: 130 - 132: 6.254 distance: 132 - 133: 8.765 distance: 133 - 134: 11.515 distance: 133 - 136: 9.747 distance: 134 - 135: 4.169 distance: 134 - 138: 6.735 distance: 136 - 137: 9.221