Starting phenix.real_space_refine on Mon Mar 18 18:43:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwn_34317/03_2024/8gwn_34317_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwn_34317/03_2024/8gwn_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_34317/03_2024/8gwn_34317.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwn_34317/03_2024/8gwn_34317.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwn_34317/03_2024/8gwn_34317_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwn_34317/03_2024/8gwn_34317_updated.pdb" } resolution = 3.38 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= 0.031 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 16.16, per 1000 atoms: 0.74 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: 9.59 Conformation dependent library (CDL) restraints added in 4.7 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: 11.08 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: 6.64 Time building geometry restraints manager: 10.16 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: 12115 25.88 - 51.76: 1192 51.76 - 77.64: 203 77.64 - 103.52: 14 103.52 - 129.40: 1 Dihedral angle restraints: 13525 sinusoidal: 5669 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 13522 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.050 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: 19.450 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 76.080 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.430 ------------------------------------------------------------------------------- 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 : 19.479 129.398 8457 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 % Allowed : 22.28 % Favored : 63.65 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 916 HIS 0.016 0.002 HIS F 33 PHE 0.031 0.003 PHE D 147 TYR 0.037 0.003 TYR E 269 ARG 0.014 0.001 ARG A 197 *********************** 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 : 2.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.8487 (t80) REVERT: A 110 MET cc_start: 0.7545 (mmp) cc_final: 0.7300 (mmm) REVERT: A 181 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.6753 (mtm180) REVERT: A 306 CYS cc_start: 0.7482 (OUTLIER) cc_final: 0.6937 (t) REVERT: A 366 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8961 (pp) REVERT: A 372 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9124 (mp) REVERT: A 391 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8597 (mtpp) REVERT: A 445 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8259 (p0) REVERT: A 511 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8720 (mtpp) REVERT: A 545 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8494 (mtmt) REVERT: A 553 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7856 (ptm-80) REVERT: A 610 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.6154 (mt-10) REVERT: A 636 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9123 (mp) REVERT: A 668 MET cc_start: 0.8595 (ttp) cc_final: 0.7997 (tmm) REVERT: A 750 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7817 (mtm-85) REVERT: A 802 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: A 914 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8475 (ptt-90) REVERT: B 65 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8425 (tm-30) REVERT: B 82 LYS cc_start: 0.8720 (tppp) cc_final: 0.8386 (tppp) REVERT: C 38 ASP cc_start: 0.7549 (m-30) cc_final: 0.7290 (m-30) REVERT: D 12 TYR cc_start: 0.8718 (t80) cc_final: 0.8460 (t80) REVERT: D 67 MET cc_start: 0.7907 (ttp) cc_final: 0.7687 (tmm) REVERT: F 65 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.8979 (tt) REVERT: F 233 MET cc_start: 0.8099 (mmm) cc_final: 0.7710 (mmm) REVERT: F 325 LEU cc_start: 0.1647 (OUTLIER) cc_final: 0.0754 (tp) REVERT: F 421 TYR cc_start: 0.9161 (m-10) cc_final: 0.8906 (m-10) REVERT: F 440 THR cc_start: -0.0091 (OUTLIER) cc_final: -0.0588 (m) REVERT: E 405 LEU cc_start: 0.4870 (OUTLIER) cc_final: 0.4667 (tp) REVERT: E 541 TYR cc_start: 0.8565 (t80) cc_final: 0.8354 (t80) REVERT: G 12 MET cc_start: 0.7792 (tpp) cc_final: 0.7195 (tpp) REVERT: G 58 LYS cc_start: 0.8592 (tptp) cc_final: 0.8143 (tptp) REVERT: G 111 ARG cc_start: 0.8510 (mmm160) cc_final: 0.8282 (mmm160) outliers start: 317 outliers final: 224 residues processed: 421 average time/residue: 0.3054 time to fit residues: 203.7897 Evaluate side-chains 354 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 111 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 483 TYR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 748 TYR Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 773 GLN Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 825 ASP Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain A residue 914 ARG Chi-restraints excluded: chain A residue 917 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 94 MET Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 31 TYR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 440 THR Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 542 ASP Chi-restraints excluded: chain E residue 9 ASN Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 75 HIS Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 164 HIS Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 86 LYS 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: 0.9990 chunk 111 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 135 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 208 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 241 optimal weight: 0.9990 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** ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 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 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22434 Z= 0.223 Angle : 0.763 10.288 30754 Z= 0.395 Chirality : 0.045 0.215 3565 Planarity : 0.005 0.095 3731 Dihedral : 15.653 126.781 4168 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.00 % Favored : 87.62 % Rotamer: Outliers : 8.43 % Allowed : 25.36 % Favored : 66.21 % 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: -4.54 (0.14), residues: 2639 helix: -2.04 (0.15), residues: 921 sheet: -4.00 (0.28), residues: 209 loop : -3.66 (0.13), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 916 HIS 0.009 0.001 HIS F 33 PHE 0.022 0.002 PHE E 357 TYR 0.034 0.002 TYR F 457 ARG 0.006 0.001 ARG G 74 *********************** 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 324 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 135 time to evaluate : 2.491 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: A 366 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8697 (pp) REVERT: A 626 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8131 (ttm) REVERT: A 735 ARG cc_start: 0.6739 (OUTLIER) cc_final: 0.6287 (mtm-85) REVERT: A 802 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: B 56 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7191 (pp30) REVERT: B 71 TYR cc_start: 0.7659 (t80) cc_final: 0.7418 (t80) REVERT: B 135 TYR cc_start: 0.8222 (t80) cc_final: 0.7907 (t80) REVERT: C 21 ARG cc_start: 0.8351 (mmm160) cc_final: 0.8145 (mmm160) REVERT: C 34 GLN cc_start: 0.8283 (tp40) cc_final: 0.7646 (tp-100) REVERT: C 38 ASP cc_start: 0.7516 (m-30) cc_final: 0.6800 (m-30) REVERT: D 64 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7948 (t70) REVERT: F 65 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8511 (tt) REVERT: F 233 MET cc_start: 0.8415 (mmm) cc_final: 0.8068 (mmm) REVERT: F 440 THR cc_start: 0.0045 (OUTLIER) cc_final: -0.0377 (m) REVERT: E 162 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7953 (mm-30) REVERT: E 277 TYR cc_start: 0.6789 (OUTLIER) cc_final: 0.6087 (p90) REVERT: E 429 MET cc_start: 0.8506 (mtp) cc_final: 0.8016 (mtt) REVERT: E 541 TYR cc_start: 0.8401 (t80) cc_final: 0.8109 (t80) REVERT: E 576 MET cc_start: 0.2257 (ptt) cc_final: 0.2007 (ptt) REVERT: G 10 ARG cc_start: 0.6288 (OUTLIER) cc_final: 0.4674 (mmp80) outliers start: 189 outliers final: 121 residues processed: 307 average time/residue: 0.3155 time to fit residues: 153.4297 Evaluate side-chains 252 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 120 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 825 ASP Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 917 GLU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 92 PHE Chi-restraints excluded: chain D residue 94 MET Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 440 THR Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 14 CYS Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 201 optimal weight: 0.6980 chunk 164 optimal weight: 0.3980 chunk 66 optimal weight: 5.9990 chunk 241 optimal weight: 0.4980 chunk 261 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 239 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 194 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 724 GLN B 176 ASN ** 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 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 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22434 Z= 0.202 Angle : 0.675 8.922 30754 Z= 0.346 Chirality : 0.042 0.259 3565 Planarity : 0.005 0.080 3731 Dihedral : 14.419 128.026 3912 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.89 % Favored : 87.85 % Rotamer: Outliers : 6.44 % Allowed : 27.35 % Favored : 66.21 % 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: -3.76 (0.15), residues: 2639 helix: -1.15 (0.16), residues: 933 sheet: -3.70 (0.26), residues: 256 loop : -3.32 (0.14), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 53 HIS 0.008 0.001 HIS F 33 PHE 0.045 0.002 PHE E 357 TYR 0.028 0.002 TYR F 476 ARG 0.007 0.001 ARG G 74 *********************** 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 282 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 137 time to evaluate : 2.470 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 116 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7324 (mpp-170) REVERT: A 153 ASP cc_start: 0.7685 (t0) cc_final: 0.7396 (t0) REVERT: A 477 ASP cc_start: 0.7554 (t70) cc_final: 0.7334 (t0) REVERT: A 626 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.8093 (ttm) REVERT: A 735 ARG cc_start: 0.6739 (OUTLIER) cc_final: 0.6230 (mtm-85) REVERT: A 802 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: B 48 GLU cc_start: 0.8605 (tt0) cc_final: 0.8294 (tt0) REVERT: B 56 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.7088 (pp30) REVERT: B 71 TYR cc_start: 0.7645 (t80) cc_final: 0.7437 (t80) REVERT: F 65 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8691 (tt) REVERT: F 233 MET cc_start: 0.8441 (mmm) cc_final: 0.8123 (mmm) REVERT: E 162 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8036 (mm-30) REVERT: E 277 TYR cc_start: 0.6755 (OUTLIER) cc_final: 0.6068 (p90) REVERT: E 429 MET cc_start: 0.8529 (mtp) cc_final: 0.8023 (mtt) REVERT: E 541 TYR cc_start: 0.8384 (t80) cc_final: 0.8122 (t80) REVERT: G 58 LYS cc_start: 0.8367 (tptp) cc_final: 0.8030 (tptp) REVERT: G 74 ARG cc_start: 0.8412 (tpt90) cc_final: 0.8159 (tpt90) REVERT: G 87 TYR cc_start: 0.7451 (m-80) cc_final: 0.7040 (m-80) REVERT: G 111 ARG cc_start: 0.7448 (mmm160) cc_final: 0.6915 (mmm160) outliers start: 145 outliers final: 92 residues processed: 271 average time/residue: 0.3383 time to fit residues: 143.4720 Evaluate side-chains 222 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 122 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 825 ASP Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 92 PHE Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 516 ASN Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain E residue 9 ASN Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 86 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 7.9990 chunk 181 optimal weight: 30.0000 chunk 125 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 162 optimal weight: 10.0000 chunk 242 optimal weight: 20.0000 chunk 257 optimal weight: 30.0000 chunk 126 optimal weight: 0.9990 chunk 230 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 312 ASN A 507 ASN ** 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 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 388 ASN ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 GLN ** 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: 0.7999 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22434 Z= 0.234 Angle : 0.656 9.511 30754 Z= 0.335 Chirality : 0.042 0.207 3565 Planarity : 0.004 0.076 3731 Dihedral : 13.881 128.091 3856 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.52 % Favored : 89.25 % Rotamer: Outliers : 6.48 % Allowed : 28.32 % Favored : 65.20 % 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: -3.41 (0.15), residues: 2639 helix: -0.79 (0.17), residues: 915 sheet: -3.62 (0.26), residues: 284 loop : -3.08 (0.14), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 53 HIS 0.007 0.001 HIS F 33 PHE 0.026 0.001 PHE E 357 TYR 0.026 0.002 TYR F 306 ARG 0.005 0.000 ARG G 74 *********************** 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 274 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 128 time to evaluate : 2.459 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 116 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7267 (mpp-170) REVERT: A 153 ASP cc_start: 0.7698 (t0) cc_final: 0.7305 (t0) REVERT: A 735 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.6267 (mtm-85) REVERT: A 802 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7103 (mp0) REVERT: B 56 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.7105 (pp30) REVERT: B 135 TYR cc_start: 0.8074 (t80) cc_final: 0.7858 (t80) REVERT: C 21 ARG cc_start: 0.7990 (mmm160) cc_final: 0.7736 (mmm160) REVERT: F 65 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8635 (tt) REVERT: F 233 MET cc_start: 0.8542 (mmm) cc_final: 0.8237 (mmm) REVERT: F 421 TYR cc_start: 0.9226 (m-10) cc_final: 0.8980 (m-10) REVERT: E 162 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8159 (mm-30) REVERT: E 277 TYR cc_start: 0.6729 (OUTLIER) cc_final: 0.6090 (p90) REVERT: E 429 MET cc_start: 0.8558 (mtp) cc_final: 0.8038 (mtt) REVERT: E 462 LYS cc_start: 0.2954 (OUTLIER) cc_final: 0.2181 (mtmm) REVERT: E 541 TYR cc_start: 0.8395 (t80) cc_final: 0.8143 (t80) REVERT: E 576 MET cc_start: 0.1957 (ptt) cc_final: 0.1652 (ptt) REVERT: G 12 MET cc_start: 0.8123 (tpp) cc_final: 0.7847 (tpp) REVERT: G 58 LYS cc_start: 0.8453 (tptp) cc_final: 0.7850 (tptp) REVERT: G 111 ARG cc_start: 0.7514 (mmm160) cc_final: 0.6899 (mmm160) outliers start: 146 outliers final: 97 residues processed: 262 average time/residue: 0.3368 time to fit residues: 137.5478 Evaluate side-chains 225 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 120 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 825 ASP Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 92 PHE Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 516 ASN Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain E residue 9 ASN Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 293 ILE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 chunk 3 optimal weight: 0.0050 chunk 191 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 219 optimal weight: 10.0000 chunk 177 optimal weight: 30.0000 chunk 0 optimal weight: 6.9990 chunk 131 optimal weight: 0.5980 chunk 230 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- 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 312 ASN A 600 ASN ** 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 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 388 ASN ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 GLN ** 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: 0.7961 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22434 Z= 0.177 Angle : 0.624 7.905 30754 Z= 0.317 Chirality : 0.041 0.178 3565 Planarity : 0.004 0.069 3731 Dihedral : 13.533 127.653 3837 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.65 % Favored : 90.13 % Rotamer: Outliers : 5.43 % Allowed : 28.67 % Favored : 65.90 % 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: -3.03 (0.15), residues: 2639 helix: -0.46 (0.17), residues: 909 sheet: -3.43 (0.27), residues: 277 loop : -2.86 (0.15), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 53 HIS 0.007 0.001 HIS F 33 PHE 0.027 0.001 PHE F 357 TYR 0.024 0.001 TYR F 306 ARG 0.009 0.000 ARG G 74 *********************** 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 249 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 127 time to evaluate : 2.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7247 (mpp-170) REVERT: A 153 ASP cc_start: 0.7616 (t0) cc_final: 0.7237 (t0) REVERT: A 477 ASP cc_start: 0.7591 (t70) cc_final: 0.7302 (t0) REVERT: A 735 ARG cc_start: 0.6827 (OUTLIER) cc_final: 0.6308 (mtm-85) REVERT: A 802 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7112 (mp0) REVERT: A 906 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6267 (mmm) REVERT: B 157 GLN cc_start: 0.7794 (pp30) cc_final: 0.7483 (pp30) REVERT: D 12 TYR cc_start: 0.8456 (t80) cc_final: 0.8188 (t80) REVERT: F 65 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8569 (tt) REVERT: F 233 MET cc_start: 0.8596 (mmm) cc_final: 0.8326 (mmm) REVERT: F 421 TYR cc_start: 0.9234 (m-10) cc_final: 0.8987 (m-10) REVERT: E 162 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8244 (mm-30) REVERT: E 277 TYR cc_start: 0.6697 (OUTLIER) cc_final: 0.6110 (p90) REVERT: E 388 ASN cc_start: 0.7558 (OUTLIER) cc_final: 0.7271 (m110) REVERT: E 429 MET cc_start: 0.8534 (mtp) cc_final: 0.7991 (mtt) REVERT: E 442 ARG cc_start: 0.4362 (OUTLIER) cc_final: 0.3132 (pmt-80) REVERT: E 462 LYS cc_start: 0.2969 (OUTLIER) cc_final: 0.2148 (mtmm) REVERT: E 541 TYR cc_start: 0.8324 (t80) cc_final: 0.8069 (t80) REVERT: G 58 LYS cc_start: 0.8549 (tptp) cc_final: 0.8015 (tptp) REVERT: G 74 ARG cc_start: 0.8110 (tpt90) cc_final: 0.7831 (tpt90) REVERT: G 111 ARG cc_start: 0.7533 (mmm160) cc_final: 0.6865 (mmm160) outliers start: 122 outliers final: 88 residues processed: 241 average time/residue: 0.3462 time to fit residues: 128.1159 Evaluate side-chains 215 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 117 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 92 PHE Chi-restraints excluded: chain D residue 94 MET Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 516 ASN Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain E residue 9 ASN Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 442 ARG Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 49 GLN Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 0.0470 chunk 231 optimal weight: 20.0000 chunk 50 optimal weight: 0.0270 chunk 150 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 257 optimal weight: 30.0000 chunk 213 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 85 optimal weight: 0.0870 chunk 135 optimal weight: 10.0000 overall best weight: 1.0318 ------------------------------------------------------------------------------- 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 898 HIS ** 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 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22434 Z= 0.179 Angle : 0.613 8.307 30754 Z= 0.312 Chirality : 0.040 0.177 3565 Planarity : 0.004 0.060 3731 Dihedral : 13.326 127.671 3824 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.87 % Favored : 89.94 % Rotamer: Outliers : 4.90 % Allowed : 29.47 % Favored : 65.64 % 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: -2.79 (0.16), residues: 2639 helix: -0.25 (0.18), residues: 906 sheet: -3.26 (0.26), residues: 288 loop : -2.71 (0.15), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 53 HIS 0.012 0.001 HIS F 33 PHE 0.027 0.001 PHE F 357 TYR 0.024 0.001 TYR B 135 ARG 0.009 0.000 ARG G 74 *********************** 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 230 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 120 time to evaluate : 2.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7203 (mpp-170) REVERT: A 153 ASP cc_start: 0.7592 (t0) cc_final: 0.7197 (t0) REVERT: A 477 ASP cc_start: 0.7576 (t70) cc_final: 0.7336 (t0) REVERT: A 735 ARG cc_start: 0.6843 (OUTLIER) cc_final: 0.6318 (mtm-85) REVERT: A 802 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: A 906 MET cc_start: 0.6780 (OUTLIER) cc_final: 0.5695 (mmm) REVERT: B 77 GLU cc_start: 0.8293 (tp30) cc_final: 0.8053 (tp30) REVERT: B 157 GLN cc_start: 0.7805 (pp30) cc_final: 0.7481 (pp30) REVERT: F 65 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8539 (tt) REVERT: F 233 MET cc_start: 0.8625 (mmm) cc_final: 0.8370 (mmm) REVERT: F 421 TYR cc_start: 0.9264 (m-10) cc_final: 0.9021 (m-10) REVERT: E 277 TYR cc_start: 0.6705 (OUTLIER) cc_final: 0.6089 (p90) REVERT: E 429 MET cc_start: 0.8487 (mtp) cc_final: 0.8129 (mtt) REVERT: E 462 LYS cc_start: 0.2883 (OUTLIER) cc_final: 0.2067 (mtmm) REVERT: E 492 GLN cc_start: 0.1828 (OUTLIER) cc_final: 0.1539 (mp10) REVERT: E 541 TYR cc_start: 0.8306 (t80) cc_final: 0.8047 (t80) REVERT: G 58 LYS cc_start: 0.8488 (tptp) cc_final: 0.7948 (tptp) REVERT: G 111 ARG cc_start: 0.7632 (mmm160) cc_final: 0.6999 (mmm160) outliers start: 110 outliers final: 85 residues processed: 223 average time/residue: 0.3438 time to fit residues: 120.6184 Evaluate side-chains 208 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 115 time to evaluate : 2.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 94 MET Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 516 ASN Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain E residue 9 ASN Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 8.9990 chunk 29 optimal weight: 0.5980 chunk 146 optimal weight: 0.0980 chunk 187 optimal weight: 0.0970 chunk 145 optimal weight: 1.9990 chunk 216 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 256 optimal weight: 6.9990 chunk 160 optimal weight: 0.0370 chunk 156 optimal weight: 40.0000 chunk 118 optimal weight: 7.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- 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** ** 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 492 GLN ** 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 243 GLN ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 GLN ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 559 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 22434 Z= 0.148 Angle : 0.590 8.951 30754 Z= 0.299 Chirality : 0.039 0.174 3565 Planarity : 0.004 0.056 3731 Dihedral : 13.007 126.758 3812 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.09 % Favored : 91.72 % Rotamer: Outliers : 3.57 % Allowed : 30.75 % Favored : 65.68 % 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: -2.46 (0.16), residues: 2639 helix: 0.03 (0.18), residues: 908 sheet: -2.89 (0.28), residues: 269 loop : -2.58 (0.15), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 53 HIS 0.012 0.001 HIS F 33 PHE 0.022 0.001 PHE F 357 TYR 0.025 0.001 TYR A 903 ARG 0.010 0.001 ARG G 74 *********************** 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 218 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 138 time to evaluate : 2.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7214 (mpp-170) REVERT: A 477 ASP cc_start: 0.7449 (t70) cc_final: 0.7238 (t0) REVERT: A 735 ARG cc_start: 0.6829 (OUTLIER) cc_final: 0.6280 (mtm-85) REVERT: A 802 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: B 56 GLN cc_start: 0.7161 (OUTLIER) cc_final: 0.6921 (pp30) REVERT: F 233 MET cc_start: 0.8614 (mmm) cc_final: 0.8262 (mmm) REVERT: F 288 LYS cc_start: 0.7193 (OUTLIER) cc_final: 0.6922 (mtmm) REVERT: F 421 TYR cc_start: 0.9253 (m-10) cc_final: 0.9021 (m-10) REVERT: E 429 MET cc_start: 0.8458 (mtp) cc_final: 0.8224 (mtm) REVERT: E 442 ARG cc_start: 0.4240 (OUTLIER) cc_final: 0.2881 (pmt-80) REVERT: E 462 LYS cc_start: 0.3003 (OUTLIER) cc_final: 0.2176 (mtmm) REVERT: E 492 GLN cc_start: 0.1995 (OUTLIER) cc_final: 0.1752 (mp10) REVERT: E 541 TYR cc_start: 0.8278 (t80) cc_final: 0.8014 (t80) REVERT: G 53 TRP cc_start: 0.7484 (m100) cc_final: 0.7270 (m100) REVERT: G 58 LYS cc_start: 0.8449 (tptp) cc_final: 0.7950 (tptp) REVERT: G 89 TYR cc_start: 0.4307 (m-10) cc_final: 0.3950 (m-80) REVERT: G 111 ARG cc_start: 0.7664 (mmm160) cc_final: 0.6990 (mmm160) outliers start: 80 outliers final: 47 residues processed: 211 average time/residue: 0.3610 time to fit residues: 117.9233 Evaluate side-chains 177 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 122 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 442 ARG Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 20.0000 chunk 102 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 174 optimal weight: 0.0570 chunk 126 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 201 optimal weight: 8.9990 overall best weight: 1.1700 ------------------------------------------------------------------------------- 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** A 898 HIS B 109 ASN ** 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 492 GLN ** 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 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 GLN ** 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: 0.7946 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22434 Z= 0.189 Angle : 0.629 16.157 30754 Z= 0.311 Chirality : 0.040 0.174 3565 Planarity : 0.004 0.054 3731 Dihedral : 12.848 127.571 3788 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.00 % Favored : 90.81 % Rotamer: Outliers : 3.53 % Allowed : 30.92 % Favored : 65.55 % 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: -2.40 (0.16), residues: 2639 helix: 0.01 (0.18), residues: 908 sheet: -2.68 (0.30), residues: 253 loop : -2.55 (0.15), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 916 HIS 0.009 0.001 HIS F 33 PHE 0.019 0.001 PHE F 357 TYR 0.035 0.001 TYR A 903 ARG 0.008 0.000 ARG G 74 *********************** REFINEMENT MACRO_CYCLE 8 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 202 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 123 time to evaluate : 2.512 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: A 116 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7182 (mpp-170) REVERT: A 477 ASP cc_start: 0.7601 (t70) cc_final: 0.7389 (t0) REVERT: A 735 ARG cc_start: 0.6866 (OUTLIER) cc_final: 0.6322 (mtm-85) REVERT: A 802 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: A 906 MET cc_start: 0.5549 (tpp) cc_final: 0.4727 (mmm) REVERT: B 94 MET cc_start: 0.8544 (ttp) cc_final: 0.8287 (tmm) REVERT: B 157 GLN cc_start: 0.7683 (pp30) cc_final: 0.7393 (pp30) REVERT: F 65 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8367 (tt) REVERT: F 233 MET cc_start: 0.8613 (mmm) cc_final: 0.8258 (mmm) REVERT: F 421 TYR cc_start: 0.9251 (m-10) cc_final: 0.9018 (m-10) REVERT: E 429 MET cc_start: 0.8428 (mtp) cc_final: 0.8067 (mtt) REVERT: E 462 LYS cc_start: 0.3047 (OUTLIER) cc_final: 0.2221 (mtmm) REVERT: E 492 GLN cc_start: 0.1777 (OUTLIER) cc_final: 0.1499 (mp10) REVERT: E 541 TYR cc_start: 0.8275 (t80) cc_final: 0.8025 (t80) REVERT: G 53 TRP cc_start: 0.7456 (m100) cc_final: 0.7198 (m100) REVERT: G 58 LYS cc_start: 0.8417 (tptp) cc_final: 0.7911 (tptp) REVERT: G 89 TYR cc_start: 0.4697 (m-80) cc_final: 0.4080 (m-80) REVERT: G 111 ARG cc_start: 0.7781 (mmm160) cc_final: 0.7127 (mmm160) outliers start: 79 outliers final: 55 residues processed: 200 average time/residue: 0.3411 time to fit residues: 108.0144 Evaluate side-chains 179 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 118 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 825 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 21 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 0.8980 chunk 245 optimal weight: 10.0000 chunk 224 optimal weight: 20.0000 chunk 238 optimal weight: 8.9990 chunk 143 optimal weight: 0.4980 chunk 104 optimal weight: 0.6980 chunk 187 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 215 optimal weight: 30.0000 chunk 225 optimal weight: 3.9990 chunk 156 optimal weight: 0.0980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** ** 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 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 GLN ** 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** G 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22434 Z= 0.177 Angle : 0.612 13.139 30754 Z= 0.304 Chirality : 0.040 0.174 3565 Planarity : 0.004 0.054 3731 Dihedral : 12.708 127.493 3777 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.77 % Favored : 91.11 % Rotamer: Outliers : 3.04 % Allowed : 31.41 % Favored : 65.55 % 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: -2.29 (0.16), residues: 2639 helix: 0.11 (0.18), residues: 904 sheet: -2.56 (0.30), residues: 253 loop : -2.49 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.009 0.001 HIS F 33 PHE 0.018 0.001 PHE F 357 TYR 0.030 0.001 TYR A 903 ARG 0.008 0.000 ARG G 74 *********************** REFINEMENT MACRO_CYCLE 9 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 187 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 119 time to evaluate : 2.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7215 (mpp-170) REVERT: A 477 ASP cc_start: 0.7598 (t70) cc_final: 0.7381 (t0) REVERT: A 735 ARG cc_start: 0.6849 (OUTLIER) cc_final: 0.6314 (mtm-85) REVERT: A 802 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: A 906 MET cc_start: 0.5291 (tpp) cc_final: 0.4533 (mmm) REVERT: B 157 GLN cc_start: 0.7700 (pp30) cc_final: 0.7418 (pp30) REVERT: F 95 ASN cc_start: 0.8761 (OUTLIER) cc_final: 0.8309 (p0) REVERT: F 233 MET cc_start: 0.8600 (mmm) cc_final: 0.8248 (mmm) REVERT: F 421 TYR cc_start: 0.9246 (m-10) cc_final: 0.9009 (m-10) REVERT: E 429 MET cc_start: 0.8442 (mtp) cc_final: 0.8191 (mtm) REVERT: E 462 LYS cc_start: 0.3053 (OUTLIER) cc_final: 0.2247 (mtmm) REVERT: E 492 GLN cc_start: 0.1992 (OUTLIER) cc_final: 0.1732 (mp10) REVERT: E 541 TYR cc_start: 0.8290 (t80) cc_final: 0.8024 (t80) REVERT: G 53 TRP cc_start: 0.7471 (m100) cc_final: 0.7207 (m100) REVERT: G 58 LYS cc_start: 0.8308 (tptp) cc_final: 0.7824 (tptp) REVERT: G 89 TYR cc_start: 0.4569 (m-80) cc_final: 0.4035 (m-80) REVERT: G 111 ARG cc_start: 0.7825 (mmm160) cc_final: 0.7212 (mmm160) outliers start: 68 outliers final: 55 residues processed: 185 average time/residue: 0.3256 time to fit residues: 96.4247 Evaluate side-chains 176 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 115 time to evaluate : 2.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 8.9990 chunk 154 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 175 optimal weight: 7.9990 chunk 265 optimal weight: 2.9990 chunk 243 optimal weight: 0.7980 chunk 211 optimal weight: 0.6980 chunk 21 optimal weight: 0.2980 chunk 163 optimal weight: 0.0470 chunk 129 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 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 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN ** E 268 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22434 Z= 0.150 Angle : 0.595 11.706 30754 Z= 0.295 Chirality : 0.039 0.172 3565 Planarity : 0.004 0.055 3731 Dihedral : 12.579 127.229 3773 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.94 % Favored : 91.95 % Rotamer: Outliers : 2.69 % Allowed : 31.63 % Favored : 65.68 % 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: -2.13 (0.16), residues: 2639 helix: 0.25 (0.18), residues: 908 sheet: -2.49 (0.30), residues: 259 loop : -2.39 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 916 HIS 0.007 0.001 HIS F 33 PHE 0.016 0.001 PHE F 357 TYR 0.028 0.001 TYR A 903 ARG 0.008 0.000 ARG G 74 ********************** REFINEMENT MACRO_CYCLE 10 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 183 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 123 time to evaluate : 2.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7190 (mpp-170) REVERT: A 477 ASP cc_start: 0.7500 (t70) cc_final: 0.7291 (t0) REVERT: A 735 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6314 (mtm-85) REVERT: A 802 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: B 157 GLN cc_start: 0.7637 (pp30) cc_final: 0.7352 (pp30) REVERT: F 95 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8398 (p0) REVERT: F 233 MET cc_start: 0.8652 (mmm) cc_final: 0.8330 (mmm) REVERT: F 421 TYR cc_start: 0.9246 (m-10) cc_final: 0.9016 (m-10) REVERT: E 429 MET cc_start: 0.8422 (mtp) cc_final: 0.7874 (mtt) REVERT: E 462 LYS cc_start: 0.3179 (OUTLIER) cc_final: 0.2312 (mtmm) REVERT: E 492 GLN cc_start: 0.1976 (OUTLIER) cc_final: 0.1742 (mp10) REVERT: E 541 TYR cc_start: 0.8294 (t80) cc_final: 0.8006 (t80) REVERT: G 12 MET cc_start: 0.8019 (mtp) cc_final: 0.7785 (mtp) REVERT: G 53 TRP cc_start: 0.7439 (m100) cc_final: 0.7162 (m100) REVERT: G 58 LYS cc_start: 0.8273 (tptp) cc_final: 0.7875 (tptp) REVERT: G 89 TYR cc_start: 0.4269 (m-80) cc_final: 0.3874 (m-80) REVERT: G 111 ARG cc_start: 0.7955 (mmm160) cc_final: 0.7342 (mmm160) outliers start: 60 outliers final: 49 residues processed: 182 average time/residue: 0.3384 time to fit residues: 98.0618 Evaluate side-chains 176 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 121 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 825 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 194 optimal weight: 7.9990 chunk 31 optimal weight: 0.0980 chunk 58 optimal weight: 4.9990 chunk 211 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 217 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 185 optimal weight: 20.0000 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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** ** 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 537 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.121146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.080238 restraints weight = 88911.548| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 5.12 r_work: 0.3168 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22434 Z= 0.262 Angle : 0.651 14.750 30754 Z= 0.323 Chirality : 0.041 0.189 3565 Planarity : 0.004 0.054 3731 Dihedral : 12.638 128.520 3772 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.80 % Favored : 90.09 % Rotamer: Outliers : 3.09 % Allowed : 31.41 % Favored : 65.51 % 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: -2.20 (0.16), residues: 2639 helix: 0.16 (0.18), residues: 906 sheet: -2.48 (0.30), residues: 271 loop : -2.41 (0.15), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 916 HIS 0.011 0.001 HIS F 33 PHE 0.015 0.001 PHE F 357 TYR 0.029 0.001 TYR D 12 ARG 0.008 0.000 ARG G 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5460.76 seconds wall clock time: 99 minutes 22.35 seconds (5962.35 seconds total)