Starting phenix.real_space_refine on Sun Apr 7 04:04:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvw_41653/04_2024/8tvw_41653_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvw_41653/04_2024/8tvw_41653.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvw_41653/04_2024/8tvw_41653_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvw_41653/04_2024/8tvw_41653_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvw_41653/04_2024/8tvw_41653_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvw_41653/04_2024/8tvw_41653.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvw_41653/04_2024/8tvw_41653.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvw_41653/04_2024/8tvw_41653_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvw_41653/04_2024/8tvw_41653_trim_updated.pdb" } resolution = 3.6 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= 0.127 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 8 6.06 5 P 57 5.49 5 Mg 1 5.21 5 S 179 5.16 5 C 19360 2.51 5 N 5386 2.21 5 O 5972 1.98 5 H 30468 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 307": "OD1" <-> "OD2" Residue "A TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A GLU 618": "OE1" <-> "OE2" Residue "A GLU 678": "OE1" <-> "OE2" Residue "A PHE 787": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 801": "OE1" <-> "OE2" Residue "A GLU 822": "OE1" <-> "OE2" Residue "A ASP 871": "OD1" <-> "OD2" Residue "A GLU 932": "OE1" <-> "OE2" Residue "A ASP 1334": "OD1" <-> "OD2" Residue "A TYR 1349": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1407": "OE1" <-> "OE2" Residue "B PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 696": "OE1" <-> "OE2" Residue "B TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 785": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 859": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1004": "OE1" <-> "OE2" Residue "B GLU 1041": "OE1" <-> "OE2" Residue "B TYR 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1091": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 1186": "OD1" <-> "OD2" Residue "B TYR 1192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 4": "OE1" <-> "OE2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 194": "OE1" <-> "OE2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 140": "OD1" <-> "OD2" Residue "D ASP 205": "OD1" <-> "OD2" Residue "E GLU 21": "OE1" <-> "OE2" Residue "E PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 182": "OD1" <-> "OD2" Residue "F ASP 77": "OD1" <-> "OD2" Residue "F TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 89": "OE1" <-> "OE2" Residue "F ASP 154": "OD1" <-> "OD2" Residue "G PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 45": "OE1" <-> "OE2" Residue "H GLU 105": "OE1" <-> "OE2" Residue "H TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 94": "OD1" <-> "OD2" Residue "J GLU 32": "OE1" <-> "OE2" Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 106": "OE1" <-> "OE2" Residue "L TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 61431 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 21595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1367, 21595 Classifications: {'peptide': 1367} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1304} Chain breaks: 6 Chain: "B" Number of atoms: 16597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 16597 Classifications: {'peptide': 1041} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 45, 'TRANS': 995} Chain breaks: 10 Chain: "C" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 4147 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2276 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain breaks: 1 Chain: "E" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3548 Classifications: {'peptide': 215} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1330 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 75} Chain: "G" Number of atoms: 2687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 2687 Classifications: {'peptide': 171} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 2090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2090 Classifications: {'peptide': 133} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 2 Chain: "I" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1860 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "J" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1074 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1673 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "L" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 751 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "N" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 550 Classifications: {'DNA': 17} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 16} Chain: "T" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 914 Unusual residues: {'TTD': 1} Classifications: {'DNA': 28, 'undetermined': 1} Link IDs: {'p': 1, 'rna3p': 26, None: 1} Not linked: pdbres=" DC T 17 " pdbres="TTD T 18 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "R" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 330 Classifications: {'RNA': 10} Modifications used: {'3*END': 1, 'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2450 SG CYS A 167 95.107 73.571 120.930 1.00193.34 S ATOM 1041 SG CYS A 77 48.135 71.488 103.853 1.00144.81 S ATOM 37199 SG CYS B1163 57.943 83.312 111.227 1.00139.25 S ATOM 37235 SG CYS B1166 60.634 80.725 110.236 1.00144.77 S ATOM 37485 SG CYS B1182 57.320 79.649 111.736 1.00144.04 S ATOM 37524 SG CYS B1185 59.972 81.424 113.859 1.00149.18 S ATOM 39529 SG CYS C 88 12.823 62.735 50.364 1.00147.90 S ATOM 39584 SG CYS C 92 10.721 61.603 47.764 1.00143.82 S ATOM 39628 SG CYS C 95 14.591 63.489 47.473 1.00135.28 S ATOM 54295 SG CYS I 7 132.464 43.058 70.137 1.00253.41 S ATOM 54341 SG CYS I 10 130.291 40.763 71.986 1.00257.18 S ATOM 55350 SG CYS I 75 116.854 58.459 28.656 1.00222.13 S ATOM 55397 SG CYS I 78 118.151 54.379 27.331 1.00224.27 S ATOM 55821 SG CYS I 103 114.388 55.415 28.227 1.00223.16 S ATOM 55860 SG CYS I 106 118.363 54.403 29.801 1.00228.96 S ATOM 56244 SG CYS J 7 42.170 63.860 32.758 1.00 96.94 S ATOM 56841 SG CYS J 45 43.939 66.025 30.051 1.00100.23 S ATOM 56851 SG CYS J 46 41.799 63.015 29.054 1.00103.48 S ATOM 58987 SG CYS L 31 38.547 27.390 60.302 1.00168.52 S ATOM 59022 SG CYS L 34 40.273 25.987 57.116 1.00173.26 S ATOM 59281 SG CYS L 51 41.238 26.355 59.118 1.00171.06 S Time building chain proxies: 20.42, per 1000 atoms: 0.33 Number of scatterers: 61431 At special positions: 0 Unit cell: (156.6, 155.44, 163.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 8 29.99 S 179 16.00 P 57 15.00 Mg 1 11.99 O 5972 8.00 N 5386 7.00 C 19360 6.00 H 30468 1.00 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: 37.95 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " Number of angles added : 12 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7040 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 141 helices and 36 sheets defined 35.3% alpha, 13.4% beta 25 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 26.80 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 93 through 103 removed outlier: 5.127A pdb=" N ALA A 97 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS A 103 " --> pdb=" O LYS A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 131 through 144 removed outlier: 4.504A pdb=" N THR A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 216 through 222 removed outlier: 3.531A pdb=" N SER A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 261 through 281 Processing helix chain 'A' and resid 286 through 304 Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 368 through 371 No H-bonds generated for 'chain 'A' and resid 368 through 371' Processing helix chain 'A' and resid 385 through 394 Processing helix chain 'A' and resid 415 through 417 No H-bonds generated for 'chain 'A' and resid 415 through 417' Processing helix chain 'A' and resid 420 through 422 No H-bonds generated for 'chain 'A' and resid 420 through 422' Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 472 through 478 removed outlier: 3.815A pdb=" N SER A 476 " --> pdb=" O SER A 473 " (cutoff:3.500A) Proline residue: A 477 - end of helix Processing helix chain 'A' and resid 495 through 505 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 525 through 535 removed outlier: 3.557A pdb=" N THR A 535 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 552 removed outlier: 3.855A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 581 removed outlier: 3.507A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 622 No H-bonds generated for 'chain 'A' and resid 619 through 622' Processing helix chain 'A' and resid 629 through 637 removed outlier: 3.858A pdb=" N ARG A 635 " --> pdb=" O HIS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 660 removed outlier: 4.432A pdb=" N LYS A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 673 through 698 Processing helix chain 'A' and resid 710 through 735 removed outlier: 3.653A pdb=" N ARG A 731 " --> pdb=" O ASP A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 749 Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 794 through 797 No H-bonds generated for 'chain 'A' and resid 794 through 797' Processing helix chain 'A' and resid 810 through 844 removed outlier: 3.991A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY A 835 " --> pdb=" O THR A 831 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR A 836 " --> pdb=" O ALA A 832 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 837 " --> pdb=" O GLU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 870 No H-bonds generated for 'chain 'A' and resid 868 through 870' Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 890 through 897 Processing helix chain 'A' and resid 910 through 912 No H-bonds generated for 'chain 'A' and resid 910 through 912' Processing helix chain 'A' and resid 923 through 946 removed outlier: 3.714A pdb=" N GLU A 945 " --> pdb=" O LYS A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 983 through 996 Processing helix chain 'A' and resid 1005 through 1014 Processing helix chain 'A' and resid 1016 through 1025 Processing helix chain 'A' and resid 1028 through 1033 Processing helix chain 'A' and resid 1039 through 1056 Processing helix chain 'A' and resid 1064 through 1077 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1099 through 1105 Processing helix chain 'A' and resid 1122 through 1124 No H-bonds generated for 'chain 'A' and resid 1122 through 1124' Processing helix chain 'A' and resid 1128 through 1138 Processing helix chain 'A' and resid 1143 through 1145 No H-bonds generated for 'chain 'A' and resid 1143 through 1145' Processing helix chain 'A' and resid 1199 through 1205 Processing helix chain 'A' and resid 1209 through 1219 Processing helix chain 'A' and resid 1258 through 1270 removed outlier: 3.780A pdb=" N MET A1267 " --> pdb=" O ILE A1263 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU A1268 " --> pdb=" O GLU A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1318 removed outlier: 4.618A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1338 Processing helix chain 'A' and resid 1341 through 1359 removed outlier: 4.285A pdb=" N ASP A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1374 Processing helix chain 'A' and resid 1396 through 1401 removed outlier: 4.358A pdb=" N SER A1401 " --> pdb=" O LEU A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1406 through 1415 Processing helix chain 'A' and resid 1424 through 1430 Processing helix chain 'A' and resid 1437 through 1439 No H-bonds generated for 'chain 'A' and resid 1437 through 1439' Processing helix chain 'A' and resid 1447 through 1452 Processing helix chain 'B' and resid 27 through 41 removed outlier: 3.542A pdb=" N TRP B 31 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 38 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS B 41 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 56 removed outlier: 4.508A pdb=" N SER B 50 " --> pdb=" O GLN B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 64 Processing helix chain 'B' and resid 114 through 120 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 282 through 288 Processing helix chain 'B' and resid 294 through 301 Processing helix chain 'B' and resid 308 through 323 Proline residue: B 316 - end of helix removed outlier: 4.628A pdb=" N VAL B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 338 Processing helix chain 'B' and resid 349 through 358 Processing helix chain 'B' and resid 368 through 389 removed outlier: 5.113A pdb=" N LYS B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 378 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 409 through 434 Processing helix chain 'B' and resid 443 through 463 removed outlier: 3.542A pdb=" N ALA B 447 " --> pdb=" O ASN B 443 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 495 Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 530 through 532 No H-bonds generated for 'chain 'B' and resid 530 through 532' Processing helix chain 'B' and resid 552 through 560 Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 593 through 606 Processing helix chain 'B' and resid 655 through 670 Processing helix chain 'B' and resid 681 through 687 Processing helix chain 'B' and resid 695 through 700 removed outlier: 3.684A pdb=" N GLU B 699 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 695 through 700' Processing helix chain 'B' and resid 707 through 709 No H-bonds generated for 'chain 'B' and resid 707 through 709' Processing helix chain 'B' and resid 712 through 715 No H-bonds generated for 'chain 'B' and resid 712 through 715' Processing helix chain 'B' and resid 745 through 748 Processing helix chain 'B' and resid 751 through 755 removed outlier: 3.762A pdb=" N ILE B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 751 through 755' Processing helix chain 'B' and resid 759 through 761 No H-bonds generated for 'chain 'B' and resid 759 through 761' Processing helix chain 'B' and resid 764 through 774 Processing helix chain 'B' and resid 807 through 810 Processing helix chain 'B' and resid 843 through 847 Processing helix chain 'B' and resid 1014 through 1018 Proline residue: B1018 - end of helix Processing helix chain 'B' and resid 1023 through 1038 Processing helix chain 'B' and resid 1052 through 1062 removed outlier: 3.629A pdb=" N HIS B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1132 through 1141 Processing helix chain 'B' and resid 1144 through 1152 Processing helix chain 'B' and resid 1175 through 1177 No H-bonds generated for 'chain 'B' and resid 1175 through 1177' Processing helix chain 'B' and resid 1198 through 1209 Processing helix chain 'C' and resid 27 through 39 Processing helix chain 'C' and resid 60 through 69 removed outlier: 3.570A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 79 No H-bonds generated for 'chain 'C' and resid 77 through 79' Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 197 through 200 No H-bonds generated for 'chain 'C' and resid 197 through 200' Processing helix chain 'C' and resid 205 through 209 removed outlier: 3.671A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 265 Processing helix chain 'D' and resid 52 through 71 removed outlier: 3.560A pdb=" N ARG D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D 57 " --> pdb=" O SER D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 133 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 157 through 170 removed outlier: 4.488A pdb=" N ALA D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL D 163 " --> pdb=" O THR D 159 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 182 Processing helix chain 'D' and resid 188 through 194 Processing helix chain 'D' and resid 196 through 201 removed outlier: 4.288A pdb=" N ASN D 200 " --> pdb=" O SER D 197 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS D 201 " --> pdb=" O LEU D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 219 Processing helix chain 'E' and resid 6 through 26 Processing helix chain 'E' and resid 32 through 35 No H-bonds generated for 'chain 'E' and resid 32 through 35' Processing helix chain 'E' and resid 39 through 46 Processing helix chain 'E' and resid 56 through 58 No H-bonds generated for 'chain 'E' and resid 56 through 58' Processing helix chain 'E' and resid 66 through 71 Processing helix chain 'E' and resid 90 through 103 removed outlier: 3.602A pdb=" N GLN E 101 " --> pdb=" O VAL E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 125 Proline residue: E 125 - end of helix Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 158 through 168 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'F' and resid 87 through 102 Processing helix chain 'F' and resid 117 through 127 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 20 through 34 removed outlier: 3.690A pdb=" N LYS G 23 " --> pdb=" O PRO G 20 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN G 24 " --> pdb=" O ARG G 21 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU G 32 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL G 34 " --> pdb=" O LEU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 117 through 121 Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 32 through 38 Processing helix chain 'J' and resid 44 through 51 removed outlier: 4.259A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 62 removed outlier: 3.780A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 52 removed outlier: 4.543A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 116 removed outlier: 3.699A pdb=" N ALA K 115 " --> pdb=" O LEU K 111 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 82 through 85 Processing sheet with id= B, first strand: chain 'A' and resid 151 through 153 Processing sheet with id= C, first strand: chain 'A' and resid 173 through 177 Processing sheet with id= D, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.581A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.071A pdb=" N PHE A 468 " --> pdb=" O SER A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 363 through 367 removed outlier: 6.277A pdb=" N ARG A 459 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL A 366 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS A 461 " --> pdb=" O VAL A 366 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 375 through 379 Processing sheet with id= H, first strand: chain 'A' and resid 404 through 406 Processing sheet with id= I, first strand: chain 'A' and resid 540 through 542 Processing sheet with id= J, first strand: chain 'A' and resid 587 through 590 Processing sheet with id= K, first strand: chain 'A' and resid 878 through 882 Processing sheet with id= L, first strand: chain 'A' and resid 1115 through 1119 Processing sheet with id= M, first strand: chain 'A' and resid 1147 through 1151 removed outlier: 6.494A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 68 through 71 removed outlier: 3.887A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 95 through 97 Processing sheet with id= P, first strand: chain 'B' and resid 203 through 205 Processing sheet with id= Q, first strand: chain 'B' and resid 498 through 500 removed outlier: 6.029A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 222 through 227 removed outlier: 3.792A pdb=" N ARG B 241 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 256 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS B 270 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 543 through 545 Processing sheet with id= T, first strand: chain 'B' and resid 614 through 618 removed outlier: 6.376A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 793 through 796 removed outlier: 5.956A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 1010 through 1012 Processing sheet with id= W, first strand: chain 'B' and resid 1159 through 1163 Processing sheet with id= X, first strand: chain 'B' and resid 839 through 842 removed outlier: 7.599A pdb=" N MET B 841 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR B 993 " --> pdb=" O MET B 841 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 176 through 179 removed outlier: 3.641A pdb=" N GLU C 177 " --> pdb=" O ASN C 231 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN C 231 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 97 through 104 removed outlier: 6.255A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 111 through 114 removed outlier: 3.618A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 78 through 82 removed outlier: 7.203A pdb=" N THR E 107 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N GLU E 81 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE E 109 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR E 131 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N PHE E 110 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU E 133 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N TYR E 112 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N PHE E 135 " --> pdb=" O TYR E 112 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'E' and resid 152 through 155 Processing sheet with id= AD, first strand: chain 'F' and resid 133 through 137 Processing sheet with id= AE, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.893A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 142 through 146 removed outlier: 6.664A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'H' and resid 7 through 11 removed outlier: 6.570A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N PHE H 104 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ALA H 113 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLU H 106 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU H 111 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS H 37 " --> pdb=" O GLU H 126 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'I' and resid 16 through 19 Processing sheet with id= AI, first strand: chain 'I' and resid 100 through 103 removed outlier: 3.575A pdb=" N HIS I 108 " --> pdb=" O CYS I 103 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'K' and resid 19 through 23 1009 hydrogen bonds defined for protein. 2727 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 64 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 23.12 Time building geometry restraints manager: 40.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 30418 1.03 - 1.22: 66 1.22 - 1.42: 13000 1.42 - 1.62: 18327 1.62 - 1.81: 286 Bond restraints: 62097 Sorted by residual: bond pdb=" C2 TTD T 18 " pdb=" N3 TTD T 18 " ideal model delta sigma weight residual 1.510 1.332 0.178 2.00e-02 2.50e+03 7.92e+01 bond pdb=" C2T TTD T 18 " pdb=" N3T TTD T 18 " ideal model delta sigma weight residual 1.494 1.330 0.164 2.00e-02 2.50e+03 6.72e+01 bond pdb=" C4T TTD T 18 " pdb=" N3T TTD T 18 " ideal model delta sigma weight residual 1.484 1.326 0.158 2.00e-02 2.50e+03 6.25e+01 bond pdb=" N1 TTD T 18 " pdb=" C2 TTD T 18 " ideal model delta sigma weight residual 1.480 1.331 0.149 2.00e-02 2.50e+03 5.52e+01 bond pdb=" N3 TTD T 18 " pdb=" C4 TTD T 18 " ideal model delta sigma weight residual 1.477 1.332 0.145 2.00e-02 2.50e+03 5.28e+01 ... (remaining 62092 not shown) Histogram of bond angle deviations from ideal: 88.01 - 97.20: 5 97.20 - 106.40: 1181 106.40 - 115.60: 79384 115.60 - 124.79: 29195 124.79 - 133.99: 2655 Bond angle restraints: 112420 Sorted by residual: angle pdb=" O3' TTD T 18 " pdb=" P DT T 19 " pdb=" OP1 DT T 19 " ideal model delta sigma weight residual 108.00 130.26 -22.26 3.00e+00 1.11e-01 5.50e+01 angle pdb=" O3' TTD T 18 " pdb=" P DT T 19 " pdb=" OP2 DT T 19 " ideal model delta sigma weight residual 108.00 88.49 19.51 3.00e+00 1.11e-01 4.23e+01 angle pdb=" C3' TTD T 18 " pdb=" O3' TTD T 18 " pdb=" P DT T 19 " ideal model delta sigma weight residual 120.00 101.60 18.40 3.00e+00 1.11e-01 3.76e+01 angle pdb=" O4P TTD T 18 " pdb=" PB TTD T 18 " pdb=" O5P TTD T 18 " ideal model delta sigma weight residual 106.80 119.99 -13.19 3.00e+00 1.11e-01 1.93e+01 angle pdb=" C5R TTD T 18 " pdb=" O5R TTD T 18 " pdb=" PB TTD T 18 " ideal model delta sigma weight residual 109.83 121.92 -12.09 3.00e+00 1.11e-01 1.62e+01 ... (remaining 112415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 28042 35.50 - 71.01: 754 71.01 - 106.51: 24 106.51 - 142.02: 2 142.02 - 177.52: 5 Dihedral angle restraints: 28827 sinusoidal: 16325 harmonic: 12502 Sorted by residual: dihedral pdb=" C4' TTD T 18 " pdb=" C5R TTD T 18 " pdb=" O5R TTD T 18 " pdb=" PB TTD T 18 " ideal model delta sinusoidal sigma weight residual 241.46 90.64 150.82 1 3.00e+01 1.11e-03 2.00e+01 dihedral pdb=" CA PHE A 614 " pdb=" C PHE A 614 " pdb=" N GLY A 615 " pdb=" CA GLY A 615 " ideal model delta harmonic sigma weight residual 180.00 158.23 21.77 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" O4R TTD T 18 " pdb=" C4' TTD T 18 " pdb=" C5R TTD T 18 " pdb=" O5R TTD T 18 " ideal model delta sinusoidal sigma weight residual -87.02 24.77 -111.79 1 3.00e+01 1.11e-03 1.46e+01 ... (remaining 28824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3397 0.034 - 0.068: 966 0.068 - 0.103: 288 0.103 - 0.137: 180 0.137 - 0.171: 3 Chirality restraints: 4834 Sorted by residual: chirality pdb=" C3R TTD T 18 " pdb=" C2' TTD T 18 " pdb=" C4R TTD T 18 " pdb=" O3R TTD T 18 " both_signs ideal model delta sigma weight residual False -2.44 -2.61 0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" C6T TTD T 18 " pdb=" C6 TTD T 18 " pdb=" C5T TTD T 18 " pdb=" N1T TTD T 18 " both_signs ideal model delta sigma weight residual False 2.63 2.79 -0.16 2.00e-01 2.50e+01 6.39e-01 chirality pdb=" CA ILE B 280 " pdb=" N ILE B 280 " pdb=" C ILE B 280 " pdb=" CB ILE B 280 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 ... (remaining 4831 not shown) Planarity restraints: 8960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1R TTD T 18 " -0.476 2.00e-02 2.50e+03 2.16e-01 1.05e+03 pdb=" C2T TTD T 18 " 0.123 2.00e-02 2.50e+03 pdb=" C4T TTD T 18 " -0.045 2.00e-02 2.50e+03 pdb=" C5T TTD T 18 " 0.110 2.00e-02 2.50e+03 pdb=" C6T TTD T 18 " 0.100 2.00e-02 2.50e+03 pdb=" N1T TTD T 18 " 0.310 2.00e-02 2.50e+03 pdb=" N3T TTD T 18 " -0.032 2.00e-02 2.50e+03 pdb=" O2T TTD T 18 " 0.114 2.00e-02 2.50e+03 pdb=" O4T TTD T 18 " -0.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' TTD T 18 " 0.009 2.00e-02 2.50e+03 2.43e-02 1.33e+01 pdb=" N1 TTD T 18 " 0.004 2.00e-02 2.50e+03 pdb=" C2 TTD T 18 " 0.006 2.00e-02 2.50e+03 pdb=" O2 TTD T 18 " -0.003 2.00e-02 2.50e+03 pdb=" N3 TTD T 18 " -0.001 2.00e-02 2.50e+03 pdb=" C4 TTD T 18 " 0.003 2.00e-02 2.50e+03 pdb=" O4 TTD T 18 " -0.018 2.00e-02 2.50e+03 pdb=" C5 TTD T 18 " 0.048 2.00e-02 2.50e+03 pdb=" C6 TTD T 18 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A1098 " -0.044 5.00e-02 4.00e+02 6.62e-02 7.02e+00 pdb=" N PRO A1099 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A1099 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1099 " -0.038 5.00e-02 4.00e+02 ... (remaining 8957 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 1217 2.06 - 2.69: 99379 2.69 - 3.33: 182390 3.33 - 3.96: 233611 3.96 - 4.60: 365982 Nonbonded interactions: 882579 Sorted by model distance: nonbonded pdb=" HB2 CYS I 10 " pdb="ZN ZN I 201 " model vdw 1.423 1.544 nonbonded pdb=" O THR A1394 " pdb="HH12 ARG A1399 " model vdw 1.485 1.850 nonbonded pdb=" O GLU B 711 " pdb=" H ALA B 715 " model vdw 1.527 1.850 nonbonded pdb=" OE1 GLU A 795 " pdb=" H GLU A 795 " model vdw 1.546 1.850 nonbonded pdb=" HG SER A 663 " pdb=" O ILE B 827 " model vdw 1.555 1.850 ... (remaining 882574 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 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: 0.670 Extract box with map and model: 12.720 Check model and map are aligned: 0.670 Set scattering table: 0.420 Process input model: 183.780 Find NCS groups from input model: 0.830 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: 0.020 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 204.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 : 0.004 0.178 31629 Z= 0.262 Angle : 0.580 22.256 42949 Z= 0.317 Chirality : 0.040 0.171 4834 Planarity : 0.005 0.216 5359 Dihedral : 13.744 150.816 12158 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.04 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.14), residues: 3686 helix: 1.14 (0.15), residues: 1285 sheet: -0.66 (0.21), residues: 542 loop : -0.08 (0.15), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 656 HIS 0.004 0.001 HIS J 53 PHE 0.017 0.001 PHE A 971 TYR 0.018 0.001 TYR G 51 ARG 0.008 0.001 ARG A1399 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 168 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 415 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 415 time to evaluate : 3.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.8524 (mtm) cc_final: 0.8285 (mtt) REVERT: A 445 ASN cc_start: 0.7825 (t0) cc_final: 0.7366 (t0) REVERT: A 605 MET cc_start: 0.9062 (tpt) cc_final: 0.8492 (tpt) REVERT: A 973 ILE cc_start: 0.7950 (mp) cc_final: 0.7699 (mp) REVERT: A 1110 ASN cc_start: 0.9113 (t0) cc_final: 0.8723 (p0) REVERT: A 1239 ARG cc_start: 0.9402 (mmt-90) cc_final: 0.9191 (mmm160) REVERT: A 1442 ASP cc_start: 0.8054 (m-30) cc_final: 0.7713 (m-30) REVERT: B 396 ASP cc_start: 0.8167 (t0) cc_final: 0.7561 (p0) REVERT: B 860 MET cc_start: 0.8600 (ppp) cc_final: 0.8360 (ppp) REVERT: B 978 ASP cc_start: 0.8099 (m-30) cc_final: 0.7858 (m-30) REVERT: B 1092 TYR cc_start: 0.8113 (m-10) cc_final: 0.7375 (m-80) REVERT: D 156 ASP cc_start: 0.9301 (t0) cc_final: 0.9057 (t0) REVERT: E 29 PHE cc_start: 0.9119 (t80) cc_final: 0.8772 (t80) REVERT: E 93 MET cc_start: 0.9635 (mmp) cc_final: 0.9410 (mmm) REVERT: G 9 LEU cc_start: 0.7996 (mm) cc_final: 0.7769 (mm) REVERT: G 111 THR cc_start: 0.9086 (t) cc_final: 0.8526 (t) REVERT: G 113 HIS cc_start: 0.9297 (m90) cc_final: 0.9022 (m90) REVERT: I 13 MET cc_start: 0.5768 (tpt) cc_final: 0.5367 (tpt) REVERT: I 36 GLU cc_start: 0.9208 (tp30) cc_final: 0.8679 (tm-30) REVERT: I 87 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7914 (tm-30) outliers start: 0 outliers final: 0 residues processed: 415 average time/residue: 0.8203 time to fit residues: 552.6471 Evaluate side-chains 352 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 352 time to evaluate : 3.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 315 optimal weight: 2.9990 chunk 283 optimal weight: 5.9990 chunk 157 optimal weight: 0.0980 chunk 96 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 293 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 chunk 218 optimal weight: 0.8980 chunk 339 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN D 40 HIS ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31629 Z= 0.273 Angle : 0.562 6.935 42949 Z= 0.304 Chirality : 0.042 0.170 4834 Planarity : 0.005 0.062 5359 Dihedral : 12.719 154.627 4704 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.94 % Favored : 95.01 % Rotamer: Outliers : 1.03 % Allowed : 3.52 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3686 helix: 0.73 (0.14), residues: 1288 sheet: -0.70 (0.21), residues: 552 loop : -0.15 (0.15), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 13 HIS 0.008 0.001 HIS G 158 PHE 0.029 0.001 PHE D 175 TYR 0.013 0.001 TYR A1349 ARG 0.005 0.000 ARG G 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 168 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 397 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 363 time to evaluate : 3.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7151 (mmp) cc_final: 0.6750 (mmp) REVERT: A 291 GLU cc_start: 0.9201 (mm-30) cc_final: 0.8972 (tm-30) REVERT: A 304 MET cc_start: 0.8539 (mtm) cc_final: 0.8177 (mtt) REVERT: A 605 MET cc_start: 0.9100 (tpt) cc_final: 0.8772 (tpt) REVERT: A 1110 ASN cc_start: 0.9110 (t0) cc_final: 0.8708 (p0) REVERT: B 241 ARG cc_start: 0.7343 (mmm-85) cc_final: 0.6911 (tpt170) REVERT: B 396 ASP cc_start: 0.8143 (t0) cc_final: 0.7657 (p0) REVERT: B 408 LEU cc_start: 0.8471 (mm) cc_final: 0.8255 (mp) REVERT: D 156 ASP cc_start: 0.9331 (t0) cc_final: 0.9064 (t0) REVERT: E 29 PHE cc_start: 0.9147 (t80) cc_final: 0.8814 (t80) REVERT: E 93 MET cc_start: 0.9540 (mmp) cc_final: 0.9196 (mmm) REVERT: G 69 GLU cc_start: 0.7446 (tm-30) cc_final: 0.7138 (tm-30) REVERT: G 113 HIS cc_start: 0.9297 (m90) cc_final: 0.9072 (m90) REVERT: H 5 LEU cc_start: 0.6200 (OUTLIER) cc_final: 0.5843 (tt) REVERT: I 13 MET cc_start: 0.5853 (tpt) cc_final: 0.5424 (tpt) outliers start: 34 outliers final: 28 residues processed: 380 average time/residue: 0.7922 time to fit residues: 482.6121 Evaluate side-chains 369 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 340 time to evaluate : 3.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 971 PHE Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 666 TYR Chi-restraints excluded: chain B residue 874 PHE Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1134 GLU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 175 PHE Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 42 PHE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 31 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 188 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 282 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 340 optimal weight: 10.0000 chunk 367 optimal weight: 7.9990 chunk 303 optimal weight: 2.9990 chunk 337 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 272 optimal weight: 9.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 ASN ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 31629 Z= 0.377 Angle : 0.564 5.671 42949 Z= 0.307 Chirality : 0.041 0.166 4834 Planarity : 0.004 0.072 5359 Dihedral : 12.795 153.598 4704 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.53 % Favored : 94.41 % Rotamer: Outliers : 1.06 % Allowed : 4.92 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3686 helix: 0.50 (0.14), residues: 1278 sheet: -0.81 (0.21), residues: 549 loop : -0.36 (0.15), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 31 HIS 0.006 0.001 HIS G 158 PHE 0.023 0.001 PHE D 175 TYR 0.013 0.001 TYR B1092 ARG 0.004 0.000 ARG L 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 168 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 379 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 344 time to evaluate : 3.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7360 (mmp) cc_final: 0.7075 (mmp) REVERT: A 304 MET cc_start: 0.8612 (mtm) cc_final: 0.8224 (mtt) REVERT: A 1110 ASN cc_start: 0.9143 (t0) cc_final: 0.8725 (p0) REVERT: B 239 GLU cc_start: 0.8441 (tt0) cc_final: 0.7688 (tm-30) REVERT: B 396 ASP cc_start: 0.8190 (t0) cc_final: 0.7617 (p0) REVERT: B 408 LEU cc_start: 0.8560 (mm) cc_final: 0.8303 (mt) REVERT: B 1092 TYR cc_start: 0.8785 (m-10) cc_final: 0.8526 (m-80) REVERT: D 156 ASP cc_start: 0.9303 (t0) cc_final: 0.9016 (t0) REVERT: E 29 PHE cc_start: 0.9165 (t80) cc_final: 0.8827 (t80) REVERT: E 93 MET cc_start: 0.9524 (mmt) cc_final: 0.9244 (mmm) REVERT: F 86 THR cc_start: 0.8767 (m) cc_final: 0.8179 (p) REVERT: G 138 THR cc_start: 0.8383 (t) cc_final: 0.8171 (m) REVERT: I 13 MET cc_start: 0.6043 (tpt) cc_final: 0.5567 (tpt) REVERT: I 47 GLU cc_start: 0.5707 (mp0) cc_final: 0.5492 (mp0) outliers start: 35 outliers final: 27 residues processed: 360 average time/residue: 0.8260 time to fit residues: 479.8657 Evaluate side-chains 353 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 326 time to evaluate : 3.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 666 TYR Chi-restraints excluded: chain B residue 874 PHE Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 175 PHE Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 52 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 336 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 228 optimal weight: 2.9990 chunk 341 optimal weight: 9.9990 chunk 361 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 323 optimal weight: 30.0000 chunk 97 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN ** A 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 ASN ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 31629 Z= 0.357 Angle : 0.555 5.319 42949 Z= 0.300 Chirality : 0.041 0.172 4834 Planarity : 0.004 0.065 5359 Dihedral : 12.855 150.868 4704 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.64 % Favored : 94.30 % Rotamer: Outliers : 1.18 % Allowed : 5.86 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.14), residues: 3686 helix: 0.48 (0.14), residues: 1277 sheet: -0.95 (0.21), residues: 562 loop : -0.50 (0.15), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 31 HIS 0.005 0.001 HIS A 490 PHE 0.026 0.001 PHE D 175 TYR 0.028 0.002 TYR G 25 ARG 0.004 0.000 ARG L 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 168 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 377 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 338 time to evaluate : 3.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7271 (mmp) cc_final: 0.7034 (mmp) REVERT: A 304 MET cc_start: 0.8686 (mtm) cc_final: 0.8407 (mtt) REVERT: A 1110 ASN cc_start: 0.9179 (t0) cc_final: 0.8786 (p0) REVERT: A 1111 MET cc_start: 0.8855 (mtm) cc_final: 0.8640 (mtm) REVERT: A 1442 ASP cc_start: 0.8085 (m-30) cc_final: 0.7863 (m-30) REVERT: B 239 GLU cc_start: 0.8298 (tt0) cc_final: 0.7743 (tm-30) REVERT: B 396 ASP cc_start: 0.8240 (t0) cc_final: 0.7667 (p0) REVERT: B 408 LEU cc_start: 0.8539 (mm) cc_final: 0.8290 (mt) REVERT: B 615 MET cc_start: 0.8129 (mpp) cc_final: 0.7778 (mpp) REVERT: B 1092 TYR cc_start: 0.8664 (m-10) cc_final: 0.8458 (m-80) REVERT: D 156 ASP cc_start: 0.9209 (t0) cc_final: 0.8884 (t0) REVERT: E 25 ASP cc_start: 0.8700 (m-30) cc_final: 0.8289 (m-30) REVERT: E 29 PHE cc_start: 0.9181 (t80) cc_final: 0.8853 (t80) REVERT: E 93 MET cc_start: 0.9527 (mmt) cc_final: 0.9206 (mmm) REVERT: F 86 THR cc_start: 0.8809 (m) cc_final: 0.8269 (p) REVERT: G 49 LEU cc_start: 0.9207 (tt) cc_final: 0.8787 (mp) REVERT: G 69 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7292 (tm-30) REVERT: G 94 CYS cc_start: 0.3941 (m) cc_final: 0.3716 (m) REVERT: I 13 MET cc_start: 0.6187 (tpt) cc_final: 0.5676 (tpt) REVERT: I 36 GLU cc_start: 0.8872 (tp30) cc_final: 0.8447 (tm-30) REVERT: I 87 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7795 (tm-30) outliers start: 39 outliers final: 30 residues processed: 355 average time/residue: 0.7823 time to fit residues: 450.1986 Evaluate side-chains 359 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 329 time to evaluate : 3.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 666 TYR Chi-restraints excluded: chain B residue 874 PHE Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 1134 GLU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 175 PHE Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain J residue 52 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 301 optimal weight: 0.4980 chunk 205 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 269 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 308 optimal weight: 1.9990 chunk 249 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 324 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 ASN ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 44 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 31629 Z= 0.239 Angle : 0.503 5.315 42949 Z= 0.270 Chirality : 0.041 0.179 4834 Planarity : 0.004 0.061 5359 Dihedral : 12.822 147.257 4704 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.15 % Favored : 94.79 % Rotamer: Outliers : 1.06 % Allowed : 6.62 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3686 helix: 0.89 (0.15), residues: 1270 sheet: -0.92 (0.21), residues: 552 loop : -0.36 (0.15), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 31 HIS 0.004 0.001 HIS A 399 PHE 0.026 0.001 PHE D 175 TYR 0.012 0.001 TYR H 95 ARG 0.002 0.000 ARG L 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 168 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 390 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 355 time to evaluate : 3.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7287 (mmp) cc_final: 0.7087 (mmp) REVERT: A 304 MET cc_start: 0.8675 (mtm) cc_final: 0.8376 (mtt) REVERT: A 1110 ASN cc_start: 0.9146 (t0) cc_final: 0.8723 (p0) REVERT: A 1111 MET cc_start: 0.8879 (mtm) cc_final: 0.8660 (mtm) REVERT: A 1228 TRP cc_start: 0.7729 (p90) cc_final: 0.7483 (p90) REVERT: A 1442 ASP cc_start: 0.8080 (m-30) cc_final: 0.7821 (m-30) REVERT: B 239 GLU cc_start: 0.8274 (tt0) cc_final: 0.7766 (tm-30) REVERT: B 408 LEU cc_start: 0.8537 (mm) cc_final: 0.8297 (mt) REVERT: B 417 PHE cc_start: 0.8753 (t80) cc_final: 0.8481 (t80) REVERT: B 1092 TYR cc_start: 0.8666 (m-10) cc_final: 0.8391 (m-80) REVERT: C 17 ASN cc_start: 0.8555 (OUTLIER) cc_final: 0.7947 (p0) REVERT: D 156 ASP cc_start: 0.9206 (t0) cc_final: 0.8884 (t0) REVERT: E 25 ASP cc_start: 0.8631 (m-30) cc_final: 0.8184 (m-30) REVERT: E 29 PHE cc_start: 0.9150 (t80) cc_final: 0.8821 (t80) REVERT: E 93 MET cc_start: 0.9510 (mmt) cc_final: 0.9191 (mmm) REVERT: F 86 THR cc_start: 0.8786 (m) cc_final: 0.8308 (p) REVERT: G 49 LEU cc_start: 0.9219 (tt) cc_final: 0.8825 (mp) REVERT: G 69 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7289 (tm-30) REVERT: G 94 CYS cc_start: 0.4547 (m) cc_final: 0.4327 (m) REVERT: I 13 MET cc_start: 0.6261 (tpt) cc_final: 0.5738 (tpt) outliers start: 35 outliers final: 28 residues processed: 367 average time/residue: 0.7972 time to fit residues: 473.4625 Evaluate side-chains 366 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 337 time to evaluate : 3.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 706 HIS Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 666 TYR Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 874 PHE Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1216 LEU Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 182 ASP Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain J residue 52 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 121 optimal weight: 6.9990 chunk 325 optimal weight: 20.0000 chunk 71 optimal weight: 0.9980 chunk 212 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 361 optimal weight: 1.9990 chunk 300 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN D 132 GLN ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31629 Z= 0.288 Angle : 0.517 5.790 42949 Z= 0.277 Chirality : 0.041 0.163 4834 Planarity : 0.004 0.061 5359 Dihedral : 12.819 145.392 4704 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.67 % Favored : 94.25 % Rotamer: Outliers : 1.03 % Allowed : 7.35 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.14), residues: 3686 helix: 0.86 (0.14), residues: 1276 sheet: -0.95 (0.21), residues: 552 loop : -0.40 (0.15), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 31 HIS 0.005 0.001 HIS A 109 PHE 0.031 0.001 PHE D 175 TYR 0.013 0.001 TYR B 486 ARG 0.008 0.000 ARG G 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 168 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 373 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 339 time to evaluate : 3.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.8696 (mtm) cc_final: 0.8384 (mtt) REVERT: A 1110 ASN cc_start: 0.9163 (t0) cc_final: 0.8817 (p0) REVERT: A 1111 MET cc_start: 0.8905 (mtm) cc_final: 0.8691 (mtm) REVERT: A 1209 MET cc_start: 0.6388 (ttt) cc_final: 0.6072 (ttt) REVERT: A 1228 TRP cc_start: 0.7711 (p90) cc_final: 0.7433 (p90) REVERT: A 1267 MET cc_start: 0.9379 (mpp) cc_final: 0.9175 (mpp) REVERT: A 1284 MET cc_start: 0.8403 (mtp) cc_final: 0.8016 (ttm) REVERT: A 1442 ASP cc_start: 0.8095 (m-30) cc_final: 0.7860 (m-30) REVERT: B 239 GLU cc_start: 0.8271 (tt0) cc_final: 0.7783 (tm-30) REVERT: B 267 ARG cc_start: 0.8556 (mtm180) cc_final: 0.8182 (mtm180) REVERT: B 408 LEU cc_start: 0.8540 (mm) cc_final: 0.8313 (mt) REVERT: B 417 PHE cc_start: 0.8729 (t80) cc_final: 0.8445 (t80) REVERT: B 1092 TYR cc_start: 0.8658 (m-10) cc_final: 0.8453 (m-80) REVERT: C 75 MET cc_start: 0.8853 (tpp) cc_final: 0.8535 (mmm) REVERT: D 156 ASP cc_start: 0.9213 (t0) cc_final: 0.8891 (t0) REVERT: E 25 ASP cc_start: 0.8627 (m-30) cc_final: 0.8183 (m-30) REVERT: E 29 PHE cc_start: 0.9171 (t80) cc_final: 0.8827 (t80) REVERT: E 93 MET cc_start: 0.9510 (mmt) cc_final: 0.9201 (mmm) REVERT: F 86 THR cc_start: 0.8793 (m) cc_final: 0.8323 (p) REVERT: G 49 LEU cc_start: 0.9218 (tt) cc_final: 0.8823 (mp) REVERT: G 94 CYS cc_start: 0.4481 (m) cc_final: 0.4199 (m) REVERT: I 13 MET cc_start: 0.6342 (tpt) cc_final: 0.5795 (tpt) outliers start: 34 outliers final: 33 residues processed: 355 average time/residue: 0.7885 time to fit residues: 451.6774 Evaluate side-chains 369 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 336 time to evaluate : 3.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 706 HIS Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 666 TYR Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 874 PHE Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain B residue 1216 LEU Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 182 ASP Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 130 TYR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 52 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 348 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 206 optimal weight: 0.9990 chunk 264 optimal weight: 1.9990 chunk 204 optimal weight: 0.3980 chunk 304 optimal weight: 4.9990 chunk 202 optimal weight: 1.9990 chunk 360 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 219 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31629 Z= 0.213 Angle : 0.493 6.912 42949 Z= 0.262 Chirality : 0.040 0.175 4834 Planarity : 0.004 0.063 5359 Dihedral : 12.789 142.201 4704 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.69 % Favored : 95.25 % Rotamer: Outliers : 1.03 % Allowed : 7.56 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.14), residues: 3686 helix: 1.11 (0.15), residues: 1276 sheet: -0.89 (0.21), residues: 552 loop : -0.29 (0.15), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 656 HIS 0.003 0.001 HIS A 490 PHE 0.034 0.001 PHE D 175 TYR 0.013 0.001 TYR H 95 ARG 0.013 0.000 ARG D 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 168 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 387 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 353 time to evaluate : 3.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.8681 (mtm) cc_final: 0.8371 (mtt) REVERT: A 1110 ASN cc_start: 0.9225 (t0) cc_final: 0.8734 (p0) REVERT: A 1111 MET cc_start: 0.8931 (mtm) cc_final: 0.8709 (mtm) REVERT: A 1209 MET cc_start: 0.6393 (ttt) cc_final: 0.6041 (ttt) REVERT: A 1228 TRP cc_start: 0.7804 (p90) cc_final: 0.7546 (p90) REVERT: A 1284 MET cc_start: 0.8329 (mtp) cc_final: 0.8038 (ttm) REVERT: A 1442 ASP cc_start: 0.8079 (m-30) cc_final: 0.7832 (m-30) REVERT: B 239 GLU cc_start: 0.8262 (tt0) cc_final: 0.7774 (tm-30) REVERT: B 267 ARG cc_start: 0.8515 (mtm180) cc_final: 0.8134 (mtm180) REVERT: B 408 LEU cc_start: 0.8490 (mm) cc_final: 0.8282 (mt) REVERT: B 417 PHE cc_start: 0.8696 (t80) cc_final: 0.8404 (t80) REVERT: B 444 MET cc_start: 0.4982 (mpp) cc_final: 0.4567 (pmm) REVERT: B 1072 MET cc_start: 0.8849 (mtt) cc_final: 0.8647 (mtp) REVERT: B 1092 TYR cc_start: 0.8654 (m-10) cc_final: 0.8404 (m-80) REVERT: D 156 ASP cc_start: 0.9214 (t0) cc_final: 0.8901 (t0) REVERT: E 25 ASP cc_start: 0.8560 (m-30) cc_final: 0.8072 (m-30) REVERT: E 29 PHE cc_start: 0.9160 (t80) cc_final: 0.8823 (t80) REVERT: F 86 THR cc_start: 0.8822 (m) cc_final: 0.8398 (p) REVERT: G 69 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7369 (tm-30) REVERT: G 94 CYS cc_start: 0.4293 (m) cc_final: 0.3974 (m) REVERT: I 13 MET cc_start: 0.6376 (tpt) cc_final: 0.5816 (tpt) outliers start: 34 outliers final: 31 residues processed: 370 average time/residue: 0.8128 time to fit residues: 482.6807 Evaluate side-chains 375 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 344 time to evaluate : 3.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 706 HIS Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 666 TYR Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 874 PHE Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain B residue 1216 LEU Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 182 ASP Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 130 TYR Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain J residue 52 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 223 optimal weight: 2.9990 chunk 143 optimal weight: 0.0570 chunk 215 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 229 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 283 optimal weight: 0.3980 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 31629 Z= 0.161 Angle : 0.480 7.280 42949 Z= 0.253 Chirality : 0.040 0.160 4834 Planarity : 0.004 0.057 5359 Dihedral : 12.751 140.123 4704 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.26 % Favored : 95.69 % Rotamer: Outliers : 0.82 % Allowed : 8.17 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.14), residues: 3686 helix: 1.34 (0.15), residues: 1281 sheet: -0.79 (0.21), residues: 558 loop : -0.20 (0.15), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 656 HIS 0.003 0.001 HIS A 118 PHE 0.033 0.001 PHE D 175 TYR 0.011 0.001 TYR H 95 ARG 0.004 0.000 ARG G 58 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 168 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 387 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 360 time to evaluate : 3.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.8675 (mtm) cc_final: 0.8374 (mtt) REVERT: A 1110 ASN cc_start: 0.9150 (t0) cc_final: 0.8744 (p0) REVERT: A 1111 MET cc_start: 0.8917 (mtm) cc_final: 0.8696 (mtm) REVERT: A 1209 MET cc_start: 0.6330 (ttt) cc_final: 0.5950 (ttt) REVERT: A 1228 TRP cc_start: 0.7784 (p90) cc_final: 0.7526 (p90) REVERT: A 1284 MET cc_start: 0.8338 (mtp) cc_final: 0.8016 (ttm) REVERT: B 239 GLU cc_start: 0.8251 (tt0) cc_final: 0.7765 (tm-30) REVERT: B 267 ARG cc_start: 0.8514 (mtm180) cc_final: 0.8096 (mtm180) REVERT: B 396 ASP cc_start: 0.8120 (t0) cc_final: 0.7391 (p0) REVERT: B 403 LYS cc_start: 0.8942 (mmtp) cc_final: 0.8670 (mmtt) REVERT: B 417 PHE cc_start: 0.8643 (t80) cc_final: 0.8341 (t80) REVERT: B 444 MET cc_start: 0.4808 (mpp) cc_final: 0.4443 (pmm) REVERT: B 615 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7755 (mpp) REVERT: B 1092 TYR cc_start: 0.8589 (m-10) cc_final: 0.8266 (m-80) REVERT: D 156 ASP cc_start: 0.9210 (t0) cc_final: 0.8896 (t0) REVERT: E 25 ASP cc_start: 0.8548 (m-30) cc_final: 0.8044 (m-30) REVERT: E 29 PHE cc_start: 0.9172 (t80) cc_final: 0.8806 (t80) REVERT: F 86 THR cc_start: 0.8791 (m) cc_final: 0.8380 (p) REVERT: F 110 ASP cc_start: 0.8624 (p0) cc_final: 0.8354 (p0) REVERT: G 69 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7347 (tm-30) REVERT: G 94 CYS cc_start: 0.4275 (m) cc_final: 0.3936 (m) REVERT: I 13 MET cc_start: 0.6359 (tpt) cc_final: 0.5801 (tpt) outliers start: 27 outliers final: 22 residues processed: 372 average time/residue: 0.8129 time to fit residues: 487.8781 Evaluate side-chains 369 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 346 time to evaluate : 3.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 666 TYR Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 874 PHE Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1216 LEU Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 130 TYR Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 52 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 327 optimal weight: 3.9990 chunk 345 optimal weight: 0.8980 chunk 315 optimal weight: 3.9990 chunk 335 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 263 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 303 optimal weight: 1.9990 chunk 317 optimal weight: 4.9990 chunk 334 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 HIS ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 31629 Z= 0.285 Angle : 0.520 7.316 42949 Z= 0.276 Chirality : 0.040 0.148 4834 Planarity : 0.004 0.060 5359 Dihedral : 12.763 139.076 4704 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.67 % Favored : 94.28 % Rotamer: Outliers : 0.88 % Allowed : 8.41 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.14), residues: 3686 helix: 1.14 (0.15), residues: 1287 sheet: -0.88 (0.21), residues: 548 loop : -0.33 (0.15), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 656 HIS 0.005 0.001 HIS J 53 PHE 0.033 0.001 PHE D 175 TYR 0.018 0.001 TYR D 147 ARG 0.003 0.000 ARG E 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 168 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 370 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 341 time to evaluate : 3.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8950 (mtm) cc_final: 0.8666 (ptm) REVERT: A 304 MET cc_start: 0.8700 (mtm) cc_final: 0.8377 (mtt) REVERT: A 1110 ASN cc_start: 0.9171 (t0) cc_final: 0.8791 (p0) REVERT: A 1111 MET cc_start: 0.8943 (mtm) cc_final: 0.8728 (mtm) REVERT: A 1228 TRP cc_start: 0.7812 (p90) cc_final: 0.7569 (p90) REVERT: A 1284 MET cc_start: 0.8272 (mtp) cc_final: 0.8007 (ttm) REVERT: B 239 GLU cc_start: 0.8317 (tt0) cc_final: 0.7785 (tm-30) REVERT: B 396 ASP cc_start: 0.8161 (t0) cc_final: 0.7589 (p0) REVERT: B 403 LYS cc_start: 0.8947 (mmtp) cc_final: 0.8742 (mmtt) REVERT: B 417 PHE cc_start: 0.8659 (t80) cc_final: 0.8387 (t80) REVERT: B 444 MET cc_start: 0.5039 (mpp) cc_final: 0.4742 (pmm) REVERT: B 1092 TYR cc_start: 0.8726 (m-10) cc_final: 0.8463 (m-80) REVERT: D 156 ASP cc_start: 0.9258 (t0) cc_final: 0.8964 (t0) REVERT: E 25 ASP cc_start: 0.8557 (m-30) cc_final: 0.8068 (m-30) REVERT: E 29 PHE cc_start: 0.9198 (t80) cc_final: 0.8813 (t80) REVERT: F 86 THR cc_start: 0.8813 (m) cc_final: 0.8395 (p) REVERT: F 110 ASP cc_start: 0.8684 (p0) cc_final: 0.8411 (p0) REVERT: F 130 ILE cc_start: 0.9592 (mt) cc_final: 0.9060 (tt) REVERT: G 69 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7445 (tm-30) REVERT: G 94 CYS cc_start: 0.4320 (m) cc_final: 0.3980 (m) REVERT: G 106 MET cc_start: 0.6634 (ttm) cc_final: 0.6195 (ttm) REVERT: I 13 MET cc_start: 0.6175 (tpt) cc_final: 0.5724 (tpt) outliers start: 29 outliers final: 24 residues processed: 354 average time/residue: 0.8139 time to fit residues: 467.7222 Evaluate side-chains 361 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 337 time to evaluate : 3.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 666 TYR Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 874 PHE Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1216 LEU Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 182 ASP Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 130 TYR Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 220 optimal weight: 0.9980 chunk 355 optimal weight: 0.1980 chunk 216 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 246 optimal weight: 0.9980 chunk 372 optimal weight: 5.9990 chunk 342 optimal weight: 20.0000 chunk 296 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 229 optimal weight: 0.0570 chunk 181 optimal weight: 0.4980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 HIS I 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 31629 Z= 0.155 Angle : 0.483 7.961 42949 Z= 0.253 Chirality : 0.040 0.150 4834 Planarity : 0.004 0.057 5359 Dihedral : 12.724 137.068 4704 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.10 % Favored : 95.85 % Rotamer: Outliers : 0.58 % Allowed : 8.75 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.14), residues: 3686 helix: 1.40 (0.15), residues: 1289 sheet: -0.78 (0.21), residues: 548 loop : -0.16 (0.15), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 656 HIS 0.004 0.001 HIS I 108 PHE 0.037 0.001 PHE D 175 TYR 0.019 0.001 TYR D 147 ARG 0.004 0.000 ARG E 7 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 168 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 365 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 346 time to evaluate : 3.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8959 (mtm) cc_final: 0.8692 (ptm) REVERT: A 304 MET cc_start: 0.8675 (mtm) cc_final: 0.8369 (mtt) REVERT: A 1110 ASN cc_start: 0.9143 (t0) cc_final: 0.8747 (p0) REVERT: A 1111 MET cc_start: 0.8923 (mtm) cc_final: 0.8705 (mtm) REVERT: A 1228 TRP cc_start: 0.7790 (p90) cc_final: 0.7534 (p90) REVERT: A 1267 MET cc_start: 0.9229 (mpp) cc_final: 0.8944 (pmm) REVERT: A 1284 MET cc_start: 0.8195 (mtp) cc_final: 0.7956 (ttm) REVERT: B 239 GLU cc_start: 0.8288 (tt0) cc_final: 0.7751 (tm-30) REVERT: B 267 ARG cc_start: 0.8517 (mtm180) cc_final: 0.8095 (mtm180) REVERT: B 310 MET cc_start: 0.8685 (ttm) cc_final: 0.8165 (ptm) REVERT: B 396 ASP cc_start: 0.8122 (t0) cc_final: 0.7586 (p0) REVERT: B 403 LYS cc_start: 0.8935 (mmtp) cc_final: 0.8728 (mmtt) REVERT: B 417 PHE cc_start: 0.8612 (t80) cc_final: 0.8323 (t80) REVERT: B 444 MET cc_start: 0.4956 (mpp) cc_final: 0.4699 (pmm) REVERT: B 1092 TYR cc_start: 0.8597 (m-10) cc_final: 0.8349 (m-80) REVERT: C 75 MET cc_start: 0.8847 (tpp) cc_final: 0.8582 (mmm) REVERT: D 156 ASP cc_start: 0.9205 (t0) cc_final: 0.8895 (t0) REVERT: E 7 ARG cc_start: 0.8691 (tmt170) cc_final: 0.8226 (tpt90) REVERT: E 25 ASP cc_start: 0.8512 (m-30) cc_final: 0.8013 (m-30) REVERT: E 29 PHE cc_start: 0.9191 (t80) cc_final: 0.8815 (t80) REVERT: F 86 THR cc_start: 0.8792 (m) cc_final: 0.8390 (p) REVERT: F 110 ASP cc_start: 0.8630 (p0) cc_final: 0.8364 (p0) REVERT: F 130 ILE cc_start: 0.9588 (mt) cc_final: 0.9022 (tt) REVERT: G 69 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7388 (tm-30) REVERT: G 94 CYS cc_start: 0.4215 (m) cc_final: 0.3848 (m) REVERT: G 106 MET cc_start: 0.6633 (ttm) cc_final: 0.6193 (ttm) REVERT: I 13 MET cc_start: 0.6370 (tpt) cc_final: 0.5792 (tpt) outliers start: 19 outliers final: 19 residues processed: 357 average time/residue: 0.8082 time to fit residues: 464.4654 Evaluate side-chains 358 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 339 time to evaluate : 3.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 666 TYR Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 874 PHE Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1216 LEU Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 130 TYR Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 235 optimal weight: 5.9990 chunk 316 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 273 optimal weight: 3.9990 chunk 43 optimal weight: 0.0670 chunk 82 optimal weight: 1.9990 chunk 297 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 305 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.116407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.079168 restraints weight = 233249.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.082823 restraints weight = 84632.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.085011 restraints weight = 49553.264| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31629 Z= 0.188 Angle : 0.489 8.472 42949 Z= 0.255 Chirality : 0.040 0.151 4834 Planarity : 0.004 0.057 5359 Dihedral : 12.700 136.096 4704 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.75 % Favored : 95.20 % Rotamer: Outliers : 0.64 % Allowed : 8.84 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.14), residues: 3686 helix: 1.46 (0.15), residues: 1283 sheet: -0.77 (0.21), residues: 554 loop : -0.17 (0.15), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 656 HIS 0.004 0.001 HIS I 108 PHE 0.038 0.001 PHE D 175 TYR 0.014 0.001 TYR B 488 ARG 0.003 0.000 ARG D 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10260.76 seconds wall clock time: 178 minutes 42.09 seconds (10722.09 seconds total)