Starting phenix.real_space_refine on Tue Feb 20 07:42:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m7j_9047/02_2024/6m7j_9047_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m7j_9047/02_2024/6m7j_9047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m7j_9047/02_2024/6m7j_9047.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m7j_9047/02_2024/6m7j_9047.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m7j_9047/02_2024/6m7j_9047_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m7j_9047/02_2024/6m7j_9047_neut_trim_updated.pdb" } resolution = 4.4 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= 0.006 sd= 0.082 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 55 5.49 5 Mg 1 5.21 5 S 98 5.16 5 C 16871 2.51 5 N 4836 2.21 5 O 5320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ARG 223": "NH1" <-> "NH2" Residue "B PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 205": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C ARG 259": "NH1" <-> "NH2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C ARG 467": "NH1" <-> "NH2" Residue "C ARG 482": "NH1" <-> "NH2" Residue "C ARG 791": "NH1" <-> "NH2" Residue "C ARG 855": "NH1" <-> "NH2" Residue "C ARG 925": "NH1" <-> "NH2" Residue "C TYR 1027": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1067": "NH1" <-> "NH2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 572": "NH1" <-> "NH2" Residue "D ARG 841": "NH1" <-> "NH2" Residue "D ARG 876": "NH1" <-> "NH2" Residue "D ARG 940": "NH1" <-> "NH2" Residue "D PHE 1061": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 213": "NH1" <-> "NH2" Residue "F ARG 229": "NH1" <-> "NH2" Residue "F ARG 278": "NH1" <-> "NH2" Residue "F ARG 279": "NH1" <-> "NH2" Residue "F ARG 290": "NH1" <-> "NH2" Residue "F ARG 384": "NH1" <-> "NH2" Residue "F ARG 418": "NH1" <-> "NH2" Residue "F ARG 500": "NH1" <-> "NH2" Residue "F ARG 524": "NH1" <-> "NH2" Residue "J ARG 109": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27183 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1716 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 210} Chain: "B" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1759 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 220} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 8586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8586 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1048} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 9873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1266, 9873 Classifications: {'peptide': 1266} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 57, 'TRANS': 1204} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 76} Chain: "F" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2518 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 310} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "J" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 881 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "O" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 526 Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "D" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Unusual residues: {' MG': 1, ' ZN': 2, 'C0L': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19125 SG CYS D 891 110.355 57.512 85.944 1.00199.50 S ATOM 19692 SG CYS D 968 106.381 58.194 87.216 1.00203.67 S ATOM 19734 SG CYS D 975 107.880 59.453 84.373 1.00192.01 S ATOM 19752 SG CYS D 978 108.130 56.056 83.748 1.00186.92 S ATOM 12567 SG CYS D 60 75.458 104.029 122.731 1.00238.85 S ATOM 12585 SG CYS D 62 73.867 104.451 125.750 1.00228.37 S Time building chain proxies: 14.15, per 1000 atoms: 0.52 Number of scatterers: 27183 At special positions: 0 Unit cell: (132.6, 159.9, 195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 98 16.00 P 55 15.00 Mg 1 11.99 O 5320 8.00 N 4836 7.00 C 16871 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.60 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1401 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 968 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 978 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 891 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 975 " pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 60 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 62 " Number of angles added : 6 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6168 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 114 helices and 31 sheets defined 37.5% alpha, 7.7% beta 26 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 13.08 Creating SS restraints... Processing helix chain 'A' and resid 31 through 44 removed outlier: 3.938A pdb=" N SER A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 82 Processing helix chain 'A' and resid 107 through 109 No H-bonds generated for 'chain 'A' and resid 107 through 109' Processing helix chain 'A' and resid 204 through 223 removed outlier: 3.630A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 44 removed outlier: 4.420A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 81 Processing helix chain 'B' and resid 204 through 223 removed outlier: 3.992A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 65 removed outlier: 3.914A pdb=" N VAL C 56 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASP C 59 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 85 through 93 Processing helix chain 'C' and resid 119 through 125 Processing helix chain 'C' and resid 234 through 240 Processing helix chain 'C' and resid 245 through 251 Processing helix chain 'C' and resid 256 through 263 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 291 through 300 removed outlier: 3.819A pdb=" N LEU C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASN C 298 " --> pdb=" O THR C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 320 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 381 through 406 removed outlier: 3.572A pdb=" N ARG C 395 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU C 402 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 417 No H-bonds generated for 'chain 'C' and resid 414 through 417' Processing helix chain 'C' and resid 421 through 431 Processing helix chain 'C' and resid 445 through 451 Processing helix chain 'C' and resid 470 through 473 Processing helix chain 'C' and resid 477 through 479 No H-bonds generated for 'chain 'C' and resid 477 through 479' Processing helix chain 'C' and resid 533 through 538 removed outlier: 3.532A pdb=" N ARG C 538 " --> pdb=" O ASP C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 593 Processing helix chain 'C' and resid 597 through 599 No H-bonds generated for 'chain 'C' and resid 597 through 599' Processing helix chain 'C' and resid 602 through 614 removed outlier: 3.662A pdb=" N ARG C 613 " --> pdb=" O ALA C 609 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN C 614 " --> pdb=" O ASN C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 638 removed outlier: 4.107A pdb=" N ALA C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 779 through 781 No H-bonds generated for 'chain 'C' and resid 779 through 781' Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 919 through 925 Proline residue: C 923 - end of helix Processing helix chain 'C' and resid 928 through 942 Processing helix chain 'C' and resid 954 through 956 No H-bonds generated for 'chain 'C' and resid 954 through 956' Processing helix chain 'C' and resid 982 through 990 Processing helix chain 'C' and resid 1072 through 1079 removed outlier: 3.657A pdb=" N GLN C1077 " --> pdb=" O CYS C1073 " (cutoff:3.500A) Processing helix chain 'C' and resid 1083 through 1091 Processing helix chain 'C' and resid 1096 through 1108 removed outlier: 4.007A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1119 through 1130 Processing helix chain 'D' and resid 17 through 23 Processing helix chain 'D' and resid 49 through 52 No H-bonds generated for 'chain 'D' and resid 49 through 52' Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing helix chain 'D' and resid 104 through 108 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 122 through 129 removed outlier: 3.650A pdb=" N LYS D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 146 Processing helix chain 'D' and resid 148 through 184 Processing helix chain 'D' and resid 191 through 227 Processing helix chain 'D' and resid 239 through 245 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 258 through 266 Processing helix chain 'D' and resid 270 through 283 Processing helix chain 'D' and resid 286 through 304 removed outlier: 3.794A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 312 Processing helix chain 'D' and resid 323 through 325 No H-bonds generated for 'chain 'D' and resid 323 through 325' Processing helix chain 'D' and resid 341 through 360 Processing helix chain 'D' and resid 364 through 383 Processing helix chain 'D' and resid 402 through 405 Processing helix chain 'D' and resid 445 through 462 removed outlier: 4.097A pdb=" N LYS D 453 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Proline residue: D 454 - end of helix Processing helix chain 'D' and resid 469 through 478 Processing helix chain 'D' and resid 481 through 491 Processing helix chain 'D' and resid 506 through 508 No H-bonds generated for 'chain 'D' and resid 506 through 508' Processing helix chain 'D' and resid 527 through 532 removed outlier: 3.605A pdb=" N GLU D 530 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 557 Processing helix chain 'D' and resid 579 through 589 Processing helix chain 'D' and resid 615 through 623 Processing helix chain 'D' and resid 644 through 650 Processing helix chain 'D' and resid 668 through 676 Processing helix chain 'D' and resid 690 through 703 Processing helix chain 'D' and resid 706 through 727 removed outlier: 3.692A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 735 No H-bonds generated for 'chain 'D' and resid 733 through 735' Processing helix chain 'D' and resid 742 through 761 Processing helix chain 'D' and resid 767 through 792 Processing helix chain 'D' and resid 798 through 805 removed outlier: 4.762A pdb=" N VAL D 803 " --> pdb=" O ILE D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 817 Processing helix chain 'D' and resid 846 through 880 removed outlier: 3.705A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA D 864 " --> pdb=" O LEU D 860 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU D 865 " --> pdb=" O ALA D 861 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR D 867 " --> pdb=" O THR D 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 917 through 920 No H-bonds generated for 'chain 'D' and resid 917 through 920' Processing helix chain 'D' and resid 946 through 955 Processing helix chain 'D' and resid 965 through 967 No H-bonds generated for 'chain 'D' and resid 965 through 967' Processing helix chain 'D' and resid 976 through 979 No H-bonds generated for 'chain 'D' and resid 976 through 979' Processing helix chain 'D' and resid 995 through 1009 Proline residue: D1006 - end of helix removed outlier: 4.805A pdb=" N GLN D1009 " --> pdb=" O GLU D1005 " (cutoff:3.500A) Processing helix chain 'D' and resid 1028 through 1036 Processing helix chain 'D' and resid 1118 through 1144 Proline residue: D1127 - end of helix Processing helix chain 'D' and resid 1151 through 1161 Processing helix chain 'D' and resid 1183 through 1194 Processing helix chain 'D' and resid 1210 through 1216 Processing helix chain 'D' and resid 1220 through 1225 removed outlier: 3.901A pdb=" N SER D1225 " --> pdb=" O LEU D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1229 through 1239 removed outlier: 3.594A pdb=" N ASP D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) Processing helix chain 'D' and resid 1248 through 1254 Processing helix chain 'D' and resid 1265 through 1268 No H-bonds generated for 'chain 'D' and resid 1265 through 1268' Processing helix chain 'D' and resid 1276 through 1281 Processing helix chain 'E' and resid 34 through 36 No H-bonds generated for 'chain 'E' and resid 34 through 36' Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.901A pdb=" N ASP E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 71 Processing helix chain 'E' and resid 91 through 101 Processing helix chain 'F' and resid 210 through 223 removed outlier: 3.723A pdb=" N ARG F 213 " --> pdb=" O GLU F 210 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG F 216 " --> pdb=" O ARG F 213 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP F 218 " --> pdb=" O ALA F 215 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA F 219 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU F 221 " --> pdb=" O ASP F 218 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR F 222 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA F 223 " --> pdb=" O GLU F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 237 Processing helix chain 'F' and resid 243 through 267 Processing helix chain 'F' and resid 275 through 310 removed outlier: 4.386A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ARG F 309 " --> pdb=" O SER F 305 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N TYR F 310 " --> pdb=" O LEU F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 333 Processing helix chain 'F' and resid 343 through 362 removed outlier: 4.021A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TRP F 350 " --> pdb=" O TYR F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 390 Processing helix chain 'F' and resid 396 through 402 Processing helix chain 'F' and resid 407 through 416 Processing helix chain 'F' and resid 435 through 438 removed outlier: 3.503A pdb=" N PHE F 438 " --> pdb=" O LEU F 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 435 through 438' Processing helix chain 'F' and resid 448 through 465 Processing helix chain 'F' and resid 469 through 479 Processing helix chain 'F' and resid 489 through 496 Processing helix chain 'F' and resid 500 through 514 Processing helix chain 'F' and resid 517 through 520 No H-bonds generated for 'chain 'F' and resid 517 through 520' Processing helix chain 'F' and resid 523 through 526 Processing helix chain 'J' and resid 81 through 86 Processing helix chain 'J' and resid 91 through 107 Processing sheet with id= A, first strand: chain 'A' and resid 8 through 13 removed outlier: 3.607A pdb=" N THR A 175 " --> pdb=" O ASP A 195 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 47 through 51 Processing sheet with id= C, first strand: chain 'A' and resid 96 through 100 Processing sheet with id= D, first strand: chain 'A' and resid 145 through 147 Processing sheet with id= E, first strand: chain 'A' and resid 103 through 106 Processing sheet with id= F, first strand: chain 'B' and resid 8 through 12 Processing sheet with id= G, first strand: chain 'B' and resid 47 through 51 Processing sheet with id= H, first strand: chain 'B' and resid 53 through 55 Processing sheet with id= I, first strand: chain 'B' and resid 97 through 99 Processing sheet with id= J, first strand: chain 'B' and resid 103 through 106 Processing sheet with id= K, first strand: chain 'C' and resid 104 through 106 Processing sheet with id= L, first strand: chain 'C' and resid 110 through 112 Processing sheet with id= M, first strand: chain 'C' and resid 166 through 168 removed outlier: 3.862A pdb=" N PHE C 166 " --> pdb=" O ARG C 173 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 178 through 181 Processing sheet with id= O, first strand: chain 'C' and resid 187 through 189 Processing sheet with id= P, first strand: chain 'C' and resid 454 through 456 Processing sheet with id= Q, first strand: chain 'C' and resid 717 through 722 removed outlier: 3.563A pdb=" N LYS C 717 " --> pdb=" O ILE C1030 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA C 886 " --> pdb=" O MET C1031 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 752 through 758 Processing sheet with id= S, first strand: chain 'C' and resid 806 through 808 Processing sheet with id= T, first strand: chain 'C' and resid 642 through 644 removed outlier: 3.648A pdb=" N ALA C 703 " --> pdb=" O VAL C 642 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ALA C 644 " --> pdb=" O VAL C 701 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL C 701 " --> pdb=" O ALA C 644 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 648 through 653 removed outlier: 6.329A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 735 through 738 removed outlier: 7.109A pdb=" N LEU C 737 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE C 898 " --> pdb=" O LEU C 737 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 73 through 75 removed outlier: 4.811A pdb=" N ILE D 73 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS D 75 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL D 80 " --> pdb=" O CYS D 75 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 93 through 96 Processing sheet with id= Y, first strand: chain 'D' and resid 234 through 236 removed outlier: 6.174A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 425 through 429 Processing sheet with id= AA, first strand: chain 'D' and resid 430 through 432 removed outlier: 5.564A pdb=" N ILE D 522 " --> pdb=" O VAL D 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'D' and resid 497 through 499 removed outlier: 3.811A pdb=" N GLN D 510 " --> pdb=" O LEU D 498 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 632 through 637 Processing sheet with id= AD, first strand: chain 'D' and resid 1180 through 1182 Processing sheet with id= AE, first strand: chain 'J' and resid 27 through 33 902 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 9.52 Time building geometry restraints manager: 13.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 4621 1.30 - 1.43: 6811 1.43 - 1.56: 16034 1.56 - 1.68: 115 1.68 - 1.81: 173 Bond restraints: 27754 Sorted by residual: bond pdb=" C23 C0L D1404 " pdb=" O24 C0L D1404 " ideal model delta sigma weight residual 1.204 1.389 -0.185 2.00e-02 2.50e+03 8.60e+01 bond pdb=" C18 C0L D1404 " pdb=" O19 C0L D1404 " ideal model delta sigma weight residual 1.224 1.392 -0.168 2.00e-02 2.50e+03 7.02e+01 bond pdb=" C PHE C1068 " pdb=" N GLY C1069 " ideal model delta sigma weight residual 1.331 1.450 -0.119 1.46e-02 4.69e+03 6.66e+01 bond pdb=" CA PHE C1068 " pdb=" C PHE C1068 " ideal model delta sigma weight residual 1.523 1.618 -0.095 1.34e-02 5.57e+03 5.04e+01 bond pdb=" CA TRP C1074 " pdb=" CB TRP C1074 " ideal model delta sigma weight residual 1.530 1.642 -0.111 1.69e-02 3.50e+03 4.34e+01 ... (remaining 27749 not shown) Histogram of bond angle deviations from ideal: 94.65 - 103.79: 613 103.79 - 112.92: 16080 112.92 - 122.06: 15639 122.06 - 131.19: 5425 131.19 - 140.33: 77 Bond angle restraints: 37834 Sorted by residual: angle pdb=" C ALA F 447 " pdb=" N VAL F 448 " pdb=" CA VAL F 448 " ideal model delta sigma weight residual 120.47 103.02 17.45 1.58e+00 4.01e-01 1.22e+02 angle pdb=" CA TRP C1074 " pdb=" CB TRP C1074 " pdb=" CG TRP C1074 " ideal model delta sigma weight residual 113.60 133.87 -20.27 1.90e+00 2.77e-01 1.14e+02 angle pdb=" C ARG C 282 " pdb=" N PRO C 283 " pdb=" CA PRO C 283 " ideal model delta sigma weight residual 119.83 108.80 11.03 1.08e+00 8.57e-01 1.04e+02 angle pdb=" N TRP C1074 " pdb=" CA TRP C1074 " pdb=" CB TRP C1074 " ideal model delta sigma weight residual 110.49 127.45 -16.96 1.69e+00 3.50e-01 1.01e+02 angle pdb=" N CYS C1073 " pdb=" CA CYS C1073 " pdb=" C CYS C1073 " ideal model delta sigma weight residual 110.80 94.65 16.15 2.13e+00 2.20e-01 5.75e+01 ... (remaining 37829 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 16522 35.54 - 71.07: 331 71.07 - 106.61: 24 106.61 - 142.14: 1 142.14 - 177.68: 5 Dihedral angle restraints: 16883 sinusoidal: 7293 harmonic: 9590 Sorted by residual: dihedral pdb=" N TRP C1074 " pdb=" C TRP C1074 " pdb=" CA TRP C1074 " pdb=" CB TRP C1074 " ideal model delta harmonic sigma weight residual 122.80 137.25 -14.45 0 2.50e+00 1.60e-01 3.34e+01 dihedral pdb=" CA ARG D 480 " pdb=" C ARG D 480 " pdb=" N PRO D 481 " pdb=" CA PRO D 481 " ideal model delta harmonic sigma weight residual 180.00 -152.24 -27.76 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA ARG D 578 " pdb=" C ARG D 578 " pdb=" N LEU D 579 " pdb=" CA LEU D 579 " ideal model delta harmonic sigma weight residual -180.00 -152.67 -27.33 0 5.00e+00 4.00e-02 2.99e+01 ... (remaining 16880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 4136 0.100 - 0.200: 161 0.200 - 0.299: 4 0.299 - 0.399: 1 0.399 - 0.499: 3 Chirality restraints: 4305 Sorted by residual: chirality pdb=" CA ALA F 225 " pdb=" N ALA F 225 " pdb=" C ALA F 225 " pdb=" CB ALA F 225 " both_signs ideal model delta sigma weight residual False 2.48 1.99 0.50 2.00e-01 2.50e+01 6.22e+00 chirality pdb=" CA GLN D 657 " pdb=" N GLN D 657 " pdb=" C GLN D 657 " pdb=" CB GLN D 657 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.96e+00 chirality pdb=" CA VAL F 446 " pdb=" N VAL F 446 " pdb=" C VAL F 446 " pdb=" CB VAL F 446 " both_signs ideal model delta sigma weight residual False 2.44 2.85 -0.41 2.00e-01 2.50e+01 4.28e+00 ... (remaining 4302 not shown) Planarity restraints: 4789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA F 223 " -0.017 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C ALA F 223 " 0.062 2.00e-02 2.50e+03 pdb=" O ALA F 223 " -0.023 2.00e-02 2.50e+03 pdb=" N SER F 224 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C1056 " -0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C PRO C1056 " 0.061 2.00e-02 2.50e+03 pdb=" O PRO C1056 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU C1057 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C1074 " 0.024 2.00e-02 2.50e+03 2.20e-02 1.21e+01 pdb=" CG TRP C1074 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP C1074 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP C1074 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C1074 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP C1074 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C1074 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1074 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1074 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C1074 " -0.000 2.00e-02 2.50e+03 ... (remaining 4786 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.21: 140 2.21 - 2.89: 11495 2.89 - 3.56: 47560 3.56 - 4.23: 69579 4.23 - 4.90: 107152 Nonbonded interactions: 235926 Sorted by model distance: nonbonded pdb=" O ARG C 230 " pdb=" CG ARG C 231 " model vdw 1.543 3.440 nonbonded pdb=" CE MET C1051 " pdb=" CA ASP F 441 " model vdw 1.553 3.890 nonbonded pdb=" O CYS C1073 " pdb=" N ALA C1075 " model vdw 1.622 2.520 nonbonded pdb=" CE MET C1051 " pdb=" CB ASP F 441 " model vdw 1.827 3.860 nonbonded pdb=" N GLU F 440 " pdb=" O LEU J 6 " model vdw 1.944 2.520 ... (remaining 235921 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 or (resid 186 \ and (name N or name CA or name C or name O or name CB )) or resid 187 through 2 \ 23 or (resid 224 and (name N or name CA or name C or name O or name CB )) or res \ id 225 through 226)) selection = (chain 'B' and resid 2 through 226) } 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.160 Check model and map are aligned: 0.450 Set scattering table: 0.250 Process input model: 84.090 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 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 : 0.008 0.185 27754 Z= 0.519 Angle : 1.073 22.001 37834 Z= 0.604 Chirality : 0.049 0.499 4305 Planarity : 0.005 0.072 4789 Dihedral : 13.779 177.678 10715 Min Nonbonded Distance : 1.543 Molprobity Statistics. All-atom Clashscore : 73.63 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.31 % Favored : 87.45 % Rotamer: Outliers : 0.22 % Allowed : 3.44 % Favored : 96.34 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.06 % 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: -4.19 (0.12), residues: 3331 helix: -2.26 (0.12), residues: 1231 sheet: -3.63 (0.22), residues: 329 loop : -3.04 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.004 TRP C1074 HIS 0.018 0.004 HIS C 751 PHE 0.021 0.003 PHE D 7 TYR 0.033 0.003 TYR D 134 ARG 0.021 0.001 ARG D 334 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 215 time to evaluate : 3.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.9239 (tp30) cc_final: 0.8983 (tm-30) REVERT: B 194 LEU cc_start: 0.9488 (mt) cc_final: 0.9078 (mp) REVERT: C 159 MET cc_start: 0.8831 (mmm) cc_final: 0.8479 (mmm) REVERT: C 611 MET cc_start: 0.9454 (mtm) cc_final: 0.8788 (mtp) REVERT: C 630 MET cc_start: 0.9284 (mmm) cc_final: 0.8869 (mmm) REVERT: C 661 MET cc_start: 0.8758 (tpt) cc_final: 0.8510 (tpt) REVERT: C 713 MET cc_start: 0.8873 (mmm) cc_final: 0.8461 (mmm) REVERT: C 724 MET cc_start: 0.9285 (ptm) cc_final: 0.8913 (ptm) REVERT: C 741 LEU cc_start: 0.9555 (mt) cc_final: 0.9342 (tt) REVERT: C 783 ASP cc_start: 0.9339 (m-30) cc_final: 0.9063 (t0) REVERT: C 904 MET cc_start: 0.9385 (tpp) cc_final: 0.8381 (mmm) REVERT: C 1028 MET cc_start: 0.9322 (ttt) cc_final: 0.8945 (tpp) REVERT: C 1031 MET cc_start: 0.7752 (mtm) cc_final: 0.7533 (mpp) REVERT: C 1127 GLU cc_start: 0.9583 (mt-10) cc_final: 0.9263 (mt-10) REVERT: D 120 LEU cc_start: 0.9059 (mp) cc_final: 0.8805 (tp) REVERT: D 373 MET cc_start: 0.9161 (mtp) cc_final: 0.8731 (mtp) REVERT: D 379 ASP cc_start: 0.9382 (m-30) cc_final: 0.9089 (m-30) REVERT: D 657 GLN cc_start: 0.6542 (OUTLIER) cc_final: 0.5935 (mp10) REVERT: D 733 MET cc_start: 0.9103 (pp-130) cc_final: 0.8878 (ppp) REVERT: D 983 MET cc_start: 0.8937 (mmm) cc_final: 0.8581 (mmt) REVERT: E 99 ILE cc_start: 0.9365 (mt) cc_final: 0.9118 (mt) REVERT: F 282 MET cc_start: 0.9765 (mmt) cc_final: 0.9554 (mmt) REVERT: F 343 PHE cc_start: 0.9252 (t80) cc_final: 0.8996 (t80) REVERT: J 69 LEU cc_start: 0.8849 (mt) cc_final: 0.8468 (tp) outliers start: 6 outliers final: 2 residues processed: 220 average time/residue: 0.4215 time to fit residues: 145.4641 Evaluate side-chains 130 residues out of total 2831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 127 time to evaluate : 3.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 0.3980 chunk 254 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 171 optimal weight: 8.9990 chunk 136 optimal weight: 9.9990 chunk 263 optimal weight: 20.0000 chunk 101 optimal weight: 4.9990 chunk 160 optimal weight: 0.3980 chunk 196 optimal weight: 5.9990 chunk 305 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 ASN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 ASN C 729 HIS C 875 GLN C 920 HIS C1034 HIS C1054 GLN D 307 ASN D 352 ASN D 465 HIS ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 HIS D 771 ASN D1145 GLN ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 322 GLN F 325 ASN F 377 ASN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27754 Z= 0.229 Angle : 0.688 12.043 37834 Z= 0.358 Chirality : 0.045 0.268 4305 Planarity : 0.005 0.072 4789 Dihedral : 16.280 177.765 4348 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 22.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.72 % Favored : 93.16 % Rotamer: Outliers : 0.04 % Allowed : 2.69 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.14), residues: 3331 helix: -0.54 (0.14), residues: 1255 sheet: -3.06 (0.24), residues: 333 loop : -2.42 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 70 HIS 0.014 0.002 HIS C 755 PHE 0.019 0.002 PHE A 63 TYR 0.033 0.002 TYR E 56 ARG 0.011 0.001 ARG C 584 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 3.159 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: B 1 MET cc_start: 0.8489 (tpp) cc_final: 0.7925 (mtp) REVERT: C 159 MET cc_start: 0.8951 (mmm) cc_final: 0.8500 (mmm) REVERT: C 440 MET cc_start: 0.8858 (tmm) cc_final: 0.8017 (tmm) REVERT: C 483 MET cc_start: 0.8691 (tmm) cc_final: 0.8458 (tmm) REVERT: C 607 MET cc_start: 0.9614 (mmp) cc_final: 0.9124 (mmm) REVERT: C 611 MET cc_start: 0.9663 (mtm) cc_final: 0.9141 (mtp) REVERT: C 661 MET cc_start: 0.9001 (tpt) cc_final: 0.8592 (tpt) REVERT: C 713 MET cc_start: 0.8568 (mmm) cc_final: 0.8353 (mmm) REVERT: C 724 MET cc_start: 0.9429 (ptm) cc_final: 0.9029 (ttt) REVERT: C 741 LEU cc_start: 0.9639 (mt) cc_final: 0.9372 (tt) REVERT: C 783 ASP cc_start: 0.9362 (m-30) cc_final: 0.9057 (p0) REVERT: C 1031 MET cc_start: 0.8486 (mtm) cc_final: 0.7901 (mpp) REVERT: C 1076 MET cc_start: 0.9321 (ttt) cc_final: 0.8922 (tpp) REVERT: C 1127 GLU cc_start: 0.9674 (mt-10) cc_final: 0.9370 (mt-10) REVERT: D 114 LEU cc_start: 0.9708 (mt) cc_final: 0.9497 (mt) REVERT: D 120 LEU cc_start: 0.9013 (mp) cc_final: 0.8734 (tp) REVERT: D 143 MET cc_start: 0.8986 (mtp) cc_final: 0.8563 (mtp) REVERT: D 373 MET cc_start: 0.9297 (mtp) cc_final: 0.8953 (mtp) REVERT: D 379 ASP cc_start: 0.9383 (m-30) cc_final: 0.9003 (m-30) REVERT: D 422 VAL cc_start: 0.8886 (m) cc_final: 0.8673 (p) REVERT: D 447 MET cc_start: 0.9081 (ttm) cc_final: 0.8859 (ttt) REVERT: D 457 MET cc_start: 0.9661 (mtp) cc_final: 0.9429 (mtt) REVERT: D 515 MET cc_start: 0.8175 (ptp) cc_final: 0.7928 (ptp) REVERT: D 559 MET cc_start: 0.9458 (mpp) cc_final: 0.8859 (mpp) REVERT: D 1161 MET cc_start: 0.8917 (tpp) cc_final: 0.8670 (tpp) REVERT: D 1208 MET cc_start: 0.9251 (pmm) cc_final: 0.8485 (pmm) REVERT: F 269 ARG cc_start: 0.9110 (pmt-80) cc_final: 0.8835 (mmm160) REVERT: F 281 MET cc_start: 0.9496 (ptp) cc_final: 0.9179 (ptm) REVERT: F 282 MET cc_start: 0.9772 (mmt) cc_final: 0.9464 (mmt) REVERT: F 343 PHE cc_start: 0.9246 (t80) cc_final: 0.9025 (t80) REVERT: F 511 MET cc_start: 0.9491 (tpt) cc_final: 0.9234 (tpt) REVERT: J 68 ASP cc_start: 0.8294 (m-30) cc_final: 0.7657 (t0) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.4203 time to fit residues: 114.0506 Evaluate side-chains 115 residues out of total 2831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 3.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 10.0000 chunk 94 optimal weight: 0.0270 chunk 253 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 305 optimal weight: 8.9990 chunk 330 optimal weight: 7.9990 chunk 272 optimal weight: 10.0000 chunk 303 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 245 optimal weight: 0.9980 overall best weight: 2.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 ASN C 612 GLN ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 875 GLN D 465 HIS ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 687 GLN D 882 GLN D1190 ASN ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 HIS ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27754 Z= 0.206 Angle : 0.621 12.226 37834 Z= 0.322 Chirality : 0.042 0.217 4305 Planarity : 0.004 0.048 4789 Dihedral : 15.816 179.048 4348 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.39 % Favored : 93.55 % Rotamer: Outliers : 0.07 % Allowed : 2.55 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.14), residues: 3331 helix: 0.18 (0.14), residues: 1254 sheet: -2.59 (0.24), residues: 359 loop : -2.06 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 70 HIS 0.009 0.001 HIS F 371 PHE 0.018 0.001 PHE F 317 TYR 0.032 0.001 TYR E 56 ARG 0.014 0.000 ARG C 870 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 3.298 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: B 1 MET cc_start: 0.8428 (tpp) cc_final: 0.7995 (mtt) REVERT: B 96 TYR cc_start: 0.8662 (m-80) cc_final: 0.8300 (m-80) REVERT: C 159 MET cc_start: 0.8944 (mmm) cc_final: 0.8572 (mmm) REVERT: C 378 LEU cc_start: 0.9591 (tp) cc_final: 0.9297 (pp) REVERT: C 440 MET cc_start: 0.8861 (tmm) cc_final: 0.8645 (tmm) REVERT: C 607 MET cc_start: 0.9624 (mmp) cc_final: 0.9103 (mmm) REVERT: C 611 MET cc_start: 0.9660 (mtm) cc_final: 0.9003 (mtp) REVERT: C 661 MET cc_start: 0.8941 (tpt) cc_final: 0.8605 (tpt) REVERT: C 724 MET cc_start: 0.9452 (ptm) cc_final: 0.9225 (ppp) REVERT: C 741 LEU cc_start: 0.9692 (mt) cc_final: 0.9429 (tt) REVERT: C 783 ASP cc_start: 0.9357 (m-30) cc_final: 0.9089 (p0) REVERT: C 904 MET cc_start: 0.9224 (tpp) cc_final: 0.9004 (tpp) REVERT: C 1031 MET cc_start: 0.8508 (mtm) cc_final: 0.7996 (mpp) REVERT: C 1076 MET cc_start: 0.9307 (ttt) cc_final: 0.8991 (tpp) REVERT: C 1127 GLU cc_start: 0.9696 (mt-10) cc_final: 0.9389 (mt-10) REVERT: D 143 MET cc_start: 0.9002 (mtp) cc_final: 0.8592 (mtp) REVERT: D 373 MET cc_start: 0.9366 (mtp) cc_final: 0.9007 (mtp) REVERT: D 379 ASP cc_start: 0.9379 (m-30) cc_final: 0.9012 (m-30) REVERT: D 422 VAL cc_start: 0.9163 (m) cc_final: 0.8952 (p) REVERT: D 447 MET cc_start: 0.9194 (ttm) cc_final: 0.8968 (ttt) REVERT: D 559 MET cc_start: 0.9474 (mpp) cc_final: 0.8849 (mpp) REVERT: D 706 MET cc_start: 0.9442 (ttt) cc_final: 0.9177 (ttt) REVERT: D 1161 MET cc_start: 0.8990 (tpp) cc_final: 0.8749 (tpp) REVERT: D 1208 MET cc_start: 0.9351 (pmm) cc_final: 0.8276 (pmm) REVERT: F 231 TYR cc_start: 0.8816 (t80) cc_final: 0.8513 (t80) REVERT: F 281 MET cc_start: 0.9441 (ptp) cc_final: 0.9112 (ptm) REVERT: F 282 MET cc_start: 0.9747 (mmt) cc_final: 0.9447 (mmt) outliers start: 2 outliers final: 2 residues processed: 153 average time/residue: 0.4053 time to fit residues: 101.4470 Evaluate side-chains 116 residues out of total 2831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 3.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 7.9990 chunk 229 optimal weight: 6.9990 chunk 158 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 145 optimal weight: 8.9990 chunk 205 optimal weight: 5.9990 chunk 306 optimal weight: 10.0000 chunk 324 optimal weight: 20.0000 chunk 160 optimal weight: 0.9990 chunk 290 optimal weight: 20.0000 chunk 87 optimal weight: 9.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 36 ASN ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 HIS ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 GLN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 ASN ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1190 ASN ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 27754 Z= 0.295 Angle : 0.670 12.478 37834 Z= 0.345 Chirality : 0.042 0.197 4305 Planarity : 0.004 0.051 4789 Dihedral : 15.635 178.374 4348 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 21.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.78 % Favored : 92.16 % Rotamer: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.14), residues: 3331 helix: 0.33 (0.14), residues: 1245 sheet: -2.21 (0.26), residues: 352 loop : -1.93 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C1074 HIS 0.009 0.002 HIS C1042 PHE 0.015 0.002 PHE C 300 TYR 0.029 0.002 TYR E 56 ARG 0.007 0.000 ARG D 572 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 3.329 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: B 1 MET cc_start: 0.8533 (tpp) cc_final: 0.8059 (mtt) REVERT: C 159 MET cc_start: 0.8896 (mmm) cc_final: 0.8487 (mmm) REVERT: C 440 MET cc_start: 0.8812 (tmm) cc_final: 0.8016 (tmm) REVERT: C 607 MET cc_start: 0.9629 (mmp) cc_final: 0.9140 (mmm) REVERT: C 611 MET cc_start: 0.9678 (mtm) cc_final: 0.9047 (mtp) REVERT: C 661 MET cc_start: 0.8894 (tpt) cc_final: 0.8605 (tpt) REVERT: C 713 MET cc_start: 0.9192 (mmp) cc_final: 0.8776 (mmm) REVERT: C 724 MET cc_start: 0.9499 (ptm) cc_final: 0.9234 (ppp) REVERT: C 741 LEU cc_start: 0.9678 (mt) cc_final: 0.9403 (tt) REVERT: C 783 ASP cc_start: 0.9383 (m-30) cc_final: 0.9112 (p0) REVERT: C 904 MET cc_start: 0.9273 (tpp) cc_final: 0.8988 (tpp) REVERT: C 1031 MET cc_start: 0.8477 (mtm) cc_final: 0.8002 (mpp) REVERT: C 1051 MET cc_start: 0.8435 (mpp) cc_final: 0.8215 (mpp) REVERT: C 1076 MET cc_start: 0.9309 (ttt) cc_final: 0.8957 (tpp) REVERT: C 1127 GLU cc_start: 0.9700 (mt-10) cc_final: 0.9422 (mt-10) REVERT: D 143 MET cc_start: 0.9061 (mtp) cc_final: 0.8791 (mtp) REVERT: D 373 MET cc_start: 0.9454 (mtp) cc_final: 0.9096 (mtp) REVERT: D 379 ASP cc_start: 0.9329 (m-30) cc_final: 0.8972 (m-30) REVERT: D 447 MET cc_start: 0.9203 (ttm) cc_final: 0.8978 (ttt) REVERT: D 559 MET cc_start: 0.9459 (mpp) cc_final: 0.9078 (mpp) REVERT: D 733 MET cc_start: 0.9081 (ppp) cc_final: 0.8822 (ppp) REVERT: D 1161 MET cc_start: 0.9086 (tpp) cc_final: 0.8680 (tpt) REVERT: D 1208 MET cc_start: 0.9374 (pmm) cc_final: 0.8175 (pmm) REVERT: F 263 MET cc_start: 0.9726 (tmm) cc_final: 0.9465 (tmm) REVERT: F 269 ARG cc_start: 0.9125 (pmt-80) cc_final: 0.8864 (mmm160) REVERT: F 281 MET cc_start: 0.9435 (ptp) cc_final: 0.9112 (ptm) REVERT: F 282 MET cc_start: 0.9721 (mmt) cc_final: 0.9451 (mmt) REVERT: F 315 MET cc_start: 0.8815 (mtt) cc_final: 0.8468 (mmt) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.3926 time to fit residues: 88.9993 Evaluate side-chains 108 residues out of total 2831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 3.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 241 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 277 optimal weight: 9.9990 chunk 224 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 165 optimal weight: 2.9990 chunk 291 optimal weight: 10.0000 chunk 81 optimal weight: 0.5980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 ASN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 GLN C 442 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 HIS ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1190 ASN ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27754 Z= 0.183 Angle : 0.596 11.469 37834 Z= 0.305 Chirality : 0.042 0.193 4305 Planarity : 0.004 0.050 4789 Dihedral : 15.430 179.547 4348 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.97 % Favored : 93.97 % Rotamer: Outliers : 0.04 % Allowed : 2.51 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.15), residues: 3331 helix: 0.67 (0.15), residues: 1253 sheet: -1.99 (0.26), residues: 356 loop : -1.72 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 70 HIS 0.008 0.001 HIS E 100 PHE 0.014 0.001 PHE F 317 TYR 0.029 0.001 TYR E 56 ARG 0.002 0.000 ARG F 384 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 3.280 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: B 1 MET cc_start: 0.8468 (tpp) cc_final: 0.8072 (mtm) REVERT: B 96 TYR cc_start: 0.9115 (m-10) cc_final: 0.8863 (m-80) REVERT: C 159 MET cc_start: 0.8955 (mmm) cc_final: 0.8607 (mmm) REVERT: C 378 LEU cc_start: 0.9524 (tp) cc_final: 0.9253 (pp) REVERT: C 440 MET cc_start: 0.8909 (tmm) cc_final: 0.8198 (tmm) REVERT: C 607 MET cc_start: 0.9636 (mmp) cc_final: 0.9133 (mmm) REVERT: C 611 MET cc_start: 0.9668 (mtm) cc_final: 0.9055 (mtp) REVERT: C 713 MET cc_start: 0.9188 (mmp) cc_final: 0.8720 (mmm) REVERT: C 724 MET cc_start: 0.9421 (ptm) cc_final: 0.9209 (ppp) REVERT: C 741 LEU cc_start: 0.9672 (mt) cc_final: 0.9404 (tt) REVERT: C 783 ASP cc_start: 0.9349 (m-30) cc_final: 0.9089 (p0) REVERT: C 1076 MET cc_start: 0.9275 (ttt) cc_final: 0.8990 (tpp) REVERT: C 1087 GLU cc_start: 0.9366 (mp0) cc_final: 0.9011 (mp0) REVERT: C 1127 GLU cc_start: 0.9692 (mt-10) cc_final: 0.9397 (mt-10) REVERT: D 143 MET cc_start: 0.9060 (mtp) cc_final: 0.8659 (mtp) REVERT: D 373 MET cc_start: 0.9528 (mtp) cc_final: 0.9110 (mtp) REVERT: D 379 ASP cc_start: 0.9343 (m-30) cc_final: 0.9033 (m-30) REVERT: D 447 MET cc_start: 0.9210 (ttm) cc_final: 0.8936 (ttt) REVERT: D 516 LEU cc_start: 0.8791 (tp) cc_final: 0.8458 (tp) REVERT: D 733 MET cc_start: 0.8967 (ppp) cc_final: 0.8677 (ppp) REVERT: D 1208 MET cc_start: 0.9396 (pmm) cc_final: 0.8633 (pmm) REVERT: F 231 TYR cc_start: 0.8861 (t80) cc_final: 0.8615 (t80) REVERT: F 263 MET cc_start: 0.9709 (tmm) cc_final: 0.9436 (tmm) REVERT: F 281 MET cc_start: 0.9398 (ptp) cc_final: 0.9083 (ptm) REVERT: F 282 MET cc_start: 0.9704 (mmt) cc_final: 0.9443 (mmt) outliers start: 1 outliers final: 0 residues processed: 142 average time/residue: 0.3782 time to fit residues: 89.9770 Evaluate side-chains 112 residues out of total 2831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 3.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 8.9990 chunk 292 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 190 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 325 optimal weight: 8.9990 chunk 269 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 27 optimal weight: 0.0770 chunk 107 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 overall best weight: 2.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 674 ASN D 882 GLN D1104 HIS D1190 ASN ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27754 Z= 0.211 Angle : 0.597 12.836 37834 Z= 0.306 Chirality : 0.041 0.196 4305 Planarity : 0.004 0.052 4789 Dihedral : 15.332 179.073 4348 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.75 % Favored : 93.19 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.15), residues: 3331 helix: 0.79 (0.15), residues: 1253 sheet: -1.81 (0.26), residues: 355 loop : -1.65 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 63 HIS 0.012 0.001 HIS B 124 PHE 0.014 0.001 PHE D 673 TYR 0.027 0.001 TYR E 56 ARG 0.006 0.000 ARG F 384 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 3.141 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: A 123 MET cc_start: 0.9044 (ppp) cc_final: 0.8693 (ptm) REVERT: B 1 MET cc_start: 0.8501 (tpp) cc_final: 0.8097 (mtm) REVERT: B 96 TYR cc_start: 0.9147 (m-10) cc_final: 0.8791 (m-80) REVERT: C 159 MET cc_start: 0.9000 (mmm) cc_final: 0.8648 (mmm) REVERT: C 378 LEU cc_start: 0.9523 (tp) cc_final: 0.9255 (pp) REVERT: C 607 MET cc_start: 0.9626 (mmp) cc_final: 0.9144 (mmm) REVERT: C 611 MET cc_start: 0.9666 (mtm) cc_final: 0.9048 (mtp) REVERT: C 661 MET cc_start: 0.9117 (tpt) cc_final: 0.8734 (tpp) REVERT: C 713 MET cc_start: 0.9234 (mmp) cc_final: 0.8720 (mmm) REVERT: C 724 MET cc_start: 0.9438 (ptm) cc_final: 0.9214 (ppp) REVERT: C 741 LEU cc_start: 0.9679 (mt) cc_final: 0.9395 (tt) REVERT: C 783 ASP cc_start: 0.9353 (m-30) cc_final: 0.9112 (p0) REVERT: C 1076 MET cc_start: 0.9281 (ttt) cc_final: 0.8986 (tpp) REVERT: C 1127 GLU cc_start: 0.9702 (mt-10) cc_final: 0.9456 (mt-10) REVERT: D 143 MET cc_start: 0.8988 (mtp) cc_final: 0.8583 (mtp) REVERT: D 373 MET cc_start: 0.9529 (mtp) cc_final: 0.9090 (mtp) REVERT: D 379 ASP cc_start: 0.9364 (m-30) cc_final: 0.9121 (m-30) REVERT: D 447 MET cc_start: 0.9185 (ttm) cc_final: 0.8920 (ttt) REVERT: D 516 LEU cc_start: 0.8834 (tp) cc_final: 0.8569 (tp) REVERT: D 559 MET cc_start: 0.9448 (mpp) cc_final: 0.9048 (mpp) REVERT: D 706 MET cc_start: 0.9150 (ttp) cc_final: 0.8789 (ttt) REVERT: D 1012 MET cc_start: 0.7061 (tmm) cc_final: 0.6694 (tmm) REVERT: D 1161 MET cc_start: 0.9204 (tpp) cc_final: 0.8816 (tpt) REVERT: D 1208 MET cc_start: 0.9419 (pmm) cc_final: 0.8219 (pmm) REVERT: F 231 TYR cc_start: 0.8857 (t80) cc_final: 0.8601 (t80) REVERT: F 263 MET cc_start: 0.9707 (tmm) cc_final: 0.9431 (tmm) REVERT: F 281 MET cc_start: 0.9397 (ptp) cc_final: 0.9104 (ptm) REVERT: F 282 MET cc_start: 0.9689 (mmt) cc_final: 0.9439 (mmt) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.3785 time to fit residues: 85.8126 Evaluate side-chains 112 residues out of total 2831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 3.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 185 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 273 optimal weight: 9.9990 chunk 181 optimal weight: 8.9990 chunk 323 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 197 optimal weight: 20.0000 chunk 149 optimal weight: 2.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 539 HIS C 612 GLN ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 967 GLN ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 639 GLN D 674 ASN ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1133 HIS D1153 HIS D1190 ASN ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1269 ASN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 ASN F 425 GLN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 27754 Z= 0.381 Angle : 0.737 15.145 37834 Z= 0.379 Chirality : 0.043 0.202 4305 Planarity : 0.005 0.056 4789 Dihedral : 15.493 176.487 4348 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 26.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.65 % Favored : 91.29 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.14), residues: 3331 helix: 0.40 (0.15), residues: 1241 sheet: -1.83 (0.27), residues: 342 loop : -1.71 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 63 HIS 0.012 0.003 HIS B 124 PHE 0.019 0.002 PHE C 300 TYR 0.022 0.002 TYR E 56 ARG 0.007 0.001 ARG D 194 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 3.323 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: B 1 MET cc_start: 0.8620 (tpp) cc_final: 0.8188 (mtt) REVERT: C 159 MET cc_start: 0.9012 (mmm) cc_final: 0.8632 (mmm) REVERT: C 378 LEU cc_start: 0.9558 (tp) cc_final: 0.9199 (pp) REVERT: C 579 MET cc_start: 0.9148 (tpt) cc_final: 0.8941 (tpt) REVERT: C 607 MET cc_start: 0.9611 (mmp) cc_final: 0.9194 (mmm) REVERT: C 611 MET cc_start: 0.9675 (mtm) cc_final: 0.9055 (mtp) REVERT: C 661 MET cc_start: 0.9010 (tpt) cc_final: 0.8647 (tpp) REVERT: C 713 MET cc_start: 0.9201 (mmp) cc_final: 0.8672 (mmm) REVERT: C 724 MET cc_start: 0.9494 (ptm) cc_final: 0.9213 (ppp) REVERT: C 741 LEU cc_start: 0.9633 (mt) cc_final: 0.9401 (tt) REVERT: C 783 ASP cc_start: 0.9422 (m-30) cc_final: 0.9144 (p0) REVERT: C 904 MET cc_start: 0.9162 (ttt) cc_final: 0.8942 (tmm) REVERT: C 1076 MET cc_start: 0.9286 (ttt) cc_final: 0.8898 (tpp) REVERT: C 1127 GLU cc_start: 0.9702 (mt-10) cc_final: 0.9477 (mt-10) REVERT: D 143 MET cc_start: 0.8995 (mtp) cc_final: 0.8636 (mtp) REVERT: D 205 MET cc_start: 0.6232 (ttm) cc_final: 0.5594 (ttm) REVERT: D 373 MET cc_start: 0.9492 (mtp) cc_final: 0.9158 (mtp) REVERT: D 379 ASP cc_start: 0.9380 (m-30) cc_final: 0.9159 (m-30) REVERT: D 559 MET cc_start: 0.9443 (mpp) cc_final: 0.8834 (mpp) REVERT: D 706 MET cc_start: 0.9286 (ttp) cc_final: 0.8945 (ttt) REVERT: D 733 MET cc_start: 0.9330 (ppp) cc_final: 0.9074 (ppp) REVERT: D 1012 MET cc_start: 0.7207 (tmm) cc_final: 0.6595 (tmm) REVERT: D 1208 MET cc_start: 0.9395 (pmm) cc_final: 0.8646 (pmm) REVERT: F 231 TYR cc_start: 0.8910 (t80) cc_final: 0.8663 (t80) REVERT: F 263 MET cc_start: 0.9714 (tmm) cc_final: 0.9446 (tmm) REVERT: F 281 MET cc_start: 0.9392 (ptp) cc_final: 0.9083 (ptm) REVERT: F 282 MET cc_start: 0.9690 (mmt) cc_final: 0.9427 (mmt) REVERT: F 511 MET cc_start: 0.9568 (tpt) cc_final: 0.9366 (tpt) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.3919 time to fit residues: 80.2329 Evaluate side-chains 101 residues out of total 2831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 3.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 193 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 205 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 chunk 160 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 254 optimal weight: 0.8980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1190 ASN ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27754 Z= 0.189 Angle : 0.595 13.321 37834 Z= 0.304 Chirality : 0.041 0.200 4305 Planarity : 0.004 0.054 4789 Dihedral : 15.383 179.449 4348 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.15 % Favored : 93.79 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.15), residues: 3331 helix: 0.82 (0.15), residues: 1246 sheet: -1.64 (0.27), residues: 345 loop : -1.52 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 63 HIS 0.010 0.001 HIS F 371 PHE 0.014 0.001 PHE D 673 TYR 0.024 0.001 TYR E 56 ARG 0.003 0.000 ARG D 981 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 3.332 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: A 123 MET cc_start: 0.9025 (ppp) cc_final: 0.8615 (ptm) REVERT: A 138 LEU cc_start: 0.9705 (mp) cc_final: 0.9293 (mp) REVERT: B 1 MET cc_start: 0.8529 (tpp) cc_final: 0.8091 (mtm) REVERT: C 159 MET cc_start: 0.8995 (mmm) cc_final: 0.8668 (mmm) REVERT: C 378 LEU cc_start: 0.9512 (tp) cc_final: 0.9230 (pp) REVERT: C 607 MET cc_start: 0.9623 (mmp) cc_final: 0.9141 (mmm) REVERT: C 611 MET cc_start: 0.9662 (mtm) cc_final: 0.9055 (mtp) REVERT: C 713 MET cc_start: 0.9273 (mmp) cc_final: 0.8682 (mmm) REVERT: C 724 MET cc_start: 0.9465 (ptm) cc_final: 0.9203 (ppp) REVERT: C 741 LEU cc_start: 0.9656 (mt) cc_final: 0.9405 (tt) REVERT: C 783 ASP cc_start: 0.9374 (m-30) cc_final: 0.9103 (p0) REVERT: C 1076 MET cc_start: 0.9249 (ttt) cc_final: 0.8887 (tpp) REVERT: C 1127 GLU cc_start: 0.9641 (mt-10) cc_final: 0.9388 (mt-10) REVERT: D 143 MET cc_start: 0.8960 (mtp) cc_final: 0.8553 (mtp) REVERT: D 373 MET cc_start: 0.9520 (mtp) cc_final: 0.9106 (mtp) REVERT: D 379 ASP cc_start: 0.9341 (m-30) cc_final: 0.9090 (m-30) REVERT: D 447 MET cc_start: 0.9218 (ttt) cc_final: 0.8935 (ttt) REVERT: D 515 MET cc_start: 0.8763 (pmm) cc_final: 0.8558 (pmm) REVERT: D 559 MET cc_start: 0.9378 (mpp) cc_final: 0.8744 (mpp) REVERT: D 706 MET cc_start: 0.9225 (ttp) cc_final: 0.8895 (ttt) REVERT: D 733 MET cc_start: 0.9280 (ppp) cc_final: 0.8989 (ppp) REVERT: D 1208 MET cc_start: 0.9422 (pmm) cc_final: 0.8595 (pmm) REVERT: F 231 TYR cc_start: 0.8862 (t80) cc_final: 0.8639 (t80) REVERT: F 263 MET cc_start: 0.9692 (tmm) cc_final: 0.9413 (tmm) REVERT: F 281 MET cc_start: 0.9382 (ptp) cc_final: 0.9090 (ptm) REVERT: F 282 MET cc_start: 0.9681 (mmt) cc_final: 0.9435 (mmt) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.3830 time to fit residues: 84.6774 Evaluate side-chains 107 residues out of total 2831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 2.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 10.0000 chunk 310 optimal weight: 5.9990 chunk 283 optimal weight: 5.9990 chunk 301 optimal weight: 0.8980 chunk 181 optimal weight: 6.9990 chunk 131 optimal weight: 0.5980 chunk 236 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 272 optimal weight: 0.9990 chunk 285 optimal weight: 10.0000 chunk 300 optimal weight: 6.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 HIS ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1190 ASN ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27754 Z= 0.209 Angle : 0.603 12.762 37834 Z= 0.307 Chirality : 0.041 0.193 4305 Planarity : 0.004 0.052 4789 Dihedral : 15.250 178.974 4348 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.78 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.15), residues: 3331 helix: 0.88 (0.15), residues: 1255 sheet: -1.39 (0.27), residues: 356 loop : -1.47 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 63 HIS 0.010 0.001 HIS F 371 PHE 0.014 0.001 PHE D 673 TYR 0.024 0.001 TYR E 56 ARG 0.007 0.000 ARG F 384 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 2.973 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: A 138 LEU cc_start: 0.9712 (mp) cc_final: 0.9337 (mp) REVERT: B 1 MET cc_start: 0.8554 (tpp) cc_final: 0.8105 (mtm) REVERT: B 96 TYR cc_start: 0.8737 (m-80) cc_final: 0.8237 (m-80) REVERT: C 159 MET cc_start: 0.9006 (mmm) cc_final: 0.8672 (mmm) REVERT: C 378 LEU cc_start: 0.9499 (tp) cc_final: 0.9246 (pp) REVERT: C 440 MET cc_start: 0.8774 (tmm) cc_final: 0.8560 (tmm) REVERT: C 579 MET cc_start: 0.9105 (tpt) cc_final: 0.8893 (tpt) REVERT: C 607 MET cc_start: 0.9621 (mmp) cc_final: 0.9147 (mmm) REVERT: C 611 MET cc_start: 0.9658 (mtm) cc_final: 0.9019 (mtp) REVERT: C 713 MET cc_start: 0.9264 (mmp) cc_final: 0.8707 (mmm) REVERT: C 724 MET cc_start: 0.9449 (ptm) cc_final: 0.9196 (ppp) REVERT: C 741 LEU cc_start: 0.9639 (mt) cc_final: 0.9402 (tt) REVERT: C 783 ASP cc_start: 0.9317 (m-30) cc_final: 0.9059 (p0) REVERT: C 1087 GLU cc_start: 0.9483 (mp0) cc_final: 0.9189 (mp0) REVERT: C 1127 GLU cc_start: 0.9653 (mt-10) cc_final: 0.9405 (mt-10) REVERT: D 106 TYR cc_start: 0.9455 (m-80) cc_final: 0.9155 (m-80) REVERT: D 143 MET cc_start: 0.8951 (mtp) cc_final: 0.8543 (mtp) REVERT: D 373 MET cc_start: 0.9516 (mtp) cc_final: 0.9121 (mtp) REVERT: D 379 ASP cc_start: 0.9338 (m-30) cc_final: 0.9089 (m-30) REVERT: D 447 MET cc_start: 0.9224 (ttt) cc_final: 0.8974 (ttt) REVERT: D 515 MET cc_start: 0.8832 (pmm) cc_final: 0.8605 (pmm) REVERT: D 559 MET cc_start: 0.9375 (mpp) cc_final: 0.8737 (mpp) REVERT: D 706 MET cc_start: 0.9226 (ttp) cc_final: 0.8892 (ttt) REVERT: D 733 MET cc_start: 0.9294 (ppp) cc_final: 0.8883 (ppp) REVERT: D 1208 MET cc_start: 0.9428 (pmm) cc_final: 0.8566 (pmm) REVERT: F 231 TYR cc_start: 0.8874 (t80) cc_final: 0.8651 (t80) REVERT: F 263 MET cc_start: 0.9711 (tmm) cc_final: 0.9436 (tmm) REVERT: F 281 MET cc_start: 0.9358 (ptp) cc_final: 0.9064 (ptm) REVERT: F 282 MET cc_start: 0.9665 (mmt) cc_final: 0.9425 (mmt) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.3573 time to fit residues: 78.9009 Evaluate side-chains 111 residues out of total 2831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 3.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 6.9990 chunk 319 optimal weight: 7.9990 chunk 194 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 221 optimal weight: 0.2980 chunk 334 optimal weight: 10.0000 chunk 308 optimal weight: 9.9990 chunk 266 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 205 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1190 ASN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27754 Z= 0.256 Angle : 0.627 12.588 37834 Z= 0.322 Chirality : 0.041 0.197 4305 Planarity : 0.004 0.053 4789 Dihedral : 15.253 177.983 4348 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.39 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 3331 helix: 0.84 (0.15), residues: 1250 sheet: -1.40 (0.27), residues: 365 loop : -1.45 (0.16), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C1074 HIS 0.010 0.002 HIS F 371 PHE 0.015 0.002 PHE D 673 TYR 0.023 0.001 TYR E 56 ARG 0.006 0.000 ARG F 384 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 3.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LEU cc_start: 0.9715 (mp) cc_final: 0.9329 (mp) REVERT: B 1 MET cc_start: 0.8593 (tpp) cc_final: 0.8144 (mtm) REVERT: B 96 TYR cc_start: 0.8639 (m-80) cc_final: 0.8150 (m-80) REVERT: C 159 MET cc_start: 0.9013 (mmm) cc_final: 0.8684 (mmm) REVERT: C 378 LEU cc_start: 0.9510 (tp) cc_final: 0.9242 (pp) REVERT: C 579 MET cc_start: 0.9118 (tpt) cc_final: 0.8881 (tpt) REVERT: C 607 MET cc_start: 0.9620 (mmp) cc_final: 0.9164 (mmm) REVERT: C 611 MET cc_start: 0.9637 (mtm) cc_final: 0.9016 (mtp) REVERT: C 661 MET cc_start: 0.8963 (tpt) cc_final: 0.8514 (tpt) REVERT: C 713 MET cc_start: 0.9217 (mmp) cc_final: 0.8692 (mmm) REVERT: C 724 MET cc_start: 0.9455 (ptm) cc_final: 0.9190 (ppp) REVERT: C 741 LEU cc_start: 0.9623 (mt) cc_final: 0.9388 (tt) REVERT: C 783 ASP cc_start: 0.9374 (m-30) cc_final: 0.9098 (p0) REVERT: C 904 MET cc_start: 0.9258 (tmm) cc_final: 0.8735 (tmm) REVERT: C 1031 MET cc_start: 0.8492 (mtp) cc_final: 0.7893 (mpp) REVERT: C 1087 GLU cc_start: 0.9481 (mp0) cc_final: 0.9244 (mp0) REVERT: C 1127 GLU cc_start: 0.9688 (mt-10) cc_final: 0.9436 (mt-10) REVERT: D 106 TYR cc_start: 0.9443 (m-80) cc_final: 0.9179 (m-80) REVERT: D 143 MET cc_start: 0.8957 (mtp) cc_final: 0.8543 (mtp) REVERT: D 327 MET cc_start: 0.9396 (tpp) cc_final: 0.9123 (mmm) REVERT: D 373 MET cc_start: 0.9509 (mtp) cc_final: 0.9110 (mtp) REVERT: D 379 ASP cc_start: 0.9354 (m-30) cc_final: 0.9104 (m-30) REVERT: D 447 MET cc_start: 0.9250 (ttt) cc_final: 0.9016 (ttt) REVERT: D 559 MET cc_start: 0.9394 (mpp) cc_final: 0.8729 (mpp) REVERT: D 706 MET cc_start: 0.9270 (ttp) cc_final: 0.8924 (ttt) REVERT: D 733 MET cc_start: 0.9325 (ppp) cc_final: 0.8997 (ppp) REVERT: D 1208 MET cc_start: 0.9436 (pmm) cc_final: 0.8574 (pmm) REVERT: F 231 TYR cc_start: 0.8878 (t80) cc_final: 0.8645 (t80) REVERT: F 263 MET cc_start: 0.9709 (tmm) cc_final: 0.9436 (tmm) REVERT: F 281 MET cc_start: 0.9364 (ptp) cc_final: 0.9083 (ptm) REVERT: F 282 MET cc_start: 0.9664 (mmt) cc_final: 0.9416 (mmt) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.3928 time to fit residues: 84.0028 Evaluate side-chains 107 residues out of total 2831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 1.9990 chunk 283 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 245 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 74 optimal weight: 0.1980 chunk 266 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 274 optimal weight: 0.6980 chunk 33 optimal weight: 0.0570 chunk 49 optimal weight: 7.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 GLN ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 687 GLN ** D 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1190 ASN ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN F 261 GLN ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN F 516 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.028486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2414 r_free = 0.2414 target = 0.020474 restraints weight = 291848.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.021225 restraints weight = 183021.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.021784 restraints weight = 131065.663| |-----------------------------------------------------------------------------| r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27754 Z= 0.149 Angle : 0.577 12.947 37834 Z= 0.293 Chirality : 0.041 0.171 4305 Planarity : 0.004 0.055 4789 Dihedral : 15.106 179.483 4348 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.34 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.15), residues: 3331 helix: 1.15 (0.15), residues: 1252 sheet: -1.36 (0.27), residues: 350 loop : -1.33 (0.16), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C1074 HIS 0.012 0.001 HIS F 371 PHE 0.013 0.001 PHE F 317 TYR 0.022 0.001 TYR E 56 ARG 0.006 0.000 ARG F 384 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3995.70 seconds wall clock time: 75 minutes 45.24 seconds (4545.24 seconds total)