Starting phenix.real_space_refine on Thu Sep 26 12:15:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy7_27777/09_2024/8dy7_27777.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy7_27777/09_2024/8dy7_27777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy7_27777/09_2024/8dy7_27777.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy7_27777/09_2024/8dy7_27777.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy7_27777/09_2024/8dy7_27777.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy7_27777/09_2024/8dy7_27777.cif" } resolution = 3.18 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= 0.002 sd= 1.010 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: 9 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 3 6.06 5 P 148 5.49 5 Mg 1 5.21 5 S 110 5.16 5 C 19061 2.51 5 N 5576 2.21 5 O 6267 1.98 5 H 29915 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 61085 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3519 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 211} Chain: "B" Number of atoms: 3671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3671 Classifications: {'peptide': 236} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 221} Chain: "C" Number of atoms: 17368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1118, 17368 Classifications: {'peptide': 1118} Link IDs: {'PCIS': 1, 'PTRANS': 56, 'TRANS': 1060} Chain: "D" Number of atoms: 19789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1253, 19789 Classifications: {'peptide': 1253} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1199} Chain breaks: 1 Chain: "E" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1202 Classifications: {'peptide': 77} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 72} Chain: "F" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 4857 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 12, 'TRANS': 288} Chain: "G" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1647 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 6, 'TRANS': 96} Chain: "H" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1208 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 82} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "I" Number of atoms: 3187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3187 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 8, 'TRANS': 205} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "O" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 2365 Classifications: {'DNA': 78} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 77} Chain breaks: 1 Chain: "P" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 2260 Classifications: {'DNA': 71} Link IDs: {'rna3p': 70} Chain breaks: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 38735 SG CYS D 886 18.428 115.050 92.457 1.00 29.21 S ATOM 39874 SG CYS D 962 22.070 114.976 93.758 1.00 26.36 S ATOM 39957 SG CYS D 969 21.080 113.128 90.515 1.00 19.10 S ATOM 39997 SG CYS D 972 21.296 116.740 90.534 1.00 22.12 S ATOM 25506 SG CYS D 60 54.180 63.516 120.474 1.00 46.44 S ATOM 25537 SG CYS D 62 56.064 62.211 123.393 1.00 51.42 S ATOM 25770 SG CYS D 75 52.264 62.266 123.577 1.00 56.90 S ATOM 25819 SG CYS D 78 54.187 65.501 123.774 1.00 55.22 S ATOM 52313 SG CYS H 25 59.811 44.995 77.495 1.00 81.13 S ATOM 52653 SG CYS H 48 61.897 39.446 75.618 1.00 88.25 S ATOM 52783 SG CYS H 57 65.543 42.749 79.833 1.00 94.87 S ATOM 52692 SG CYS H 51 64.911 44.772 73.680 1.00 87.70 S ATOM 53538 SG CYS I 18 41.409 59.095 77.225 1.00 70.00 S ATOM 53548 SG CYS I 19 38.833 57.068 75.327 1.00 78.50 S ATOM 55071 SG CYS I 122 39.243 55.563 78.029 1.00 85.60 S Time building chain proxies: 21.06, per 1000 atoms: 0.34 Number of scatterers: 61085 At special positions: 0 Unit cell: (129.96, 173.28, 202.521, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 3 29.99 Fe 4 26.01 S 110 16.00 P 148 15.00 Mg 1 11.99 O 6267 8.00 N 5576 7.00 C 19061 6.00 H 29915 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=0, symmetry=0 Time building additional restraints: 11.63 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 H 101 " pdb="FE2 SF4 H 101 " - pdb=" SG CYS H 48 " pdb="FE4 SF4 H 101 " - pdb=" SG CYS H 51 " pdb="FE1 SF4 H 101 " - pdb=" SG CYS H 25 " pdb="FE3 SF4 H 101 " - pdb=" SG CYS H 57 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 972 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 969 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 886 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 962 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 75 " pdb=" ZN I2000 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 122 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 18 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 19 " Number of angles added : 12 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6652 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 42 sheets defined 43.4% alpha, 14.5% beta 61 base pairs and 108 stacking pairs defined. Time for finding SS restraints: 22.17 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 removed outlier: 3.553A pdb=" N LEU A 34 " --> pdb=" O PHE A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 81 removed outlier: 3.656A pdb=" N LEU A 78 " --> pdb=" O THR A 74 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 203 through 224 removed outlier: 3.839A pdb=" N GLU A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A 218 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 45 Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.836A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 67 removed outlier: 4.256A pdb=" N SER C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 79 Processing helix chain 'C' and resid 89 through 99 Processing helix chain 'C' and resid 123 through 131 Processing helix chain 'C' and resid 238 through 247 removed outlier: 3.536A pdb=" N LEU C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 257 Processing helix chain 'C' and resid 260 through 269 removed outlier: 4.133A pdb=" N ARG C 264 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 Processing helix chain 'C' and resid 293 through 305 Processing helix chain 'C' and resid 314 through 326 Processing helix chain 'C' and resid 337 through 354 Processing helix chain 'C' and resid 383 through 410 removed outlier: 3.654A pdb=" N ARG C 398 " --> pdb=" O THR C 394 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR C 408 " --> pdb=" O ARG C 404 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN C 410 " --> pdb=" O ARG C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 420 Processing helix chain 'C' and resid 423 through 435 Processing helix chain 'C' and resid 447 through 455 removed outlier: 3.528A pdb=" N LYS C 455 " --> pdb=" O GLY C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 542 Processing helix chain 'C' and resid 593 through 597 removed outlier: 3.568A pdb=" N MET C 596 " --> pdb=" O ALA C 593 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE C 597 " --> pdb=" O THR C 594 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 593 through 597' Processing helix chain 'C' and resid 604 through 615 Processing helix chain 'C' and resid 633 through 642 removed outlier: 3.968A pdb=" N GLY C 642 " --> pdb=" O ALA C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 737 removed outlier: 4.234A pdb=" N ASP C 736 " --> pdb=" O ASN C 733 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA C 737 " --> pdb=" O TYR C 734 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 733 through 737' Processing helix chain 'C' and resid 742 through 747 Processing helix chain 'C' and resid 782 through 786 removed outlier: 4.470A pdb=" N ASP C 786 " --> pdb=" O VAL C 783 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 829 Processing helix chain 'C' and resid 859 through 861 No H-bonds generated for 'chain 'C' and resid 859 through 861' Processing helix chain 'C' and resid 903 through 907 removed outlier: 3.805A pdb=" N ASP C 906 " --> pdb=" O PRO C 903 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET C 907 " --> pdb=" O ILE C 904 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 903 through 907' Processing helix chain 'C' and resid 923 through 929 removed outlier: 4.215A pdb=" N SER C 927 " --> pdb=" O LEU C 923 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG C 928 " --> pdb=" O GLY C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 931 through 946 removed outlier: 3.576A pdb=" N LEU C 935 " --> pdb=" O PRO C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 962 removed outlier: 3.794A pdb=" N ARG C 959 " --> pdb=" O GLU C 955 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 960 " --> pdb=" O TRP C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 991 Processing helix chain 'C' and resid 1038 through 1042 Processing helix chain 'C' and resid 1071 through 1082 Processing helix chain 'C' and resid 1083 through 1093 removed outlier: 3.893A pdb=" N LEU C1087 " --> pdb=" O ALA C1083 " (cutoff:3.500A) Processing helix chain 'C' and resid 1097 through 1111 removed outlier: 4.453A pdb=" N VAL C1102 " --> pdb=" O VAL C1098 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS C1103 " --> pdb=" O THR C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1120 through 1132 removed outlier: 3.844A pdb=" N LYS C1124 " --> pdb=" O PRO C1120 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 7 Processing helix chain 'D' and resid 16 through 24 removed outlier: 3.604A pdb=" N SER D 24 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 84 through 90 removed outlier: 3.942A pdb=" N VAL D 87 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 109 removed outlier: 3.784A pdb=" N GLY D 109 " --> pdb=" O TRP D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 140 through 184 Proline residue: D 149 - end of helix Processing helix chain 'D' and resid 190 through 228 removed outlier: 4.927A pdb=" N VAL D 197 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ARG D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 249 Processing helix chain 'D' and resid 256 through 267 removed outlier: 3.679A pdb=" N ALA D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.529A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.827A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE D 302 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 303 " --> pdb=" O VAL D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 339 through 361 removed outlier: 3.820A pdb=" N LEU D 343 " --> pdb=" O ASP D 339 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 removed outlier: 3.528A pdb=" N VAL D 367 " --> pdb=" O PRO D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 481 through 491 removed outlier: 3.688A pdb=" N ASP D 485 " --> pdb=" O THR D 481 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 removed outlier: 3.597A pdb=" N ASN D 563 " --> pdb=" O LEU D 560 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN D 564 " --> pdb=" O SER D 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 560 through 564' Processing helix chain 'D' and resid 581 through 589 Processing helix chain 'D' and resid 606 through 616 removed outlier: 3.638A pdb=" N ALA D 616 " --> pdb=" O MET D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 669 Processing helix chain 'D' and resid 685 through 699 Processing helix chain 'D' and resid 700 through 721 removed outlier: 3.767A pdb=" N ARG D 721 " --> pdb=" O TYR D 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 757 Processing helix chain 'D' and resid 761 through 788 Processing helix chain 'D' and resid 792 through 800 Processing helix chain 'D' and resid 805 through 813 removed outlier: 3.767A pdb=" N MET D 809 " --> pdb=" O ASN D 805 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 876 removed outlier: 3.945A pdb=" N HIS D 849 " --> pdb=" O PHE D 845 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY D 850 " --> pdb=" O ILE D 846 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA D 863 " --> pdb=" O ALA D 859 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY D 866 " --> pdb=" O THR D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 950 Processing helix chain 'D' and resid 958 through 962 Processing helix chain 'D' and resid 969 through 974 Processing helix chain 'D' and resid 988 through 999 removed outlier: 3.776A pdb=" N ILE D 992 " --> pdb=" O ALA D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1003 Processing helix chain 'D' and resid 1022 through 1031 Processing helix chain 'D' and resid 1100 through 1128 removed outlier: 3.550A pdb=" N VAL D1104 " --> pdb=" O ASN D1100 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N GLN D1110 " --> pdb=" O ARG D1106 " (cutoff:3.500A) removed outlier: 9.669A pdb=" N ARG D1111 " --> pdb=" O ILE D1107 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA D1112 " --> pdb=" O LEU D1108 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL D1113 " --> pdb=" O GLY D1109 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL D1124 " --> pdb=" O GLU D1120 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR D1125 " --> pdb=" O VAL D1121 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN D1128 " --> pdb=" O VAL D1124 " (cutoff:3.500A) Processing helix chain 'D' and resid 1133 through 1145 removed outlier: 4.074A pdb=" N ILE D1137 " --> pdb=" O HIS D1133 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE D1140 " --> pdb=" O HIS D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1166 through 1178 removed outlier: 3.626A pdb=" N THR D1178 " --> pdb=" O ARG D1174 " (cutoff:3.500A) Processing helix chain 'D' and resid 1192 through 1199 Processing helix chain 'D' and resid 1202 through 1210 removed outlier: 3.547A pdb=" N GLN D1210 " --> pdb=" O ALA D1206 " (cutoff:3.500A) Processing helix chain 'D' and resid 1211 through 1223 removed outlier: 3.703A pdb=" N ILE D1221 " --> pdb=" O THR D1217 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN D1222 " --> pdb=" O ASP D1218 " (cutoff:3.500A) Processing helix chain 'D' and resid 1230 through 1238 removed outlier: 3.872A pdb=" N ASN D1234 " --> pdb=" O GLY D1230 " (cutoff:3.500A) Processing helix chain 'D' and resid 1243 through 1246 Processing helix chain 'D' and resid 1247 through 1252 removed outlier: 3.738A pdb=" N ASN D1252 " --> pdb=" O SER D1248 " (cutoff:3.500A) Processing helix chain 'D' and resid 1258 through 1265 Processing helix chain 'E' and resid 15 through 21 Processing helix chain 'E' and resid 25 through 46 removed outlier: 3.686A pdb=" N ILE E 31 " --> pdb=" O TYR E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 78 Processing helix chain 'F' and resid 217 through 227 removed outlier: 3.874A pdb=" N ASP F 221 " --> pdb=" O ASP F 217 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY F 227 " --> pdb=" O LEU F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 256 Processing helix chain 'F' and resid 261 through 295 removed outlier: 4.706A pdb=" N ARG F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LEU F 289 " --> pdb=" O ALA F 285 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL F 290 " --> pdb=" O ASN F 286 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS F 295 " --> pdb=" O VAL F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 298 No H-bonds generated for 'chain 'F' and resid 296 through 298' Processing helix chain 'F' and resid 303 through 321 Processing helix chain 'F' and resid 330 through 349 Processing helix chain 'F' and resid 356 through 378 Processing helix chain 'F' and resid 382 through 391 Processing helix chain 'F' and resid 393 through 404 removed outlier: 3.693A pdb=" N GLY F 404 " --> pdb=" O VAL F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 426 removed outlier: 3.717A pdb=" N LEU F 425 " --> pdb=" O PHE F 422 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE F 426 " --> pdb=" O GLY F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 453 removed outlier: 3.686A pdb=" N HIS F 448 " --> pdb=" O GLN F 444 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER F 449 " --> pdb=" O GLU F 445 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR F 453 " --> pdb=" O SER F 449 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 467 Processing helix chain 'F' and resid 475 through 484 removed outlier: 3.800A pdb=" N VAL F 482 " --> pdb=" O GLU F 478 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR F 483 " --> pdb=" O ILE F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 486 through 502 Processing helix chain 'F' and resid 507 through 512 removed outlier: 4.388A pdb=" N ASP F 512 " --> pdb=" O GLN F 508 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 90 removed outlier: 3.790A pdb=" N MET G 85 " --> pdb=" O THR G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 108 removed outlier: 3.591A pdb=" N LEU G 95 " --> pdb=" O THR G 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 8 removed outlier: 3.661A pdb=" N GLU H 7 " --> pdb=" O GLU H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 28 Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 42 through 50 removed outlier: 3.640A pdb=" N ALA H 50 " --> pdb=" O LYS H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 65 Processing helix chain 'H' and resid 75 through 85 Processing helix chain 'I' and resid 2 through 12 Processing helix chain 'I' and resid 16 through 31 Processing helix chain 'I' and resid 49 through 64 removed outlier: 3.972A pdb=" N ALA I 53 " --> pdb=" O THR I 49 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG I 54 " --> pdb=" O ALA I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 99 Processing helix chain 'I' and resid 120 through 135 Processing helix chain 'I' and resid 152 through 167 removed outlier: 4.463A pdb=" N ALA I 156 " --> pdb=" O PRO I 152 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA I 157 " --> pdb=" O GLY I 153 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 198 removed outlier: 3.618A pdb=" N GLY I 198 " --> pdb=" O LEU I 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 214 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 15 removed outlier: 6.716A pdb=" N ARG A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.742A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.866A pdb=" N ALA A 126 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 15 removed outlier: 6.501A pdb=" N ARG B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ARG B 18 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N THR B 198 " --> pdb=" O ARG B 18 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ARG B 20 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL B 196 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL B 22 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL B 194 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLU B 24 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU B 192 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.606A pdb=" N ALA B 111 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TYR B 96 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N THR B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 40 through 41 removed outlier: 6.611A pdb=" N ILE C 40 " --> pdb=" O ALA C 975 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 101 through 102 removed outlier: 4.435A pdb=" N HIS C 115 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N PHE C 139 " --> pdb=" O HIS C 115 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE C 117 " --> pdb=" O PRO C 137 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY C 160 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL C 140 " --> pdb=" O PHE C 158 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N PHE C 158 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ALA C 142 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N THR C 156 " --> pdb=" O ALA C 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 171 through 173 Processing sheet with id=AB5, first strand: chain 'C' and resid 379 through 382 removed outlier: 3.591A pdb=" N SER C 182 " --> pdb=" O ARG C 457 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 189 through 197 removed outlier: 3.615A pdb=" N LYS C 202 " --> pdb=" O ASP C 197 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE C 205 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU C 217 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 357 through 358 Processing sheet with id=AB8, first strand: chain 'C' and resid 508 through 509 removed outlier: 4.931A pdb=" N GLU C 530 " --> pdb=" O LYS C 521 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL C 523 " --> pdb=" O THR C 528 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N THR C 528 " --> pdb=" O VAL C 523 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 508 through 509 Processing sheet with id=AC1, first strand: chain 'C' and resid 562 through 565 Processing sheet with id=AC2, first strand: chain 'C' and resid 645 through 646 removed outlier: 6.838A pdb=" N LEU C 645 " --> pdb=" O LEU C 705 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 670 through 674 removed outlier: 6.194A pdb=" N ALA C 664 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL C 653 " --> pdb=" O ALA C 664 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 679 through 680 removed outlier: 3.556A pdb=" N VAL C 687 " --> pdb=" O SER C 679 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 711 through 712 removed outlier: 3.607A pdb=" N GLU C 715 " --> pdb=" O GLU C 712 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1009 through 1010 removed outlier: 6.803A pdb=" N ILE C 738 " --> pdb=" O SER C 899 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE C 901 " --> pdb=" O ILE C 738 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU C 740 " --> pdb=" O ILE C 901 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE C 739 " --> pdb=" O ILE C 919 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N ILE C 918 " --> pdb=" O ASN C 721 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU C 723 " --> pdb=" O ILE C 918 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LEU C 920 " --> pdb=" O LEU C 723 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA C 725 " --> pdb=" O LEU C 920 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N SER C1026 " --> pdb=" O PHE C 726 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 768 through 769 removed outlier: 3.569A pdb=" N GLY C 768 " --> pdb=" O THR C 765 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ASP C 764 " --> pdb=" O VAL C 868 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL C 868 " --> pdb=" O ASP C 764 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N ASN C 869 " --> pdb=" O ASP C 857 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ASP C 857 " --> pdb=" O ASN C 869 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU C 871 " --> pdb=" O VAL C 855 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL C 855 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG C 873 " --> pdb=" O VAL C 853 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL C 853 " --> pdb=" O ARG C 873 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TYR C 875 " --> pdb=" O ILE C 851 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LYS C 879 " --> pdb=" O ILE C 847 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N ILE C 847 " --> pdb=" O LYS C 879 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY C 848 " --> pdb=" O VAL C 799 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 771 through 772 Processing sheet with id=AC9, first strand: chain 'C' and resid 804 through 806 removed outlier: 6.575A pdb=" N LEU C 840 " --> pdb=" O LEU C 805 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 947 through 948 Processing sheet with id=AD2, first strand: chain 'C' and resid 1044 through 1046 Processing sheet with id=AD3, first strand: chain 'C' and resid 1069 through 1070 Processing sheet with id=AD4, first strand: chain 'C' and resid 1138 through 1140 removed outlier: 3.683A pdb=" N GLU D 9 " --> pdb=" O LEU C1140 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 93 through 102 removed outlier: 10.310A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.490A pdb=" N ALA D 99 " --> pdb=" O CYS D 316 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N CYS D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 234 through 235 removed outlier: 6.269A pdb=" N ASP D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 408 through 409 removed outlier: 6.405A pdb=" N PHE D 335 " --> pdb=" O ILE F 408 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY G 8 " --> pdb=" O GLU F 427 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 603 through 604 Processing sheet with id=AD9, first strand: chain 'D' and resid 892 through 895 Processing sheet with id=AE1, first strand: chain 'D' and resid 1070 through 1074 Processing sheet with id=AE2, first strand: chain 'D' and resid 1163 through 1165 Processing sheet with id=AE3, first strand: chain 'D' and resid 1253 through 1257 Processing sheet with id=AE4, first strand: chain 'G' and resid 39 through 45 removed outlier: 3.789A pdb=" N LEU G 64 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 32 through 37 Processing sheet with id=AE6, first strand: chain 'I' and resid 149 through 151 removed outlier: 4.430A pdb=" N ASP I 180 " --> pdb=" O CYS I 151 " (cutoff:3.500A) 1273 hydrogen bonds defined for protein. 3600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 163 hydrogen bonds 326 hydrogen bond angles 0 basepair planarities 61 basepair parallelities 108 stacking parallelities Total time for adding SS restraints: 25.09 Time building geometry restraints manager: 14.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.13: 29903 1.13 - 1.41: 12782 1.41 - 1.70: 19017 1.70 - 1.99: 185 1.99 - 2.28: 12 Bond restraints: 61899 Sorted by residual: bond pdb=" C3' DG P 48 " pdb=" O3' DG P 48 " ideal model delta sigma weight residual 1.422 1.480 -0.058 3.00e-02 1.11e+03 3.77e+00 bond pdb=" N MET I 1 " pdb=" CA MET I 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" C3' DC O 64 " pdb=" O3' DC O 64 " ideal model delta sigma weight residual 1.422 1.469 -0.047 3.00e-02 1.11e+03 2.48e+00 bond pdb=" N MET I 1 " pdb=" H MET I 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" C VAL C 85 " pdb=" N PRO C 86 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.21e+00 ... (remaining 61894 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.07: 112221 8.07 - 16.14: 0 16.14 - 24.21: 0 24.21 - 32.28: 3 32.28 - 40.35: 2 Bond angle restraints: 112226 Sorted by residual: angle pdb=" OP1 DG P 49 " pdb=" P DG P 49 " pdb=" OP2 DG P 49 " ideal model delta sigma weight residual 120.00 79.65 40.35 3.00e+00 1.11e-01 1.81e+02 angle pdb=" O3' DG P 48 " pdb=" P DG P 49 " pdb=" OP2 DG P 49 " ideal model delta sigma weight residual 108.00 73.05 34.95 3.00e+00 1.11e-01 1.36e+02 angle pdb=" OP1 DG P 49 " pdb=" P DG P 49 " pdb=" O5' DG P 49 " ideal model delta sigma weight residual 109.00 76.76 32.24 3.00e+00 1.11e-01 1.15e+02 angle pdb=" OP2 DG P 49 " pdb=" P DG P 49 " pdb=" O5' DG P 49 " ideal model delta sigma weight residual 108.00 135.68 -27.68 3.00e+00 1.11e-01 8.51e+01 angle pdb=" O3' DG P 48 " pdb=" P DG P 49 " pdb=" OP1 DG P 49 " ideal model delta sigma weight residual 108.00 133.84 -25.84 3.00e+00 1.11e-01 7.42e+01 ... (remaining 112221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 26918 35.19 - 70.38: 1187 70.38 - 105.57: 34 105.57 - 140.76: 0 140.76 - 175.95: 9 Dihedral angle restraints: 28148 sinusoidal: 16672 harmonic: 11476 Sorted by residual: dihedral pdb=" CA PRO D 641 " pdb=" C PRO D 641 " pdb=" N PRO D 642 " pdb=" CA PRO D 642 " ideal model delta harmonic sigma weight residual 180.00 144.85 35.15 0 5.00e+00 4.00e-02 4.94e+01 dihedral pdb=" CA SER A 44 " pdb=" C SER A 44 " pdb=" N SER A 45 " pdb=" CA SER A 45 " ideal model delta harmonic sigma weight residual -180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA VAL A 147 " pdb=" C VAL A 147 " pdb=" N SER A 148 " pdb=" CA SER A 148 " ideal model delta harmonic sigma weight residual -180.00 -157.26 -22.74 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 28145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4228 0.055 - 0.110: 648 0.110 - 0.165: 111 0.165 - 0.220: 0 0.220 - 0.275: 1 Chirality restraints: 4988 Sorted by residual: chirality pdb=" P DG P 49 " pdb=" OP1 DG P 49 " pdb=" OP2 DG P 49 " pdb=" O5' DG P 49 " both_signs ideal model delta sigma weight residual True 2.35 2.07 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA ILE C 597 " pdb=" N ILE C 597 " pdb=" C ILE C 597 " pdb=" CB ILE C 597 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.86e-01 chirality pdb=" CA ILE D 509 " pdb=" N ILE D 509 " pdb=" C ILE D 509 " pdb=" CB ILE D 509 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 4985 not shown) Planarity restraints: 8774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C1142 " 0.029 2.00e-02 2.50e+03 5.72e-02 3.27e+01 pdb=" C SER C1142 " -0.099 2.00e-02 2.50e+03 pdb=" O SER C1142 " 0.037 2.00e-02 2.50e+03 pdb=" N ASP C1143 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 641 " -0.060 5.00e-02 4.00e+02 9.20e-02 1.35e+01 pdb=" N PRO D 642 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO D 642 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 642 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 470 " 0.252 9.50e-02 1.11e+02 8.51e-02 1.17e+01 pdb=" NE ARG C 470 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG C 470 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG C 470 " -0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG C 470 " -0.003 2.00e-02 2.50e+03 pdb="HH11 ARG C 470 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG C 470 " 0.011 2.00e-02 2.50e+03 pdb="HH21 ARG C 470 " 0.008 2.00e-02 2.50e+03 pdb="HH22 ARG C 470 " -0.006 2.00e-02 2.50e+03 ... (remaining 8771 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 992 2.13 - 2.74: 106986 2.74 - 3.36: 164700 3.36 - 3.98: 211373 3.98 - 4.60: 334101 Nonbonded interactions: 818152 Sorted by model distance: nonbonded pdb=" OD1 ASP I 123 " pdb="ZN ZN I2000 " model vdw 1.507 2.110 nonbonded pdb=" OE2 GLU D 81 " pdb="HH22 ARG D 91 " model vdw 1.602 2.450 nonbonded pdb=" OD2 ASP C 444 " pdb=" HG SER C 450 " model vdw 1.633 2.450 nonbonded pdb=" OG1 THR B 41 " pdb=" HG SER B 45 " model vdw 1.645 2.450 nonbonded pdb=" OE1 GLU F 235 " pdb=" H GLU F 235 " model vdw 1.653 2.450 ... (remaining 818147 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 3 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 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: 0.800 Extract box with map and model: 1.690 Check model and map are aligned: 0.340 Set scattering table: 0.410 Process input model: 159.750 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 168.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 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 : 0.003 0.058 31984 Z= 0.203 Angle : 0.647 40.347 43894 Z= 0.323 Chirality : 0.041 0.275 4988 Planarity : 0.004 0.114 5234 Dihedral : 17.405 175.947 12494 Min Nonbonded Distance : 1.507 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.14), residues: 3592 helix: 1.75 (0.15), residues: 1375 sheet: -0.22 (0.25), residues: 411 loop : -1.07 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 773 HIS 0.007 0.001 HIS C 482 PHE 0.027 0.001 PHE C 376 TYR 0.040 0.001 TYR E 32 ARG 0.030 0.000 ARG C 470 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 371 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 3.410 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: C 98 ILE cc_start: 0.7884 (tp) cc_final: 0.7500 (tp) REVERT: C 159 MET cc_start: 0.8306 (mmm) cc_final: 0.7997 (mmt) outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 0.9425 time to fit residues: 545.1117 Evaluate side-chains 314 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 3.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 313 optimal weight: 7.9990 chunk 281 optimal weight: 0.0970 chunk 156 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 290 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 chunk 336 optimal weight: 0.6980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 933 GLN C 958 GLN H 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.0631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31984 Z= 0.214 Angle : 0.628 40.121 43894 Z= 0.314 Chirality : 0.041 0.228 4988 Planarity : 0.004 0.078 5234 Dihedral : 18.692 175.715 5534 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.46 % Allowed : 5.04 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.14), residues: 3592 helix: 1.80 (0.14), residues: 1423 sheet: -0.24 (0.25), residues: 414 loop : -1.16 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 773 HIS 0.008 0.001 HIS C1044 PHE 0.018 0.001 PHE C 376 TYR 0.029 0.001 TYR E 32 ARG 0.007 0.000 ARG C 470 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 361 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 347 time to evaluate : 3.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 159 MET cc_start: 0.8251 (mmm) cc_final: 0.7913 (mmt) REVERT: D 1103 ASP cc_start: 0.6378 (m-30) cc_final: 0.6059 (m-30) REVERT: F 436 ASP cc_start: 0.6999 (m-30) cc_final: 0.6627 (m-30) outliers start: 14 outliers final: 10 residues processed: 353 average time/residue: 0.9046 time to fit residues: 497.6913 Evaluate side-chains 327 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 317 time to evaluate : 3.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 675 ASP Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 204 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 187 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 280 optimal weight: 3.9990 chunk 229 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 337 optimal weight: 6.9990 chunk 364 optimal weight: 20.0000 chunk 300 optimal weight: 0.8980 chunk 334 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 31984 Z= 0.309 Angle : 0.644 40.143 43894 Z= 0.323 Chirality : 0.042 0.229 4988 Planarity : 0.004 0.068 5234 Dihedral : 18.718 174.160 5534 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.56 % Allowed : 6.70 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.14), residues: 3592 helix: 1.75 (0.14), residues: 1426 sheet: -0.24 (0.25), residues: 415 loop : -1.25 (0.14), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 773 HIS 0.007 0.001 HIS C 482 PHE 0.024 0.001 PHE C 376 TYR 0.031 0.002 TYR E 32 ARG 0.004 0.000 ARG C1046 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 342 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 325 time to evaluate : 3.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 159 MET cc_start: 0.8246 (mmm) cc_final: 0.7853 (mmt) REVERT: C 1031 TYR cc_start: 0.8989 (t80) cc_final: 0.8621 (t80) REVERT: D 1103 ASP cc_start: 0.6407 (m-30) cc_final: 0.6085 (m-30) REVERT: F 436 ASP cc_start: 0.7091 (m-30) cc_final: 0.6746 (m-30) outliers start: 17 outliers final: 13 residues processed: 332 average time/residue: 0.9020 time to fit residues: 459.6364 Evaluate side-chains 324 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 311 time to evaluate : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 759 GLU Chi-restraints excluded: chain C residue 884 ASP Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 675 ASP Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain I residue 109 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 333 optimal weight: 4.9990 chunk 253 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 161 optimal weight: 3.9990 chunk 226 optimal weight: 1.9990 chunk 338 optimal weight: 4.9990 chunk 358 optimal weight: 20.0000 chunk 176 optimal weight: 9.9990 chunk 321 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN E 62 HIS F 233 ASN G 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 31984 Z= 0.441 Angle : 0.693 39.991 43894 Z= 0.351 Chirality : 0.045 0.253 4988 Planarity : 0.005 0.064 5234 Dihedral : 18.782 174.168 5534 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.83 % Allowed : 8.99 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.14), residues: 3592 helix: 1.49 (0.14), residues: 1419 sheet: -0.40 (0.25), residues: 420 loop : -1.50 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 773 HIS 0.010 0.001 HIS C1044 PHE 0.024 0.002 PHE C 376 TYR 0.033 0.002 TYR E 32 ARG 0.007 0.000 ARG C1046 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 339 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 314 time to evaluate : 3.433 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: C 159 MET cc_start: 0.8098 (mmm) cc_final: 0.7610 (mmt) REVERT: C 589 MET cc_start: 0.8284 (ptt) cc_final: 0.7865 (ptt) REVERT: D 1103 ASP cc_start: 0.6495 (m-30) cc_final: 0.6151 (m-30) REVERT: F 436 ASP cc_start: 0.7127 (m-30) cc_final: 0.6795 (m-30) outliers start: 25 outliers final: 19 residues processed: 332 average time/residue: 0.9412 time to fit residues: 480.8303 Evaluate side-chains 319 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 300 time to evaluate : 3.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 759 GLU Chi-restraints excluded: chain C residue 884 ASP Chi-restraints excluded: chain C residue 1139 VAL Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 675 ASP Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain F residue 284 GLU Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 109 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 298 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 267 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 306 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 321 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1034 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 31984 Z= 0.247 Angle : 0.633 40.162 43894 Z= 0.316 Chirality : 0.041 0.233 4988 Planarity : 0.004 0.066 5234 Dihedral : 18.740 173.959 5534 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.70 % Allowed : 9.95 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3592 helix: 1.73 (0.14), residues: 1420 sheet: -0.36 (0.25), residues: 417 loop : -1.40 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 773 HIS 0.006 0.001 HIS C1044 PHE 0.013 0.001 PHE C 144 TYR 0.021 0.001 TYR E 32 ARG 0.003 0.000 ARG C1046 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 337 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 316 time to evaluate : 3.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 159 MET cc_start: 0.8173 (mmm) cc_final: 0.7789 (mmt) REVERT: C 589 MET cc_start: 0.8253 (ptt) cc_final: 0.7758 (ptt) REVERT: D 1103 ASP cc_start: 0.6455 (m-30) cc_final: 0.6111 (m-30) REVERT: F 436 ASP cc_start: 0.7011 (m-30) cc_final: 0.6674 (m-30) REVERT: H 62 LEU cc_start: 0.8848 (tp) cc_final: 0.8647 (tt) outliers start: 21 outliers final: 16 residues processed: 330 average time/residue: 0.9329 time to fit residues: 474.8615 Evaluate side-chains 325 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 309 time to evaluate : 3.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 884 ASP Chi-restraints excluded: chain C residue 1139 VAL Chi-restraints excluded: chain D residue 675 ASP Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain F residue 284 GLU Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain I residue 68 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 120 optimal weight: 2.9990 chunk 322 optimal weight: 0.0000 chunk 70 optimal weight: 6.9990 chunk 210 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 358 optimal weight: 20.0000 chunk 297 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 188 optimal weight: 0.0270 overall best weight: 1.4048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 64 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31984 Z= 0.216 Angle : 0.615 40.079 43894 Z= 0.305 Chirality : 0.041 0.245 4988 Planarity : 0.004 0.066 5234 Dihedral : 18.703 173.772 5534 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.76 % Allowed : 10.19 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3592 helix: 1.89 (0.14), residues: 1422 sheet: -0.29 (0.25), residues: 424 loop : -1.29 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 773 HIS 0.005 0.001 HIS C1044 PHE 0.013 0.001 PHE D 226 TYR 0.018 0.001 TYR E 32 ARG 0.004 0.000 ARG H 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 343 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 320 time to evaluate : 3.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 ARG cc_start: 0.7641 (tpp-160) cc_final: 0.7251 (mtm110) REVERT: C 159 MET cc_start: 0.8203 (mmm) cc_final: 0.7794 (mmt) REVERT: D 1103 ASP cc_start: 0.6430 (m-30) cc_final: 0.6080 (m-30) REVERT: F 436 ASP cc_start: 0.6954 (m-30) cc_final: 0.6623 (m-30) REVERT: H 62 LEU cc_start: 0.8843 (tp) cc_final: 0.8632 (tt) outliers start: 23 outliers final: 19 residues processed: 332 average time/residue: 0.9534 time to fit residues: 488.4057 Evaluate side-chains 327 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 308 time to evaluate : 3.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 759 GLU Chi-restraints excluded: chain C residue 884 ASP Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 675 ASP Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain I residue 203 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 346 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 204 optimal weight: 1.9990 chunk 262 optimal weight: 4.9990 chunk 203 optimal weight: 1.9990 chunk 302 optimal weight: 1.9990 chunk 200 optimal weight: 0.7980 chunk 357 optimal weight: 20.0000 chunk 223 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31984 Z= 0.196 Angle : 0.609 40.106 43894 Z= 0.300 Chirality : 0.040 0.241 4988 Planarity : 0.004 0.063 5234 Dihedral : 18.672 173.718 5534 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.63 % Allowed : 10.78 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.14), residues: 3592 helix: 1.98 (0.14), residues: 1421 sheet: -0.22 (0.25), residues: 424 loop : -1.25 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 773 HIS 0.005 0.001 HIS E 64 PHE 0.013 0.001 PHE C 144 TYR 0.015 0.001 TYR E 32 ARG 0.005 0.000 ARG H 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 335 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 316 time to evaluate : 3.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 159 MET cc_start: 0.8210 (mmm) cc_final: 0.7795 (mmt) REVERT: C 310 ARG cc_start: 0.7795 (ttm-80) cc_final: 0.7508 (mtp-110) REVERT: D 1103 ASP cc_start: 0.6450 (m-30) cc_final: 0.6112 (m-30) REVERT: F 436 ASP cc_start: 0.6965 (m-30) cc_final: 0.6656 (m-30) REVERT: H 62 LEU cc_start: 0.8827 (tp) cc_final: 0.8622 (tt) outliers start: 19 outliers final: 19 residues processed: 327 average time/residue: 0.9339 time to fit residues: 473.3693 Evaluate side-chains 329 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 310 time to evaluate : 3.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 759 GLU Chi-restraints excluded: chain C residue 1139 VAL Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 675 ASP Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 186 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 221 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 213 optimal weight: 0.0980 chunk 107 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 chunk 227 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 281 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 508 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 31984 Z= 0.152 Angle : 0.595 40.155 43894 Z= 0.292 Chirality : 0.040 0.236 4988 Planarity : 0.004 0.063 5234 Dihedral : 18.609 173.464 5534 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.53 % Allowed : 11.05 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.14), residues: 3592 helix: 2.16 (0.14), residues: 1422 sheet: -0.20 (0.25), residues: 414 loop : -1.14 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 773 HIS 0.004 0.001 HIS E 64 PHE 0.013 0.001 PHE C 144 TYR 0.014 0.001 TYR C 319 ARG 0.004 0.000 ARG C 825 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 331 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 315 time to evaluate : 3.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LYS cc_start: 0.8443 (ptpp) cc_final: 0.8185 (ptpp) REVERT: C 159 MET cc_start: 0.8208 (mmm) cc_final: 0.7807 (mmt) REVERT: C 310 ARG cc_start: 0.7781 (ttm-80) cc_final: 0.7499 (mtp-110) REVERT: C 589 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7659 (ptt) REVERT: C 884 ASP cc_start: 0.8355 (p0) cc_final: 0.8089 (p0) REVERT: F 436 ASP cc_start: 0.6968 (m-30) cc_final: 0.6650 (m-30) REVERT: H 62 LEU cc_start: 0.8909 (tp) cc_final: 0.8690 (tt) outliers start: 16 outliers final: 13 residues processed: 322 average time/residue: 0.8884 time to fit residues: 444.6612 Evaluate side-chains 323 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 309 time to evaluate : 3.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 675 ASP Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 186 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 325 optimal weight: 5.9990 chunk 342 optimal weight: 5.9990 chunk 312 optimal weight: 2.9990 chunk 333 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 261 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 301 optimal weight: 4.9990 chunk 315 optimal weight: 0.9990 chunk 332 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 31984 Z= 0.335 Angle : 0.643 39.944 43894 Z= 0.320 Chirality : 0.042 0.263 4988 Planarity : 0.004 0.059 5234 Dihedral : 18.652 173.942 5534 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.70 % Allowed : 11.05 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3592 helix: 1.90 (0.14), residues: 1422 sheet: -0.23 (0.25), residues: 424 loop : -1.28 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 773 HIS 0.007 0.001 HIS C1044 PHE 0.014 0.001 PHE C 909 TYR 0.021 0.002 TYR E 32 ARG 0.004 0.000 ARG C1046 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 333 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 312 time to evaluate : 3.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 159 MET cc_start: 0.8248 (mmm) cc_final: 0.7816 (mmt) REVERT: C 589 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7756 (ptt) REVERT: D 1103 ASP cc_start: 0.6440 (m-30) cc_final: 0.6094 (m-30) REVERT: D 1169 PHE cc_start: 0.8581 (t80) cc_final: 0.8270 (t80) REVERT: F 436 ASP cc_start: 0.7039 (m-30) cc_final: 0.6716 (m-30) REVERT: H 62 LEU cc_start: 0.8911 (tp) cc_final: 0.8690 (tt) outliers start: 21 outliers final: 19 residues processed: 324 average time/residue: 0.9102 time to fit residues: 455.6973 Evaluate side-chains 327 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 307 time to evaluate : 3.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 759 GLU Chi-restraints excluded: chain C residue 1139 VAL Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 675 ASP Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain I residue 203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 218 optimal weight: 0.2980 chunk 352 optimal weight: 6.9990 chunk 215 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 369 optimal weight: 10.0000 chunk 340 optimal weight: 8.9990 chunk 294 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 227 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 396 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 31984 Z= 0.246 Angle : 0.622 40.089 43894 Z= 0.308 Chirality : 0.041 0.245 4988 Planarity : 0.004 0.061 5234 Dihedral : 18.643 173.706 5534 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.80 % Allowed : 11.05 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.14), residues: 3592 helix: 1.93 (0.14), residues: 1422 sheet: -0.19 (0.25), residues: 421 loop : -1.26 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 337 HIS 0.006 0.001 HIS C1044 PHE 0.013 0.001 PHE C 144 TYR 0.018 0.001 TYR E 32 ARG 0.010 0.000 ARG G 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 332 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 308 time to evaluate : 3.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 159 MET cc_start: 0.8243 (mmm) cc_final: 0.7839 (mmt) REVERT: C 589 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.7727 (ptt) REVERT: D 576 MET cc_start: 0.8001 (ttp) cc_final: 0.7797 (mtp) REVERT: D 1103 ASP cc_start: 0.6425 (m-30) cc_final: 0.6084 (m-30) REVERT: F 436 ASP cc_start: 0.7032 (m-30) cc_final: 0.6723 (m-30) REVERT: H 62 LEU cc_start: 0.8916 (tp) cc_final: 0.8692 (tt) outliers start: 24 outliers final: 20 residues processed: 322 average time/residue: 0.9213 time to fit residues: 460.7653 Evaluate side-chains 327 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 306 time to evaluate : 3.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 759 GLU Chi-restraints excluded: chain C residue 1139 VAL Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 675 ASP Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain I residue 203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 233 optimal weight: 3.9990 chunk 313 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 271 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 294 optimal weight: 10.0000 chunk 123 optimal weight: 0.9980 chunk 302 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.175019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.122082 restraints weight = 96526.879| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.07 r_work: 0.2912 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 31984 Z= 0.378 Angle : 0.664 39.905 43894 Z= 0.332 Chirality : 0.043 0.270 4988 Planarity : 0.005 0.067 5234 Dihedral : 18.694 173.993 5534 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.86 % Allowed : 11.18 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3592 helix: 1.71 (0.14), residues: 1423 sheet: -0.33 (0.25), residues: 414 loop : -1.39 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D1203 HIS 0.008 0.001 HIS C1044 PHE 0.016 0.002 PHE C 909 TYR 0.024 0.002 TYR E 32 ARG 0.009 0.000 ARG C 825 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10813.51 seconds wall clock time: 185 minutes 58.85 seconds (11158.85 seconds total)