Starting phenix.real_space_refine on Fri May 30 01:46:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7aof_11843/05_2025/7aof_11843_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aof_11843/05_2025/7aof_11843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7aof_11843/05_2025/7aof_11843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aof_11843/05_2025/7aof_11843.map" model { file = "/net/cci-nas-00/data/ceres_data/7aof_11843/05_2025/7aof_11843_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aof_11843/05_2025/7aof_11843_neut.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 3 5.49 5 Mg 1 5.21 5 S 149 5.16 5 C 21030 2.51 5 N 5424 2.21 5 O 6116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 125 residue(s): 0.51s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 32727 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 10188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1268, 10188 Classifications: {'peptide': 1268} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 1223} Chain: "B" Number of atoms: 9091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9091 Classifications: {'peptide': 1129} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1076} Chain breaks: 2 Chain: "C" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2484 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 9, 'TRANS': 294} Chain: "E" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1495 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 8, 'TRANS': 175} Chain: "F" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 849 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "G" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1192 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 3, 'TRANS': 149} Chain breaks: 1 Chain: "I" Number of atoms: 5573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5573 Classifications: {'peptide': 665} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 641} Chain breaks: 4 Chain: "J" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 490 Classifications: {'peptide': 61} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 58} Chain: "S" Number of atoms: 1360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1360 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 156} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "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 360 SG CYS A 49 88.711 102.937 62.424 1.00111.55 S ATOM 382 SG CYS A 52 92.441 103.061 61.672 1.00106.51 S ATOM 434 SG CYS A 59 90.886 99.849 63.007 1.00106.93 S ATOM 694 SG CYS A 90 75.616 100.473 109.345 1.00135.81 S ATOM 718 SG CYS A 93 76.868 104.034 109.991 1.00139.72 S ATOM 1016 SG CYS A 130 76.730 101.421 112.791 1.00141.05 S ATOM 1059 SG CYS A 135 73.554 102.962 111.495 1.00143.99 S ATOM 18688 SG CYS B1087 99.143 104.377 76.437 1.00 98.78 S ATOM 18711 SG CYS B1090 95.605 103.182 77.348 1.00101.21 S ATOM 18800 SG CYS B1103 96.072 105.670 74.621 1.00 98.37 S ATOM 18825 SG CYS B1106 96.696 106.749 78.177 1.00102.17 S ATOM 27074 SG CYS I 326 102.516 95.772 38.660 1.00149.52 S ATOM 27387 SG CYS I 363 100.239 92.636 39.608 1.00136.01 S ATOM 27411 SG CYS I 366 103.502 93.325 41.494 1.00142.53 S Time building chain proxies: 17.69, per 1000 atoms: 0.54 Number of scatterers: 32727 At special positions: 0 Unit cell: (163.779, 152.081, 152.081, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 149 16.00 P 3 15.00 Mg 1 11.99 O 6116 8.00 N 5424 7.00 C 21030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS J 7 " - pdb=" SG CYS J 39 " distance=2.04 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: 8.53 Conformation dependent library (CDL) restraints added in 4.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1302 " pdb="ZN ZN A1302 " - pdb=" NE2 HIS A 62 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 49 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 52 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 59 " pdb=" ZN A1303 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 135 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 90 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 93 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1103 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1090 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1106 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1087 " pdb=" ZN I 801 " pdb="ZN ZN I 801 " - pdb=" NE2 HIS I 328 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 366 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 363 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 326 " Number of angles added : 18 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7726 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 48 sheets defined 43.6% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.02 Creating SS restraints... Processing helix chain 'A' and resid 13 through 19 Processing helix chain 'A' and resid 78 through 88 Processing helix chain 'A' and resid 107 through 111 removed outlier: 3.554A pdb=" N LEU A 111 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 Processing helix chain 'A' and resid 161 through 171 removed outlier: 3.689A pdb=" N ILE A 165 " --> pdb=" O PRO A 161 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 removed outlier: 6.195A pdb=" N LYS A 175 " --> pdb=" O ILE A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 199 through 203 removed outlier: 4.006A pdb=" N ILE A 202 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 Processing helix chain 'A' and resid 236 through 249 removed outlier: 3.844A pdb=" N ILE A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 253 Processing helix chain 'A' and resid 261 through 267 removed outlier: 3.614A pdb=" N ILE A 265 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A 267 " --> pdb=" O TYR A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 304 through 311 Processing helix chain 'A' and resid 321 through 331 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 428 through 438 Processing helix chain 'A' and resid 440 through 445 Processing helix chain 'A' and resid 458 through 471 removed outlier: 3.615A pdb=" N VAL A 463 " --> pdb=" O GLN A 459 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 466 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 485 through 488 removed outlier: 4.181A pdb=" N ARG A 488 " --> pdb=" O LYS A 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 485 through 488' Processing helix chain 'A' and resid 499 through 508 Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.764A pdb=" N VAL A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 550 through 573 Processing helix chain 'A' and resid 577 through 582 removed outlier: 3.683A pdb=" N LEU A 581 " --> pdb=" O THR A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 615 Processing helix chain 'A' and resid 622 through 656 Processing helix chain 'A' and resid 659 through 667 Processing helix chain 'A' and resid 672 through 681 Processing helix chain 'A' and resid 712 through 715 Processing helix chain 'A' and resid 727 through 763 Processing helix chain 'A' and resid 809 through 821 Processing helix chain 'A' and resid 841 through 846 removed outlier: 3.731A pdb=" N VAL A 844 " --> pdb=" O ASN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 876 Processing helix chain 'A' and resid 882 through 893 removed outlier: 3.638A pdb=" N GLU A 886 " --> pdb=" O ILE A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 919 Processing helix chain 'A' and resid 925 through 943 Processing helix chain 'A' and resid 944 through 946 No H-bonds generated for 'chain 'A' and resid 944 through 946' Processing helix chain 'A' and resid 960 through 970 removed outlier: 3.617A pdb=" N PHE A 964 " --> pdb=" O GLY A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 996 removed outlier: 4.324A pdb=" N LEU A 988 " --> pdb=" O ASP A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1004 Processing helix chain 'A' and resid 1024 through 1030 Processing helix chain 'A' and resid 1033 through 1048 removed outlier: 3.519A pdb=" N PHE A1047 " --> pdb=" O ARG A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1093 Proline residue: A1090 - end of helix Processing helix chain 'A' and resid 1131 through 1136 removed outlier: 3.825A pdb=" N SER A1135 " --> pdb=" O GLU A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1154 Processing helix chain 'A' and resid 1155 through 1171 Processing helix chain 'A' and resid 1175 through 1177 No H-bonds generated for 'chain 'A' and resid 1175 through 1177' Processing helix chain 'A' and resid 1178 through 1190 Processing helix chain 'A' and resid 1207 through 1215 Processing helix chain 'A' and resid 1218 through 1227 Processing helix chain 'A' and resid 1234 through 1241 Processing helix chain 'A' and resid 1247 through 1252 removed outlier: 3.690A pdb=" N TYR A1252 " --> pdb=" O THR A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1263 Processing helix chain 'B' and resid 9 through 17 Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 31 through 44 Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 216 through 219 Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 245 through 253 Processing helix chain 'B' and resid 257 through 278 removed outlier: 3.686A pdb=" N LEU B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 298 Processing helix chain 'B' and resid 307 through 314 removed outlier: 3.525A pdb=" N ASN B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 344 Processing helix chain 'B' and resid 345 through 348 Processing helix chain 'B' and resid 353 through 357 removed outlier: 3.510A pdb=" N CYS B 356 " --> pdb=" O SER B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 392 removed outlier: 3.542A pdb=" N TYR B 365 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 416 Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 463 through 467 Processing helix chain 'B' and resid 498 through 515 Processing helix chain 'B' and resid 518 through 522 Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 544 through 558 removed outlier: 3.567A pdb=" N MET B 558 " --> pdb=" O ARG B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 611 removed outlier: 4.340A pdb=" N SER B 609 " --> pdb=" O PRO B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 623 Processing helix chain 'B' and resid 632 through 637 removed outlier: 3.700A pdb=" N PHE B 637 " --> pdb=" O GLU B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 649 removed outlier: 3.623A pdb=" N MET B 649 " --> pdb=" O GLN B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 656 removed outlier: 3.639A pdb=" N LYS B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 669 removed outlier: 3.906A pdb=" N ASP B 669 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 678 through 682 Processing helix chain 'B' and resid 683 through 695 removed outlier: 4.042A pdb=" N LYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 732 Processing helix chain 'B' and resid 762 through 767 Processing helix chain 'B' and resid 795 through 799 removed outlier: 3.533A pdb=" N SER B 799 " --> pdb=" O ASN B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 902 removed outlier: 3.823A pdb=" N LEU B 902 " --> pdb=" O GLU B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 923 removed outlier: 3.775A pdb=" N PHE B 921 " --> pdb=" O SER B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 941 removed outlier: 4.324A pdb=" N LEU B 929 " --> pdb=" O THR B 925 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 930 " --> pdb=" O ILE B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 977 removed outlier: 3.635A pdb=" N TYR B 965 " --> pdb=" O SER B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 990 Processing helix chain 'B' and resid 1054 through 1065 Processing helix chain 'B' and resid 1066 through 1074 Processing helix chain 'B' and resid 1077 through 1081 removed outlier: 3.706A pdb=" N TYR B1081 " --> pdb=" O GLU B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1109 Processing helix chain 'B' and resid 1121 through 1134 Processing helix chain 'C' and resid 15 through 30 Processing helix chain 'C' and resid 48 through 58 removed outlier: 3.968A pdb=" N HIS C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 64 removed outlier: 5.323A pdb=" N MET C 62 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS C 63 " --> pdb=" O PRO C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 68 through 74 Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 117 through 123 Processing helix chain 'C' and resid 152 through 157 removed outlier: 3.773A pdb=" N SER C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 152 through 157' Processing helix chain 'C' and resid 162 through 177 Processing helix chain 'C' and resid 207 through 230 removed outlier: 3.960A pdb=" N CYS C 211 " --> pdb=" O ASP C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 283 through 304 Processing helix chain 'E' and resid 4 through 22 removed outlier: 4.033A pdb=" N TYR E 8 " --> pdb=" O TYR E 4 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU E 15 " --> pdb=" O LYS E 11 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 34 removed outlier: 3.624A pdb=" N LEU E 32 " --> pdb=" O ASN E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 102 removed outlier: 4.339A pdb=" N ILE E 102 " --> pdb=" O PHE E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 146 through 153 Processing helix chain 'F' and resid 63 through 75 removed outlier: 3.774A pdb=" N ARG F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 96 Processing helix chain 'F' and resid 112 through 123 Processing helix chain 'F' and resid 140 through 142 No H-bonds generated for 'chain 'F' and resid 140 through 142' Processing helix chain 'F' and resid 143 through 161 Processing helix chain 'G' and resid 15 through 19 Processing helix chain 'G' and resid 22 through 36 Processing helix chain 'G' and resid 109 through 113 removed outlier: 3.589A pdb=" N GLY G 113 " --> pdb=" O ARG G 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 119 Processing helix chain 'I' and resid 167 through 169 No H-bonds generated for 'chain 'I' and resid 167 through 169' Processing helix chain 'I' and resid 170 through 186 removed outlier: 6.213A pdb=" N ASP I 180 " --> pdb=" O GLU I 176 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLN I 181 " --> pdb=" O LYS I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 264 removed outlier: 3.700A pdb=" N ASP I 258 " --> pdb=" O ASN I 254 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS I 261 " --> pdb=" O SER I 257 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL I 262 " --> pdb=" O ASP I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 267 No H-bonds generated for 'chain 'I' and resid 265 through 267' Processing helix chain 'I' and resid 269 through 272 Processing helix chain 'I' and resid 273 through 279 Processing helix chain 'I' and resid 283 through 285 No H-bonds generated for 'chain 'I' and resid 283 through 285' Processing helix chain 'I' and resid 286 through 291 Processing helix chain 'I' and resid 326 through 336 removed outlier: 3.867A pdb=" N ILE I 330 " --> pdb=" O CYS I 326 " (cutoff:3.500A) Processing helix chain 'I' and resid 341 through 353 Processing helix chain 'I' and resid 370 through 374 Processing helix chain 'I' and resid 391 through 396 removed outlier: 4.280A pdb=" N PHE I 395 " --> pdb=" O ASN I 391 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU I 396 " --> pdb=" O LYS I 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 391 through 396' Processing helix chain 'I' and resid 397 through 402 removed outlier: 3.793A pdb=" N TYR I 402 " --> pdb=" O GLU I 398 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 421 removed outlier: 4.325A pdb=" N ARG I 408 " --> pdb=" O VAL I 404 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE I 409 " --> pdb=" O HIS I 405 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE I 413 " --> pdb=" O PHE I 409 " (cutoff:3.500A) Processing helix chain 'I' and resid 424 through 427 removed outlier: 3.983A pdb=" N VAL I 427 " --> pdb=" O GLN I 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 424 through 427' Processing helix chain 'I' and resid 428 through 446 Processing helix chain 'I' and resid 446 through 454 removed outlier: 4.141A pdb=" N LYS I 452 " --> pdb=" O GLN I 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 454 through 459 removed outlier: 3.968A pdb=" N LYS I 459 " --> pdb=" O SER I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 482 through 501 removed outlier: 3.589A pdb=" N LEU I 490 " --> pdb=" O LYS I 486 " (cutoff:3.500A) Processing helix chain 'I' and resid 503 through 514 Processing helix chain 'I' and resid 522 through 538 Processing helix chain 'I' and resid 545 through 557 Processing helix chain 'I' and resid 561 through 581 removed outlier: 3.603A pdb=" N VAL I 579 " --> pdb=" O LEU I 575 " (cutoff:3.500A) Processing helix chain 'I' and resid 638 through 649 Processing helix chain 'I' and resid 688 through 694 removed outlier: 4.133A pdb=" N TYR I 692 " --> pdb=" O LEU I 688 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE I 693 " --> pdb=" O LYS I 689 " (cutoff:3.500A) Processing helix chain 'I' and resid 705 through 710 Processing helix chain 'I' and resid 723 through 742 Processing helix chain 'I' and resid 756 through 770 removed outlier: 3.639A pdb=" N LYS I 770 " --> pdb=" O ILE I 766 " (cutoff:3.500A) Processing helix chain 'I' and resid 773 through 793 removed outlier: 5.778A pdb=" N THR I 783 " --> pdb=" O ASP I 779 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ARG I 784 " --> pdb=" O GLU I 780 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 20 removed outlier: 3.610A pdb=" N LYS J 20 " --> pdb=" O HIS J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 36 removed outlier: 3.534A pdb=" N VAL J 31 " --> pdb=" O SER J 27 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER J 34 " --> pdb=" O ASP J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 47 Processing helix chain 'S' and resid 37 through 51 Processing helix chain 'S' and resid 59 through 63 removed outlier: 3.623A pdb=" N ILE S 63 " --> pdb=" O LYS S 60 " (cutoff:3.500A) Processing helix chain 'S' and resid 72 through 81 removed outlier: 3.594A pdb=" N ASP S 81 " --> pdb=" O GLU S 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 85 Processing helix chain 'S' and resid 102 through 110 removed outlier: 4.031A pdb=" N THR S 110 " --> pdb=" O MET S 106 " (cutoff:3.500A) Processing helix chain 'S' and resid 112 through 131 Processing helix chain 'S' and resid 144 through 148 Processing helix chain 'S' and resid 213 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 1229 through 1231 Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 67 Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 144 removed outlier: 4.264A pdb=" N PHE A 151 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 281 through 282 removed outlier: 3.580A pdb=" N LYS A 282 " --> pdb=" O ILE B1051 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE B1051 " --> pdb=" O LYS A 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 1027 through 1029 removed outlier: 7.535A pdb=" N ILE A 402 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL A 289 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE A 404 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLY A 291 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 316 removed outlier: 7.135A pdb=" N ALA A 369 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL A 334 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 518 through 519 Processing sheet with id=AA9, first strand: chain 'A' and resid 684 through 685 Processing sheet with id=AB1, first strand: chain 'A' and resid 767 through 768 removed outlier: 6.641A pdb=" N VAL A 774 " --> pdb=" O ILE A 781 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 796 through 799 Processing sheet with id=AB3, first strand: chain 'A' and resid 825 through 826 Processing sheet with id=AB4, first strand: chain 'A' and resid 1106 through 1107 Processing sheet with id=AB5, first strand: chain 'A' and resid 998 through 999 removed outlier: 3.566A pdb=" N VAL A 998 " --> pdb=" O LYS A1095 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1008 through 1012 removed outlier: 6.398A pdb=" N ASN A1065 " --> pdb=" O GLU A1061 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 136 through 138 removed outlier: 3.824A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N TYR A1254 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 136 through 138 removed outlier: 3.824A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N TYR A1254 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS G 47 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA G 77 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ALA G 45 " --> pdb=" O ALA G 77 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1264 through 1265 Processing sheet with id=AC1, first strand: chain 'B' and resid 54 through 59 removed outlier: 5.713A pdb=" N ILE B 68 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 57 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR B 99 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL B 73 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR B 97 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL B 75 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU B 95 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N PHE B 98 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLU B 121 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL B 100 " --> pdb=" O SER B 119 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER B 119 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE B 102 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 54 through 59 removed outlier: 5.713A pdb=" N ILE B 68 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 57 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR B 99 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL B 73 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR B 97 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL B 75 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU B 95 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 157 through 159 Processing sheet with id=AC4, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.954A pdb=" N ASN B 169 " --> pdb=" O GLY B 445 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 179 through 184 removed outlier: 6.367A pdb=" N SER B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AC7, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AC8, first strand: chain 'B' and resid 535 through 540 removed outlier: 6.805A pdb=" N ILE B 530 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER B 539 " --> pdb=" O PHE B 528 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N PHE B 528 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ILE B 580 " --> pdb=" O PRO B 529 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR B 531 " --> pdb=" O ILE B 580 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.816A pdb=" N ILE B 772 " --> pdb=" O ARG B 875 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 870 " --> pdb=" O ARG B 856 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ARG B 856 " --> pdb=" O LEU B 870 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N MET B 872 " --> pdb=" O VAL B 854 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N VAL B 854 " --> pdb=" O MET B 872 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N GLU B 874 " --> pdb=" O SER B 852 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N SER B 852 " --> pdb=" O GLU B 874 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER B 852 " --> pdb=" O LEU B 813 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.816A pdb=" N ILE B 772 " --> pdb=" O ARG B 875 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 870 " --> pdb=" O ARG B 856 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ARG B 856 " --> pdb=" O LEU B 870 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N MET B 872 " --> pdb=" O VAL B 854 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N VAL B 854 " --> pdb=" O MET B 872 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N GLU B 874 " --> pdb=" O SER B 852 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N SER B 852 " --> pdb=" O GLU B 874 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N ASP J 61 " --> pdb=" O GLU B 855 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL B 857 " --> pdb=" O ASP J 61 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 723 through 724 Processing sheet with id=AD3, first strand: chain 'B' and resid 992 through 993 removed outlier: 6.656A pdb=" N ILE B 758 " --> pdb=" O ALA B 894 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL B 896 " --> pdb=" O ILE B 758 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE B 760 " --> pdb=" O VAL B 896 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE B1009 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1086 through 1087 Processing sheet with id=AD5, first strand: chain 'B' and resid 1095 through 1096 Processing sheet with id=AD6, first strand: chain 'C' and resid 5 through 13 removed outlier: 3.582A pdb=" N ILE C 188 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AD8, first strand: chain 'C' and resid 37 through 43 removed outlier: 3.829A pdb=" N ILE C 37 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU C 140 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASN C 43 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR C 138 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 93 through 94 removed outlier: 3.576A pdb=" N HIS C 126 " --> pdb=" O ILE C 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 251 through 253 Processing sheet with id=AE2, first strand: chain 'E' and resid 35 through 38 Processing sheet with id=AE3, first strand: chain 'E' and resid 63 through 65 removed outlier: 6.490A pdb=" N ILE E 83 " --> pdb=" O PHE E 95 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 113 through 115 Processing sheet with id=AE5, first strand: chain 'G' and resid 84 through 91 removed outlier: 4.291A pdb=" N VAL G 97 " --> pdb=" O LEU G 108 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL G 153 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ALA G 144 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU G 155 " --> pdb=" O MET G 142 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 115 through 116 Processing sheet with id=AE7, first strand: chain 'I' and resid 121 through 123 Processing sheet with id=AE8, first strand: chain 'I' and resid 161 through 166 removed outlier: 6.592A pdb=" N ILE I 128 " --> pdb=" O LYS I 162 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE I 164 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE I 130 " --> pdb=" O ILE I 164 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE I 166 " --> pdb=" O ILE I 130 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N VAL I 132 " --> pdb=" O PHE I 166 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 209 through 217 Processing sheet with id=AF1, first strand: chain 'I' and resid 354 through 357 Processing sheet with id=AF2, first strand: chain 'I' and resid 663 through 665 removed outlier: 4.326A pdb=" N ILE I 658 " --> pdb=" O ALA I 665 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 668 through 670 1435 hydrogen bonds defined for protein. 3948 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 16.79 Time building geometry restraints manager: 9.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10437 1.34 - 1.46: 7462 1.46 - 1.58: 15244 1.58 - 1.70: 12 1.70 - 1.82: 236 Bond restraints: 33391 Sorted by residual: bond pdb=" C LEU E 13 " pdb=" N CYS E 14 " ideal model delta sigma weight residual 1.332 1.304 0.027 1.35e-02 5.49e+03 4.15e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.82e+00 bond pdb=" N GLN A 459 " pdb=" CA GLN A 459 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.29e-02 6.01e+03 2.15e+00 bond pdb=" C ILE C 177 " pdb=" N ASP C 178 " ideal model delta sigma weight residual 1.339 1.414 -0.074 5.57e-02 3.22e+02 1.78e+00 bond pdb=" N ASN B 320 " pdb=" CA ASN B 320 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.40e-01 ... (remaining 33386 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 44882 2.24 - 4.48: 254 4.48 - 6.72: 8 6.72 - 8.96: 0 8.96 - 11.20: 2 Bond angle restraints: 45146 Sorted by residual: angle pdb=" CG1 VAL E 170 " pdb=" CB VAL E 170 " pdb=" CG2 VAL E 170 " ideal model delta sigma weight residual 110.80 122.00 -11.20 2.20e+00 2.07e-01 2.59e+01 angle pdb=" CG1 VAL C 111 " pdb=" CB VAL C 111 " pdb=" CG2 VAL C 111 " ideal model delta sigma weight residual 110.80 121.62 -10.82 2.20e+00 2.07e-01 2.42e+01 angle pdb=" CA VAL C 111 " pdb=" CB VAL C 111 " pdb=" CG1 VAL C 111 " ideal model delta sigma weight residual 110.40 116.90 -6.50 1.70e+00 3.46e-01 1.46e+01 angle pdb=" CA VAL E 170 " pdb=" CB VAL E 170 " pdb=" CG1 VAL E 170 " ideal model delta sigma weight residual 110.40 116.84 -6.44 1.70e+00 3.46e-01 1.44e+01 angle pdb=" CA VAL E 170 " pdb=" CB VAL E 170 " pdb=" CG2 VAL E 170 " ideal model delta sigma weight residual 110.40 116.81 -6.41 1.70e+00 3.46e-01 1.42e+01 ... (remaining 45141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 19510 17.86 - 35.73: 630 35.73 - 53.59: 119 53.59 - 71.45: 34 71.45 - 89.31: 10 Dihedral angle restraints: 20303 sinusoidal: 8351 harmonic: 11952 Sorted by residual: dihedral pdb=" CB CYS J 7 " pdb=" SG CYS J 7 " pdb=" SG CYS J 39 " pdb=" CB CYS J 39 " ideal model delta sinusoidal sigma weight residual -86.00 -139.67 53.67 1 1.00e+01 1.00e-02 3.91e+01 dihedral pdb=" CA ILE A 458 " pdb=" C ILE A 458 " pdb=" N GLN A 459 " pdb=" CA GLN A 459 " ideal model delta harmonic sigma weight residual -180.00 -154.08 -25.92 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA ASN C 245 " pdb=" C ASN C 245 " pdb=" N PRO C 246 " pdb=" CA PRO C 246 " ideal model delta harmonic sigma weight residual 180.00 157.17 22.83 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 20300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.297: 5112 0.297 - 0.594: 0 0.594 - 0.892: 0 0.892 - 1.189: 0 1.189 - 1.486: 2 Chirality restraints: 5114 Sorted by residual: chirality pdb=" CB VAL E 170 " pdb=" CA VAL E 170 " pdb=" CG1 VAL E 170 " pdb=" CG2 VAL E 170 " both_signs ideal model delta sigma weight residual False -2.63 -1.14 -1.49 2.00e-01 2.50e+01 5.52e+01 chirality pdb=" CB VAL C 111 " pdb=" CA VAL C 111 " pdb=" CG1 VAL C 111 " pdb=" CG2 VAL C 111 " both_signs ideal model delta sigma weight residual False -2.63 -1.20 -1.43 2.00e-01 2.50e+01 5.10e+01 chirality pdb=" CA ILE C 59 " pdb=" N ILE C 59 " pdb=" C ILE C 59 " pdb=" CB ILE C 59 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.99e-01 ... (remaining 5111 not shown) Planarity restraints: 5712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 41 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.74e+00 pdb=" C PHE B 41 " 0.029 2.00e-02 2.50e+03 pdb=" O PHE B 41 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE B 42 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 938 " 0.013 2.00e-02 2.50e+03 1.15e-02 2.32e+00 pdb=" CG PHE A 938 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE A 938 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 938 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 938 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 938 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 938 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 459 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.04e+00 pdb=" C GLN A 459 " -0.025 2.00e-02 2.50e+03 pdb=" O GLN A 459 " 0.009 2.00e-02 2.50e+03 pdb=" N ASP A 460 " 0.008 2.00e-02 2.50e+03 ... (remaining 5709 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 317 2.57 - 3.15: 28623 3.15 - 3.73: 49790 3.73 - 4.32: 73158 4.32 - 4.90: 122268 Nonbonded interactions: 274156 Sorted by model distance: nonbonded pdb=" N CYS I 366 " pdb="ZN ZN I 801 " model vdw 1.984 2.310 nonbonded pdb=" OD1 ASP A 415 " pdb="MG MG A1301 " model vdw 2.009 2.170 nonbonded pdb=" OD1 ASP A 419 " pdb="MG MG A1301 " model vdw 2.015 2.170 nonbonded pdb=" OE2 GLU I 250 " pdb=" OG SER I 280 " model vdw 2.081 3.040 nonbonded pdb=" O THR B 887 " pdb=" OG SER B 888 " model vdw 2.135 3.040 ... (remaining 274151 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.340 Check model and map are aligned: 0.240 Set scattering table: 0.330 Process input model: 81.190 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 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 : 0.002 0.074 33408 Z= 0.118 Angle : 0.459 11.202 45166 Z= 0.264 Chirality : 0.050 1.486 5114 Planarity : 0.002 0.033 5712 Dihedral : 9.854 89.314 12574 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.91 % Favored : 95.04 % Rotamer: Outliers : 1.81 % Allowed : 4.16 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.14), residues: 3991 helix: 1.49 (0.14), residues: 1493 sheet: -0.09 (0.23), residues: 534 loop : -0.56 (0.15), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 365 HIS 0.003 0.001 HIS B 318 PHE 0.026 0.001 PHE A 938 TYR 0.017 0.001 TYR B 377 ARG 0.003 0.000 ARG S 250 Details of bonding type rmsd hydrogen bonds : bond 0.14185 ( 1394) hydrogen bonds : angle 6.11192 ( 3948) metal coordination : bond 0.00663 ( 16) metal coordination : angle 2.11088 ( 18) SS BOND : bond 0.00571 ( 1) SS BOND : angle 1.65910 ( 2) covalent geometry : bond 0.00232 (33391) covalent geometry : angle 0.45753 (45146) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 379 time to evaluate : 3.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 LYS cc_start: 0.9210 (ttmt) cc_final: 0.9000 (ttpm) REVERT: A 238 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8334 (mm-40) REVERT: A 1031 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8317 (mm-30) REVERT: B 67 MET cc_start: 0.8226 (mmm) cc_final: 0.7791 (mmm) REVERT: B 159 ASN cc_start: 0.8948 (OUTLIER) cc_final: 0.8145 (p0) REVERT: B 256 MET cc_start: 0.8975 (mmt) cc_final: 0.8678 (mmt) REVERT: B 506 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7534 (tm-30) REVERT: B 719 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8471 (pt0) REVERT: E 18 GLU cc_start: 0.9080 (tp30) cc_final: 0.8640 (tp30) REVERT: E 69 ILE cc_start: 0.9012 (mt) cc_final: 0.8650 (mp) REVERT: E 86 SER cc_start: 0.9536 (m) cc_final: 0.9144 (p) REVERT: G 100 GLN cc_start: 0.8822 (mt0) cc_final: 0.8517 (mp10) REVERT: G 103 ASP cc_start: 0.8719 (p0) cc_final: 0.8381 (p0) REVERT: G 124 PHE cc_start: 0.7903 (m-80) cc_final: 0.7628 (m-80) REVERT: G 131 TYR cc_start: 0.7247 (m-80) cc_final: 0.6882 (m-80) REVERT: I 121 MET cc_start: 0.8477 (mmt) cc_final: 0.7984 (mmt) REVERT: I 195 CYS cc_start: 0.9005 (m) cc_final: 0.8618 (m) REVERT: I 281 TYR cc_start: 0.8519 (t80) cc_final: 0.8235 (t80) REVERT: I 444 ASN cc_start: 0.9005 (t0) cc_final: 0.8404 (p0) REVERT: J 51 GLN cc_start: 0.8052 (tp-100) cc_final: 0.7705 (tp40) REVERT: J 61 ASP cc_start: 0.8268 (t70) cc_final: 0.7908 (t70) REVERT: S 37 LEU cc_start: 0.8072 (mt) cc_final: 0.7797 (tp) outliers start: 67 outliers final: 18 residues processed: 436 average time/residue: 1.4913 time to fit residues: 769.3467 Evaluate side-chains 248 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 227 time to evaluate : 3.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 567 HIS Chi-restraints excluded: chain I residue 638 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 13 ASP Chi-restraints excluded: chain S residue 103 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 336 optimal weight: 3.9990 chunk 302 optimal weight: 0.4980 chunk 167 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 203 optimal weight: 10.0000 chunk 161 optimal weight: 0.5980 chunk 312 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 232 optimal weight: 6.9990 chunk 362 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 HIS C 129 GLN I 197 HIS I 567 HIS ** S 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.061358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.045905 restraints weight = 104817.447| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 3.19 r_work: 0.2589 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 33408 Z= 0.177 Angle : 0.579 7.594 45166 Z= 0.306 Chirality : 0.044 0.164 5114 Planarity : 0.004 0.049 5712 Dihedral : 5.511 85.513 4450 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.81 % Favored : 95.16 % Rotamer: Outliers : 1.75 % Allowed : 9.07 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.14), residues: 3991 helix: 1.62 (0.14), residues: 1506 sheet: -0.01 (0.22), residues: 538 loop : -0.50 (0.15), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 365 HIS 0.012 0.001 HIS B 389 PHE 0.028 0.001 PHE A 938 TYR 0.021 0.001 TYR S 134 ARG 0.007 0.001 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.04584 ( 1394) hydrogen bonds : angle 4.94451 ( 3948) metal coordination : bond 0.00654 ( 16) metal coordination : angle 2.35297 ( 18) SS BOND : bond 0.00548 ( 1) SS BOND : angle 3.06564 ( 2) covalent geometry : bond 0.00406 (33391) covalent geometry : angle 0.57667 (45146) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 242 time to evaluate : 3.905 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: A 44 MET cc_start: 0.8490 (pmm) cc_final: 0.8280 (ppp) REVERT: A 226 MET cc_start: 0.9141 (mmm) cc_final: 0.8772 (mmm) REVERT: A 426 GLU cc_start: 0.8682 (tp30) cc_final: 0.8477 (tp30) REVERT: A 961 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.8579 (t80) REVERT: A 1031 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8934 (mt-10) REVERT: B 67 MET cc_start: 0.8384 (mmm) cc_final: 0.7878 (mmm) REVERT: B 159 ASN cc_start: 0.8957 (OUTLIER) cc_final: 0.8046 (p0) REVERT: B 506 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8258 (tm-30) REVERT: B 1056 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8587 (mtp) REVERT: C 247 GLU cc_start: 0.6556 (mp0) cc_final: 0.6293 (mp0) REVERT: E 18 GLU cc_start: 0.9467 (tp30) cc_final: 0.8985 (tp30) REVERT: E 86 SER cc_start: 0.9587 (m) cc_final: 0.9263 (p) REVERT: E 120 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8928 (mp0) REVERT: F 103 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7464 (tm-30) REVERT: G 86 ARG cc_start: 0.8251 (mtp180) cc_final: 0.7908 (tpt-90) REVERT: G 100 GLN cc_start: 0.9020 (mt0) cc_final: 0.8540 (mp10) REVERT: G 103 ASP cc_start: 0.8857 (p0) cc_final: 0.8348 (p0) REVERT: G 107 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8388 (mtmt) REVERT: G 124 PHE cc_start: 0.8528 (m-80) cc_final: 0.8075 (m-80) REVERT: G 129 ASN cc_start: 0.8900 (m110) cc_final: 0.8680 (t0) REVERT: G 131 TYR cc_start: 0.7134 (m-80) cc_final: 0.6548 (m-80) REVERT: I 205 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8569 (ptpp) REVERT: I 281 TYR cc_start: 0.9054 (t80) cc_final: 0.8740 (t80) REVERT: I 444 ASN cc_start: 0.9110 (t0) cc_final: 0.8574 (p0) REVERT: I 511 MET cc_start: 0.6885 (mmt) cc_final: 0.6568 (tpp) REVERT: I 569 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8791 (tp40) REVERT: I 573 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8910 (mm) REVERT: I 643 LYS cc_start: 0.9520 (OUTLIER) cc_final: 0.9236 (tptp) REVERT: I 650 CYS cc_start: 0.8290 (m) cc_final: 0.8030 (m) REVERT: J 21 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8970 (pp) REVERT: J 51 GLN cc_start: 0.8619 (tp-100) cc_final: 0.8124 (tp40) REVERT: J 61 ASP cc_start: 0.8608 (t70) cc_final: 0.8229 (t70) REVERT: S 42 GLU cc_start: 0.9580 (tt0) cc_final: 0.9354 (pt0) REVERT: S 83 ARG cc_start: 0.9002 (ttp-110) cc_final: 0.8777 (mtm-85) outliers start: 65 outliers final: 21 residues processed: 291 average time/residue: 1.4333 time to fit residues: 498.2365 Evaluate side-chains 242 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 3.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 1056 MET Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 465 LEU Chi-restraints excluded: chain I residue 567 HIS Chi-restraints excluded: chain I residue 569 GLN Chi-restraints excluded: chain I residue 573 LEU Chi-restraints excluded: chain I residue 643 LYS Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 105 ASP Chi-restraints excluded: chain S residue 151 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 388 optimal weight: 10.0000 chunk 197 optimal weight: 0.8980 chunk 266 optimal weight: 2.9990 chunk 346 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 181 optimal weight: 0.3980 chunk 239 optimal weight: 5.9990 chunk 262 optimal weight: 9.9990 chunk 382 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 567 HIS ** S 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.061194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.045733 restraints weight = 105728.429| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 3.18 r_work: 0.2585 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 33408 Z= 0.157 Angle : 0.543 11.366 45166 Z= 0.285 Chirality : 0.043 0.161 5114 Planarity : 0.003 0.053 5712 Dihedral : 5.344 83.899 4436 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.01 % Favored : 94.96 % Rotamer: Outliers : 2.08 % Allowed : 9.56 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.14), residues: 3991 helix: 1.64 (0.14), residues: 1520 sheet: 0.05 (0.23), residues: 517 loop : -0.49 (0.15), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 365 HIS 0.011 0.001 HIS I 197 PHE 0.029 0.001 PHE A 938 TYR 0.020 0.001 TYR S 134 ARG 0.006 0.000 ARG G 38 Details of bonding type rmsd hydrogen bonds : bond 0.04143 ( 1394) hydrogen bonds : angle 4.70020 ( 3948) metal coordination : bond 0.00596 ( 16) metal coordination : angle 2.76749 ( 18) SS BOND : bond 0.00446 ( 1) SS BOND : angle 1.58282 ( 2) covalent geometry : bond 0.00358 (33391) covalent geometry : angle 0.54063 (45146) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 239 time to evaluate : 4.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8527 (pmm) cc_final: 0.8322 (ppp) REVERT: A 226 MET cc_start: 0.9165 (mmm) cc_final: 0.8768 (mmm) REVERT: A 261 ASN cc_start: 0.8753 (OUTLIER) cc_final: 0.8544 (p0) REVERT: A 426 GLU cc_start: 0.8675 (tp30) cc_final: 0.8411 (tp30) REVERT: A 631 GLU cc_start: 0.8634 (pp20) cc_final: 0.8389 (pp20) REVERT: A 961 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8596 (t80) REVERT: A 1031 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8945 (mt-10) REVERT: B 67 MET cc_start: 0.8403 (mmm) cc_final: 0.7868 (mmm) REVERT: B 159 ASN cc_start: 0.8999 (OUTLIER) cc_final: 0.8153 (p0) REVERT: B 386 MET cc_start: 0.8914 (mtp) cc_final: 0.8692 (mtp) REVERT: B 506 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8511 (tm-30) REVERT: B 819 MET cc_start: 0.8992 (mmm) cc_final: 0.8687 (mtt) REVERT: C 129 GLN cc_start: 0.8606 (tp40) cc_final: 0.8398 (tp40) REVERT: E 18 GLU cc_start: 0.9443 (tp30) cc_final: 0.8946 (tp30) REVERT: E 55 ASP cc_start: 0.8318 (t70) cc_final: 0.7169 (t0) REVERT: E 86 SER cc_start: 0.9578 (m) cc_final: 0.9248 (p) REVERT: F 103 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7415 (tm-30) REVERT: G 86 ARG cc_start: 0.8204 (mtp180) cc_final: 0.7805 (tpt-90) REVERT: G 100 GLN cc_start: 0.9026 (mt0) cc_final: 0.8544 (mp10) REVERT: G 103 ASP cc_start: 0.8858 (p0) cc_final: 0.8368 (p0) REVERT: G 107 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8352 (mtmt) REVERT: G 124 PHE cc_start: 0.8489 (m-80) cc_final: 0.8076 (m-80) REVERT: G 129 ASN cc_start: 0.8674 (m110) cc_final: 0.8398 (t0) REVERT: G 131 TYR cc_start: 0.7093 (m-80) cc_final: 0.6151 (m-80) REVERT: G 145 GLN cc_start: 0.8804 (mt0) cc_final: 0.8586 (mt0) REVERT: I 121 MET cc_start: 0.8883 (mmt) cc_final: 0.8341 (mmt) REVERT: I 205 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8587 (ptpp) REVERT: I 281 TYR cc_start: 0.9088 (t80) cc_final: 0.8757 (t80) REVERT: I 444 ASN cc_start: 0.9044 (t0) cc_final: 0.8585 (p0) REVERT: I 486 LYS cc_start: 0.8769 (mttt) cc_final: 0.8215 (ptpp) REVERT: I 643 LYS cc_start: 0.9519 (OUTLIER) cc_final: 0.9229 (tptp) REVERT: I 650 CYS cc_start: 0.8383 (m) cc_final: 0.8079 (m) REVERT: J 51 GLN cc_start: 0.8704 (tp-100) cc_final: 0.8203 (tp40) REVERT: S 104 CYS cc_start: 0.9267 (m) cc_final: 0.8508 (p) REVERT: S 146 ASP cc_start: 0.9025 (OUTLIER) cc_final: 0.8722 (t0) outliers start: 77 outliers final: 29 residues processed: 299 average time/residue: 1.4254 time to fit residues: 510.4611 Evaluate side-chains 252 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 216 time to evaluate : 3.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 428 MET Chi-restraints excluded: chain I residue 465 LEU Chi-restraints excluded: chain I residue 567 HIS Chi-restraints excluded: chain I residue 643 LYS Chi-restraints excluded: chain I residue 788 LEU Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 146 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 69 optimal weight: 0.9980 chunk 272 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 260 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 chunk 81 optimal weight: 4.9990 chunk 277 optimal weight: 0.4980 chunk 303 optimal weight: 6.9990 chunk 245 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 197 HIS I 567 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.060798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.045183 restraints weight = 105793.354| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 3.20 r_work: 0.2571 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33408 Z= 0.171 Angle : 0.548 9.292 45166 Z= 0.286 Chirality : 0.044 0.233 5114 Planarity : 0.004 0.067 5712 Dihedral : 5.381 83.924 4436 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.26 % Favored : 94.71 % Rotamer: Outliers : 2.19 % Allowed : 9.77 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.14), residues: 3991 helix: 1.63 (0.14), residues: 1518 sheet: 0.01 (0.23), residues: 511 loop : -0.47 (0.15), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1054 HIS 0.008 0.001 HIS B 409 PHE 0.029 0.001 PHE A 938 TYR 0.021 0.001 TYR S 134 ARG 0.012 0.000 ARG C 90 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 1394) hydrogen bonds : angle 4.62214 ( 3948) metal coordination : bond 0.00619 ( 16) metal coordination : angle 2.86821 ( 18) SS BOND : bond 0.01579 ( 1) SS BOND : angle 2.82415 ( 2) covalent geometry : bond 0.00390 (33391) covalent geometry : angle 0.54444 (45146) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 228 time to evaluate : 4.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8536 (pmm) cc_final: 0.8321 (ppp) REVERT: A 226 MET cc_start: 0.9183 (mmm) cc_final: 0.8821 (mmm) REVERT: A 426 GLU cc_start: 0.8698 (tp30) cc_final: 0.8485 (tp30) REVERT: A 631 GLU cc_start: 0.8681 (pp20) cc_final: 0.8390 (pp20) REVERT: A 961 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8556 (t80) REVERT: A 1031 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8941 (mt-10) REVERT: B 159 ASN cc_start: 0.8960 (OUTLIER) cc_final: 0.8200 (p0) REVERT: B 386 MET cc_start: 0.8885 (mtp) cc_final: 0.8644 (mtp) REVERT: B 506 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8590 (tm-30) REVERT: B 819 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8691 (mtt) REVERT: E 18 GLU cc_start: 0.9438 (tp30) cc_final: 0.8959 (tp30) REVERT: E 55 ASP cc_start: 0.8412 (t70) cc_final: 0.7809 (t0) REVERT: E 57 MET cc_start: 0.9115 (mmm) cc_final: 0.8786 (mmm) REVERT: E 86 SER cc_start: 0.9619 (m) cc_final: 0.9301 (p) REVERT: E 120 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8899 (mp0) REVERT: E 174 GLU cc_start: 0.8767 (tp30) cc_final: 0.8561 (mm-30) REVERT: F 103 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7391 (tm-30) REVERT: G 100 GLN cc_start: 0.9034 (mt0) cc_final: 0.8537 (mp10) REVERT: G 103 ASP cc_start: 0.8833 (p0) cc_final: 0.8338 (p0) REVERT: G 124 PHE cc_start: 0.8523 (m-80) cc_final: 0.8126 (m-80) REVERT: G 129 ASN cc_start: 0.8566 (m110) cc_final: 0.8336 (t0) REVERT: G 131 TYR cc_start: 0.7135 (m-80) cc_final: 0.6256 (m-80) REVERT: I 205 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8634 (ptpp) REVERT: I 281 TYR cc_start: 0.9074 (t80) cc_final: 0.8751 (t80) REVERT: I 444 ASN cc_start: 0.9018 (t0) cc_final: 0.8544 (p0) REVERT: I 486 LYS cc_start: 0.8756 (mttt) cc_final: 0.8263 (ptpp) REVERT: I 511 MET cc_start: 0.6869 (mmt) cc_final: 0.5862 (tpp) REVERT: I 643 LYS cc_start: 0.9523 (OUTLIER) cc_final: 0.9230 (tptp) REVERT: I 650 CYS cc_start: 0.8405 (m) cc_final: 0.8103 (m) REVERT: J 51 GLN cc_start: 0.8732 (tp-100) cc_final: 0.8224 (tp40) REVERT: S 39 ASP cc_start: 0.9121 (p0) cc_final: 0.8345 (p0) REVERT: S 83 ARG cc_start: 0.9028 (ttp-110) cc_final: 0.8820 (mtm-85) REVERT: S 104 CYS cc_start: 0.9204 (m) cc_final: 0.8467 (p) REVERT: S 146 ASP cc_start: 0.9033 (OUTLIER) cc_final: 0.8723 (t0) outliers start: 81 outliers final: 39 residues processed: 291 average time/residue: 1.4650 time to fit residues: 507.2132 Evaluate side-chains 259 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 213 time to evaluate : 3.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain A residue 1123 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 819 MET Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 428 MET Chi-restraints excluded: chain I residue 465 LEU Chi-restraints excluded: chain I residue 567 HIS Chi-restraints excluded: chain I residue 643 LYS Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 146 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 342 optimal weight: 8.9990 chunk 216 optimal weight: 0.6980 chunk 380 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 HIS C 137 GLN I 197 HIS ** I 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 567 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.060867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.045240 restraints weight = 105409.271| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 3.20 r_work: 0.2572 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33408 Z= 0.157 Angle : 0.541 8.597 45166 Z= 0.281 Chirality : 0.043 0.162 5114 Planarity : 0.003 0.056 5712 Dihedral : 5.376 83.787 4436 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.54 % Favored : 94.44 % Rotamer: Outliers : 2.16 % Allowed : 10.58 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.14), residues: 3991 helix: 1.63 (0.14), residues: 1520 sheet: 0.00 (0.23), residues: 504 loop : -0.46 (0.15), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1054 HIS 0.009 0.001 HIS B 409 PHE 0.029 0.001 PHE A 938 TYR 0.024 0.001 TYR A 264 ARG 0.007 0.000 ARG I 408 Details of bonding type rmsd hydrogen bonds : bond 0.03947 ( 1394) hydrogen bonds : angle 4.57214 ( 3948) metal coordination : bond 0.00623 ( 16) metal coordination : angle 2.85328 ( 18) SS BOND : bond 0.00665 ( 1) SS BOND : angle 1.95635 ( 2) covalent geometry : bond 0.00358 (33391) covalent geometry : angle 0.53825 (45146) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 227 time to evaluate : 3.851 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: A 149 VAL cc_start: 0.9014 (OUTLIER) cc_final: 0.8786 (m) REVERT: A 226 MET cc_start: 0.9196 (mmm) cc_final: 0.8845 (mmm) REVERT: A 426 GLU cc_start: 0.8689 (tp30) cc_final: 0.8417 (tp30) REVERT: A 631 GLU cc_start: 0.8729 (pp20) cc_final: 0.8391 (pp20) REVERT: A 961 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.8559 (t80) REVERT: A 1031 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8938 (mt-10) REVERT: A 1063 GLU cc_start: 0.8201 (pm20) cc_final: 0.7916 (pm20) REVERT: B 67 MET cc_start: 0.8226 (mtp) cc_final: 0.7956 (mmm) REVERT: B 159 ASN cc_start: 0.8975 (OUTLIER) cc_final: 0.8264 (p0) REVERT: B 325 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7594 (pt0) REVERT: B 386 MET cc_start: 0.8866 (mtp) cc_final: 0.8623 (mtp) REVERT: B 506 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8590 (tm-30) REVERT: E 18 GLU cc_start: 0.9438 (tp30) cc_final: 0.8944 (tp30) REVERT: E 55 ASP cc_start: 0.8467 (t70) cc_final: 0.7383 (t0) REVERT: E 57 MET cc_start: 0.9164 (mmm) cc_final: 0.8713 (mmm) REVERT: E 86 SER cc_start: 0.9611 (m) cc_final: 0.9292 (p) REVERT: E 120 GLU cc_start: 0.9132 (OUTLIER) cc_final: 0.8876 (mp0) REVERT: E 144 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8595 (pm20) REVERT: F 103 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7444 (tm-30) REVERT: G 100 GLN cc_start: 0.9036 (mt0) cc_final: 0.8530 (mp10) REVERT: G 103 ASP cc_start: 0.8828 (p0) cc_final: 0.8361 (p0) REVERT: G 124 PHE cc_start: 0.8525 (m-80) cc_final: 0.8130 (m-80) REVERT: G 129 ASN cc_start: 0.8602 (m110) cc_final: 0.8255 (t0) REVERT: G 131 TYR cc_start: 0.7106 (m-80) cc_final: 0.6276 (m-80) REVERT: I 205 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8654 (ptpp) REVERT: I 281 TYR cc_start: 0.9081 (t80) cc_final: 0.8762 (t80) REVERT: I 444 ASN cc_start: 0.9016 (t0) cc_final: 0.8524 (p0) REVERT: I 643 LYS cc_start: 0.9524 (OUTLIER) cc_final: 0.9234 (tptp) REVERT: I 650 CYS cc_start: 0.8447 (m) cc_final: 0.8114 (m) REVERT: J 51 GLN cc_start: 0.8713 (tp-100) cc_final: 0.8225 (tp40) REVERT: S 104 CYS cc_start: 0.9158 (m) cc_final: 0.8427 (p) REVERT: S 146 ASP cc_start: 0.9042 (OUTLIER) cc_final: 0.8684 (t0) outliers start: 80 outliers final: 43 residues processed: 288 average time/residue: 1.3590 time to fit residues: 471.9808 Evaluate side-chains 264 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 212 time to evaluate : 3.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain A residue 1123 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 544 MET Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 92 HIS Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 428 MET Chi-restraints excluded: chain I residue 465 LEU Chi-restraints excluded: chain I residue 567 HIS Chi-restraints excluded: chain I residue 643 LYS Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 146 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 248 optimal weight: 4.9990 chunk 230 optimal weight: 7.9990 chunk 238 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 222 optimal weight: 0.6980 chunk 184 optimal weight: 7.9990 chunk 386 optimal weight: 6.9990 chunk 389 optimal weight: 7.9990 chunk 110 optimal weight: 0.0030 chunk 108 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 overall best weight: 1.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 ASN I 197 HIS ** I 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 567 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.061459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.045914 restraints weight = 104821.950| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 3.20 r_work: 0.2590 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33408 Z= 0.120 Angle : 0.530 10.262 45166 Z= 0.275 Chirality : 0.043 0.160 5114 Planarity : 0.003 0.061 5712 Dihedral : 5.326 83.785 4436 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.92 % Allowed : 11.34 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3991 helix: 1.65 (0.14), residues: 1528 sheet: 0.03 (0.23), residues: 502 loop : -0.46 (0.15), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1054 HIS 0.014 0.001 HIS I 197 PHE 0.028 0.001 PHE A 938 TYR 0.021 0.001 TYR S 134 ARG 0.014 0.000 ARG C 90 Details of bonding type rmsd hydrogen bonds : bond 0.03724 ( 1394) hydrogen bonds : angle 4.50107 ( 3948) metal coordination : bond 0.00661 ( 16) metal coordination : angle 2.89664 ( 18) SS BOND : bond 0.00430 ( 1) SS BOND : angle 1.29248 ( 2) covalent geometry : bond 0.00271 (33391) covalent geometry : angle 0.52640 (45146) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 227 time to evaluate : 3.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 VAL cc_start: 0.9000 (OUTLIER) cc_final: 0.8763 (m) REVERT: A 426 GLU cc_start: 0.8666 (tp30) cc_final: 0.8388 (tp30) REVERT: A 631 GLU cc_start: 0.8699 (pp20) cc_final: 0.8333 (pp20) REVERT: A 961 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8421 (t80) REVERT: B 61 ASN cc_start: 0.9159 (t0) cc_final: 0.8912 (t0) REVERT: B 67 MET cc_start: 0.8067 (mtp) cc_final: 0.7775 (mmm) REVERT: B 159 ASN cc_start: 0.8949 (OUTLIER) cc_final: 0.8233 (p0) REVERT: B 386 MET cc_start: 0.8871 (mtp) cc_final: 0.8631 (mtp) REVERT: B 478 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8154 (ptp-170) REVERT: B 506 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8584 (tm-30) REVERT: B 575 MET cc_start: 0.9485 (mpp) cc_final: 0.9249 (mpt) REVERT: E 18 GLU cc_start: 0.9448 (tp30) cc_final: 0.8965 (tp30) REVERT: E 55 ASP cc_start: 0.8481 (t70) cc_final: 0.7597 (t0) REVERT: E 57 MET cc_start: 0.9165 (mmm) cc_final: 0.8951 (mmm) REVERT: E 86 SER cc_start: 0.9616 (m) cc_final: 0.9302 (p) REVERT: E 120 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8880 (mp0) REVERT: E 144 GLU cc_start: 0.9204 (OUTLIER) cc_final: 0.8666 (pm20) REVERT: F 103 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7490 (tm-30) REVERT: G 100 GLN cc_start: 0.9034 (mt0) cc_final: 0.8529 (mp10) REVERT: G 103 ASP cc_start: 0.8799 (p0) cc_final: 0.8317 (p0) REVERT: G 124 PHE cc_start: 0.8542 (m-80) cc_final: 0.8150 (m-80) REVERT: G 131 TYR cc_start: 0.7110 (m-80) cc_final: 0.6207 (m-80) REVERT: I 205 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8700 (ptpp) REVERT: I 281 TYR cc_start: 0.9082 (t80) cc_final: 0.8739 (t80) REVERT: I 444 ASN cc_start: 0.8991 (t0) cc_final: 0.8490 (p0) REVERT: I 511 MET cc_start: 0.6907 (mmt) cc_final: 0.6559 (tpp) REVERT: I 643 LYS cc_start: 0.9518 (OUTLIER) cc_final: 0.9224 (tptp) REVERT: I 650 CYS cc_start: 0.8402 (m) cc_final: 0.8085 (m) REVERT: J 51 GLN cc_start: 0.8685 (tp-100) cc_final: 0.8123 (tp40) REVERT: S 83 ARG cc_start: 0.8954 (ttp-110) cc_final: 0.8729 (mtm110) REVERT: S 104 CYS cc_start: 0.9165 (m) cc_final: 0.8446 (p) REVERT: S 146 ASP cc_start: 0.9038 (OUTLIER) cc_final: 0.8666 (t0) outliers start: 71 outliers final: 36 residues processed: 280 average time/residue: 1.4183 time to fit residues: 475.7516 Evaluate side-chains 259 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 214 time to evaluate : 3.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain A residue 1123 MET Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 478 ARG Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 92 HIS Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 428 MET Chi-restraints excluded: chain I residue 465 LEU Chi-restraints excluded: chain I residue 567 HIS Chi-restraints excluded: chain I residue 643 LYS Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 146 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 24 optimal weight: 7.9990 chunk 372 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 283 optimal weight: 3.9990 chunk 347 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 356 optimal weight: 10.0000 chunk 168 optimal weight: 0.2980 chunk 249 optimal weight: 4.9990 chunk 217 optimal weight: 0.0020 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN I 197 HIS ** I 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 567 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.061566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.046112 restraints weight = 104534.529| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 3.19 r_work: 0.2594 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33408 Z= 0.127 Angle : 0.535 11.073 45166 Z= 0.277 Chirality : 0.043 0.186 5114 Planarity : 0.003 0.053 5712 Dihedral : 5.294 83.403 4436 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.84 % Allowed : 11.64 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.14), residues: 3991 helix: 1.69 (0.14), residues: 1522 sheet: 0.05 (0.24), residues: 499 loop : -0.47 (0.15), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 365 HIS 0.009 0.001 HIS B 409 PHE 0.028 0.001 PHE A 938 TYR 0.027 0.001 TYR A 264 ARG 0.007 0.000 ARG S 83 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 1394) hydrogen bonds : angle 4.47817 ( 3948) metal coordination : bond 0.00653 ( 16) metal coordination : angle 2.91462 ( 18) SS BOND : bond 0.01585 ( 1) SS BOND : angle 4.42858 ( 2) covalent geometry : bond 0.00290 (33391) covalent geometry : angle 0.53145 (45146) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 224 time to evaluate : 3.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 VAL cc_start: 0.8992 (OUTLIER) cc_final: 0.8747 (m) REVERT: A 426 GLU cc_start: 0.8653 (tp30) cc_final: 0.8371 (tp30) REVERT: A 631 GLU cc_start: 0.8718 (pp20) cc_final: 0.8334 (pp20) REVERT: A 691 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7913 (tm-30) REVERT: A 961 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.8456 (t80) REVERT: B 61 ASN cc_start: 0.9157 (t0) cc_final: 0.8893 (t0) REVERT: B 159 ASN cc_start: 0.8958 (OUTLIER) cc_final: 0.8260 (p0) REVERT: B 386 MET cc_start: 0.8873 (mtp) cc_final: 0.8634 (mtp) REVERT: B 478 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8165 (ptp-170) REVERT: B 506 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8591 (tm-30) REVERT: B 575 MET cc_start: 0.9475 (mpp) cc_final: 0.9240 (mpt) REVERT: B 861 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7866 (mm) REVERT: C 250 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8811 (mmm) REVERT: E 18 GLU cc_start: 0.9448 (tp30) cc_final: 0.8961 (tp30) REVERT: E 86 SER cc_start: 0.9611 (m) cc_final: 0.9294 (p) REVERT: E 120 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8884 (mp0) REVERT: E 144 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8734 (pm20) REVERT: F 103 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7521 (tm-30) REVERT: F 110 LYS cc_start: 0.9505 (mtpt) cc_final: 0.9157 (mtmm) REVERT: G 100 GLN cc_start: 0.9041 (mt0) cc_final: 0.8557 (mp10) REVERT: G 103 ASP cc_start: 0.8804 (p0) cc_final: 0.8339 (p0) REVERT: G 124 PHE cc_start: 0.8548 (m-80) cc_final: 0.8162 (m-80) REVERT: G 131 TYR cc_start: 0.6877 (m-80) cc_final: 0.6286 (m-80) REVERT: I 205 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8687 (ptpp) REVERT: I 281 TYR cc_start: 0.9048 (t80) cc_final: 0.8744 (t80) REVERT: I 444 ASN cc_start: 0.8971 (t0) cc_final: 0.8470 (p0) REVERT: I 643 LYS cc_start: 0.9515 (OUTLIER) cc_final: 0.9223 (tptp) REVERT: I 650 CYS cc_start: 0.8426 (m) cc_final: 0.8093 (m) REVERT: J 17 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8781 (mp0) REVERT: J 51 GLN cc_start: 0.8661 (tp-100) cc_final: 0.8087 (tp40) REVERT: S 83 ARG cc_start: 0.9006 (ttp-110) cc_final: 0.8694 (mtm110) REVERT: S 104 CYS cc_start: 0.9172 (m) cc_final: 0.8442 (p) REVERT: S 146 ASP cc_start: 0.9070 (OUTLIER) cc_final: 0.8638 (OUTLIER) outliers start: 68 outliers final: 39 residues processed: 274 average time/residue: 1.3871 time to fit residues: 455.9628 Evaluate side-chains 266 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 216 time to evaluate : 3.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain A residue 1123 MET Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 478 ARG Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 92 HIS Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 428 MET Chi-restraints excluded: chain I residue 465 LEU Chi-restraints excluded: chain I residue 559 ILE Chi-restraints excluded: chain I residue 567 HIS Chi-restraints excluded: chain I residue 643 LYS Chi-restraints excluded: chain I residue 793 PHE Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 146 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 393 optimal weight: 0.8980 chunk 372 optimal weight: 0.5980 chunk 207 optimal weight: 5.9990 chunk 398 optimal weight: 8.9990 chunk 297 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 288 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 236 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 197 HIS ** I 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 567 HIS ** S 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.062098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.046771 restraints weight = 104434.101| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 3.13 r_work: 0.2639 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33408 Z= 0.121 Angle : 0.543 11.433 45166 Z= 0.279 Chirality : 0.043 0.170 5114 Planarity : 0.003 0.073 5712 Dihedral : 5.231 83.178 4434 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.73 % Allowed : 11.77 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.14), residues: 3991 helix: 1.75 (0.14), residues: 1515 sheet: 0.04 (0.23), residues: 505 loop : -0.47 (0.15), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 365 HIS 0.023 0.001 HIS I 197 PHE 0.028 0.001 PHE A 938 TYR 0.021 0.001 TYR S 134 ARG 0.018 0.000 ARG C 90 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 1394) hydrogen bonds : angle 4.44269 ( 3948) metal coordination : bond 0.00682 ( 16) metal coordination : angle 2.93633 ( 18) SS BOND : bond 0.00904 ( 1) SS BOND : angle 3.63456 ( 2) covalent geometry : bond 0.00275 (33391) covalent geometry : angle 0.53928 (45146) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7982 Ramachandran restraints generated. 3991 Oldfield, 0 Emsley, 3991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 235 time to evaluate : 3.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 VAL cc_start: 0.8991 (OUTLIER) cc_final: 0.8744 (m) REVERT: A 226 MET cc_start: 0.9070 (mmm) cc_final: 0.8839 (mmm) REVERT: A 283 ASP cc_start: 0.8206 (m-30) cc_final: 0.7961 (t0) REVERT: A 426 GLU cc_start: 0.8576 (tp30) cc_final: 0.8365 (tp30) REVERT: A 631 GLU cc_start: 0.8762 (pp20) cc_final: 0.8364 (pp20) REVERT: A 691 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7969 (tm-30) REVERT: B 61 ASN cc_start: 0.9102 (t0) cc_final: 0.8862 (t0) REVERT: B 159 ASN cc_start: 0.9056 (OUTLIER) cc_final: 0.8386 (p0) REVERT: B 386 MET cc_start: 0.8850 (mtp) cc_final: 0.8612 (mtp) REVERT: B 478 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8249 (ptp-170) REVERT: B 506 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8566 (tm-30) REVERT: B 575 MET cc_start: 0.9440 (mpp) cc_final: 0.8946 (mpt) REVERT: B 861 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7887 (mm) REVERT: C 250 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.8861 (mmm) REVERT: E 18 GLU cc_start: 0.9420 (tp30) cc_final: 0.8971 (tp30) REVERT: E 55 ASP cc_start: 0.8402 (t70) cc_final: 0.7866 (t0) REVERT: E 57 MET cc_start: 0.9091 (mmm) cc_final: 0.8726 (mmm) REVERT: E 86 SER cc_start: 0.9579 (m) cc_final: 0.9295 (p) REVERT: E 120 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8730 (mp0) REVERT: E 144 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.8819 (pm20) REVERT: F 103 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7493 (tm-30) REVERT: F 110 LYS cc_start: 0.9498 (mtpt) cc_final: 0.9155 (mtmm) REVERT: G 100 GLN cc_start: 0.9039 (mt0) cc_final: 0.8617 (mp10) REVERT: G 103 ASP cc_start: 0.8791 (p0) cc_final: 0.8381 (p0) REVERT: G 124 PHE cc_start: 0.8487 (m-80) cc_final: 0.8106 (m-80) REVERT: G 131 TYR cc_start: 0.7020 (m-80) cc_final: 0.6455 (m-80) REVERT: I 205 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8674 (ptpp) REVERT: I 281 TYR cc_start: 0.9001 (t80) cc_final: 0.8771 (t80) REVERT: I 444 ASN cc_start: 0.9011 (t0) cc_final: 0.8491 (p0) REVERT: I 511 MET cc_start: 0.6813 (mmt) cc_final: 0.6434 (tpp) REVERT: I 643 LYS cc_start: 0.9490 (OUTLIER) cc_final: 0.9207 (tptp) REVERT: I 650 CYS cc_start: 0.8314 (m) cc_final: 0.7993 (m) REVERT: I 795 ASN cc_start: 0.8353 (m-40) cc_final: 0.8025 (m110) REVERT: J 51 GLN cc_start: 0.8618 (tp-100) cc_final: 0.8116 (tp40) REVERT: S 83 ARG cc_start: 0.9013 (ttp-110) cc_final: 0.8696 (mtm110) REVERT: S 104 CYS cc_start: 0.9198 (m) cc_final: 0.8502 (p) REVERT: S 146 ASP cc_start: 0.9004 (OUTLIER) cc_final: 0.8617 (OUTLIER) outliers start: 64 outliers final: 38 residues processed: 283 average time/residue: 1.4217 time to fit residues: 485.1095 Evaluate side-chains 269 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 221 time to evaluate : 4.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 1123 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 478 ARG Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 92 HIS Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 428 MET Chi-restraints excluded: chain I residue 465 LEU Chi-restraints excluded: chain I residue 567 HIS Chi-restraints excluded: chain I residue 643 LYS Chi-restraints excluded: chain I residue 666 THR Chi-restraints excluded: chain I residue 793 PHE Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 146 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.5654 > 50: distance: 91 - 95: 4.734 distance: 95 - 96: 3.478 distance: 96 - 97: 3.180 distance: 97 - 98: 5.538 distance: 97 - 103: 5.737 distance: 99 - 100: 6.474 distance: 100 - 101: 6.972 distance: 101 - 102: 11.895 distance: 103 - 104: 10.721 distance: 104 - 105: 7.953 distance: 104 - 107: 6.265 distance: 105 - 106: 21.907 distance: 105 - 109: 21.189 distance: 107 - 108: 21.007 distance: 109 - 110: 22.314 distance: 110 - 111: 8.508 distance: 110 - 113: 20.830 distance: 111 - 112: 16.173 distance: 111 - 121: 26.674 distance: 113 - 114: 3.996 distance: 114 - 115: 9.336 distance: 114 - 116: 12.180 distance: 116 - 118: 3.344 distance: 117 - 119: 11.267 distance: 118 - 119: 11.099 distance: 119 - 120: 6.009 distance: 121 - 122: 13.866 distance: 122 - 123: 18.086 distance: 122 - 125: 25.203 distance: 123 - 124: 15.599 distance: 123 - 130: 18.836 distance: 125 - 126: 8.920 distance: 126 - 127: 10.864 distance: 127 - 128: 15.504 distance: 128 - 129: 11.597 distance: 130 - 131: 18.005 distance: 132 - 133: 9.011 distance: 132 - 134: 3.003 distance: 134 - 135: 7.412 distance: 135 - 136: 7.836 distance: 135 - 138: 4.946 distance: 136 - 137: 8.659 distance: 136 - 142: 7.721 distance: 138 - 139: 6.436 distance: 138 - 140: 7.467 distance: 139 - 141: 8.407 distance: 143 - 144: 5.844 distance: 143 - 146: 3.440 distance: 144 - 150: 9.558 distance: 146 - 147: 4.117 distance: 147 - 148: 3.450 distance: 147 - 149: 3.654 distance: 151 - 154: 3.774 distance: 152 - 153: 7.752 distance: 155 - 156: 4.090 distance: 159 - 160: 6.678 distance: 160 - 163: 11.253 distance: 161 - 162: 4.146 distance: 163 - 164: 4.740 distance: 164 - 165: 8.063 distance: 165 - 166: 5.028 distance: 165 - 167: 6.479 distance: 168 - 169: 5.775 distance: 169 - 172: 4.129 distance: 170 - 171: 3.759 distance: 170 - 176: 3.325 distance: 172 - 173: 3.987 distance: 173 - 174: 3.779