Starting phenix.real_space_refine on Mon Jun 23 06:33:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rid_4889/06_2025/6rid_4889.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rid_4889/06_2025/6rid_4889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6rid_4889/06_2025/6rid_4889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rid_4889/06_2025/6rid_4889.map" model { file = "/net/cci-nas-00/data/ceres_data/6rid_4889/06_2025/6rid_4889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rid_4889/06_2025/6rid_4889.cif" } resolution = 2.9 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 34 5.49 5 Mg 1 5.21 5 S 124 5.16 5 C 17003 2.51 5 N 4468 2.21 5 O 5071 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 131 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26705 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 10042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1250, 10042 Classifications: {'peptide': 1250} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1206} Chain breaks: 2 Chain: "B" Number of atoms: 9008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1120, 9008 Classifications: {'peptide': 1120} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1067} Chain breaks: 5 Chain: "C" Number of atoms: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2475 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} 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: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} 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: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1036 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "N" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 143 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "T" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 370 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "P" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 191 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna3p': 8} 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: "J" 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 17.187 93.496 70.862 1.00 59.73 S ATOM 382 SG CYS A 52 17.760 96.548 69.797 1.00 60.08 S ATOM 434 SG CYS A 59 20.550 94.329 70.795 1.00 52.62 S ATOM 694 SG CYS A 90 24.928 81.725 118.025 1.00106.28 S ATOM 718 SG CYS A 93 22.905 84.188 119.216 1.00111.49 S ATOM 1016 SG CYS A 130 25.466 83.230 121.038 1.00121.00 S ATOM 1059 SG CYS A 135 20.674 81.865 120.706 1.00126.59 S ATOM 18459 SG CYS B1087 21.499 104.521 83.885 1.00 44.88 S ATOM 18482 SG CYS B1090 21.248 101.745 84.807 1.00 42.00 S ATOM 18571 SG CYS B1103 18.905 101.977 82.396 1.00 51.79 S ATOM 18596 SG CYS B1106 18.283 103.614 86.045 1.00 53.89 S ATOM 24518 SG CYS J 7 79.785 74.552 36.034 1.00 11.68 S ATOM 24537 SG CYS J 10 81.899 76.652 33.808 1.00 13.06 S ATOM 24774 SG CYS J 39 83.220 75.800 37.382 1.00 15.33 S ATOM 24780 SG CYS J 40 82.870 73.810 34.101 1.00 14.39 S Time building chain proxies: 15.16, per 1000 atoms: 0.57 Number of scatterers: 26705 At special positions: 0 Unit cell: (118.65, 147, 153.3, 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 124 16.00 P 34 15.00 Mg 1 11.99 O 5071 8.00 N 4468 7.00 C 17003 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 6.93 Conformation dependent library (CDL) restraints added in 3.6 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 52 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 59 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 49 " pdb=" ZN A1303 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 93 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 90 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 135 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1090 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1103 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1087 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1106 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 40 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 39 " Number of angles added : 21 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6142 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 38 sheets defined 42.2% alpha, 18.6% beta 15 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 11.92 Creating SS restraints... Processing helix chain 'A' and resid 13 through 18 Processing helix chain 'A' and resid 78 through 87 Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.686A pdb=" N ALA A 115 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A 116 " --> pdb=" O GLY A 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 112 through 116' Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 161 through 171 Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.616A pdb=" N PHE A 176 " --> pdb=" O HIS A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.749A pdb=" N ILE A 202 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 Processing helix chain 'A' and resid 236 through 249 removed outlier: 3.709A 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: 3.924A 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 405 through 412 removed outlier: 3.525A pdb=" N ILE A 408 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASN A 410 " --> pdb=" O GLY A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 438 Processing helix chain 'A' and resid 458 through 471 removed outlier: 3.849A pdb=" N VAL A 463 " --> pdb=" O GLN A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 499 through 509 Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.914A 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: 4.001A pdb=" N LEU A 581 " --> pdb=" O THR A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 615 removed outlier: 4.021A pdb=" N GLU A 600 " --> pdb=" O VAL A 596 " (cutoff:3.500A) 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 696 through 700 removed outlier: 3.588A pdb=" N ARG A 700 " --> pdb=" O VAL A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 764 removed outlier: 4.503A pdb=" N SER A 750 " --> pdb=" O VAL A 746 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ARG A 751 " --> pdb=" O CYS A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 788 Processing helix chain 'A' and resid 809 through 821 Processing helix chain 'A' and resid 842 through 846 removed outlier: 3.534A pdb=" N VAL A 846 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 875 Processing helix chain 'A' and resid 882 through 893 removed outlier: 3.619A pdb=" N GLU A 886 " --> pdb=" O ILE A 882 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 893 " --> pdb=" O PHE A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 919 removed outlier: 3.675A pdb=" N THR A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 944 Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 984 through 996 removed outlier: 4.288A pdb=" N LEU A 988 " --> pdb=" O ASP A 984 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 991 " --> pdb=" O LYS A 987 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN A 994 " --> pdb=" O SER A 990 " (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 Processing helix chain 'A' and resid 1077 through 1093 Proline residue: A1090 - end of helix removed outlier: 3.506A pdb=" N ALA A1093 " --> pdb=" O LEU A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1136 removed outlier: 4.103A 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 1170 removed outlier: 3.579A pdb=" N THR A1170 " --> pdb=" O ALA A1166 " (cutoff:3.500A) 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 removed outlier: 3.514A pdb=" N LEU A1188 " --> pdb=" O LEU A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1215 Processing helix chain 'A' and resid 1218 through 1226 Processing helix chain 'A' and resid 1234 through 1241 removed outlier: 3.656A pdb=" N PHE A1240 " --> pdb=" O SER A1236 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A1241 " --> pdb=" O SER A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1252 removed outlier: 3.733A pdb=" N TYR A1252 " --> pdb=" O THR A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1264 removed outlier: 3.763A pdb=" N MET A1264 " --> pdb=" O LEU A1260 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 19 removed outlier: 3.754A pdb=" N PHE B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 18 " --> pdb=" O GLY B 14 " (cutoff:3.500A) 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 233 through 242 Processing helix chain 'B' and resid 244 through 253 Processing helix chain 'B' and resid 257 through 277 removed outlier: 3.718A pdb=" N TYR B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 298 Processing helix chain 'B' and resid 303 through 314 removed outlier: 3.721A pdb=" N ASN B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 removed outlier: 3.511A pdb=" N ASN B 320 " --> pdb=" O PRO B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 344 removed outlier: 3.611A pdb=" N LYS B 327 " --> pdb=" O PRO B 323 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 357 removed outlier: 3.730A pdb=" N CYS B 356 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS B 357 " --> pdb=" O MET B 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 353 through 357' Processing helix chain 'B' and resid 361 through 392 removed outlier: 3.934A pdb=" N TYR B 365 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 403 Processing helix chain 'B' and resid 407 through 414 Processing helix chain 'B' and resid 415 through 417 No H-bonds generated for 'chain 'B' and resid 415 through 417' 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 516 Processing helix chain 'B' and resid 544 through 558 removed outlier: 3.760A pdb=" N THR B 550 " --> pdb=" O CYS B 546 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP B 551 " --> pdb=" O ASP B 547 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET B 558 " --> pdb=" O ARG B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 604 removed outlier: 3.913A pdb=" N CYS B 604 " --> pdb=" O MET B 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 601 through 604' Processing helix chain 'B' and resid 606 through 611 Processing helix chain 'B' and resid 615 through 623 Processing helix chain 'B' and resid 632 through 637 Processing helix chain 'B' and resid 643 through 649 Processing helix chain 'B' and resid 664 through 669 removed outlier: 3.781A 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 removed outlier: 3.620A pdb=" N ASN B 682 " --> pdb=" O ILE B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 695 removed outlier: 4.031A pdb=" N LYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 731 removed outlier: 3.606A pdb=" N GLU B 729 " --> pdb=" O SER B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 767 Processing helix chain 'B' and resid 784 through 788 Processing helix chain 'B' and resid 898 through 902 removed outlier: 3.909A pdb=" N LEU B 902 " --> pdb=" O GLU B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 923 removed outlier: 3.795A pdb=" N PHE B 921 " --> pdb=" O SER B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 941 removed outlier: 4.447A pdb=" N LEU B 929 " --> pdb=" O THR B 925 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 930 " --> pdb=" O ILE B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 977 removed outlier: 3.557A pdb=" N TYR B 965 " --> pdb=" O SER B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 981 through 990 Processing helix chain 'B' and resid 1054 through 1064 Processing helix chain 'B' and resid 1066 through 1075 Processing helix chain 'B' and resid 1103 through 1109 Processing helix chain 'B' and resid 1121 through 1135 Processing helix chain 'C' and resid 15 through 30 Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.535A pdb=" N TRP C 52 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 59 No H-bonds generated for 'chain 'C' and resid 58 through 59' Processing helix chain 'C' and resid 60 through 64 removed outlier: 3.574A 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 117 through 122 Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 162 through 174 Processing helix chain 'C' and resid 191 through 193 No H-bonds generated for 'chain 'C' and resid 191 through 193' Processing helix chain 'C' and resid 207 through 229 removed outlier: 4.052A pdb=" N CYS C 211 " --> pdb=" O ASP C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 removed outlier: 3.531A pdb=" N PHE C 265 " --> pdb=" O ILE C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 304 removed outlier: 3.567A pdb=" N ARG C 304 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 22 removed outlier: 4.180A pdb=" N TYR E 8 " --> pdb=" O TYR E 4 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU E 9 " --> pdb=" O ASN E 5 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU E 15 " --> pdb=" O LYS E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 33 Processing helix chain 'E' and resid 117 through 128 Processing helix chain 'E' and resid 146 through 152 Processing helix chain 'F' and resid 63 through 74 Processing helix chain 'F' and resid 78 through 95 Processing helix chain 'F' and resid 106 through 110 Processing helix chain 'F' and resid 112 through 123 removed outlier: 3.656A pdb=" N VAL F 116 " --> pdb=" O ASN F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 161 removed outlier: 3.667A pdb=" N TYR F 153 " --> pdb=" O PHE F 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 19 Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'J' and resid 14 through 23 Processing helix chain 'J' and resid 27 through 32 Processing helix chain 'J' and resid 33 through 35 No H-bonds generated for 'chain 'J' and resid 33 through 35' Processing helix chain 'J' and resid 37 through 47 Processing helix chain 'S' and resid 24 through 32 Processing helix chain 'S' and resid 37 through 51 Processing helix chain 'S' and resid 69 through 80 removed outlier: 4.445A pdb=" N GLY S 75 " --> pdb=" O LYS S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 107 Processing helix chain 'S' and resid 112 through 131 removed outlier: 4.069A pdb=" N GLU S 116 " --> pdb=" O GLY S 112 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1229 through 1231 removed outlier: 3.537A pdb=" N LYS A 6 " --> pdb=" O ASP B1141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 24 removed outlier: 4.405A pdb=" N SER A 67 " --> pdb=" O ILE A 24 " (cutoff:3.500A) 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: 4.339A pdb=" N PHE A 151 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE A 158 " --> pdb=" O ASN A 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 280 through 282 removed outlier: 3.977A pdb=" N ILE B1051 " --> pdb=" O LYS A 282 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1027 through 1029 removed outlier: 7.526A pdb=" N ILE A 402 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL A 289 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE A 404 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 5.881A 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: 7.457A pdb=" N ALA A 369 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 8.577A 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 766 through 768 removed outlier: 6.529A 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 1111 Processing sheet with id=AB5, first strand: chain 'A' and resid 998 through 999 Processing sheet with id=AB6, first strand: chain 'A' and resid 1006 through 1012 Processing sheet with id=AB7, first strand: chain 'F' and resid 135 through 137 removed outlier: 3.807A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N TYR A1254 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 135 through 137 removed outlier: 3.807A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N TYR A1254 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR G 75 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS G 47 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS G 43 " --> pdb=" O ILE G 40 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA G 45 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG G 38 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.644A pdb=" N ARG B 54 " --> pdb=" O ILE B 68 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 66 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N SER B 58 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLU B 64 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL B 73 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR B 97 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL B 75 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU B 95 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS B 104 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N LYS B 116 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL B 106 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ILE B 114 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.644A pdb=" N ARG B 54 " --> pdb=" O ILE B 68 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 66 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N SER B 58 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLU B 64 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL B 73 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR B 97 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL B 75 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU B 95 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 157 through 158 Processing sheet with id=AC3, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.785A pdb=" N ASN B 169 " --> pdb=" O GLY B 445 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 179 through 182 Processing sheet with id=AC5, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AC6, first strand: chain 'B' and resid 598 through 599 removed outlier: 3.688A pdb=" N GLU B 598 " --> pdb=" O ASP B 595 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 535 through 540 removed outlier: 6.716A pdb=" N ILE B 530 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER B 539 " --> pdb=" O PHE B 528 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N PHE B 528 " --> pdb=" O SER B 539 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 712 through 715 removed outlier: 6.692A pdb=" N LYS B 866 " --> pdb=" O VAL B 859 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL B 859 " --> pdb=" O LYS B 866 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG B 868 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL B 857 " --> pdb=" O ARG B 868 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU B 870 " --> pdb=" O GLU B 855 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER B 852 " --> pdb=" O LEU B 813 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 715 removed outlier: 6.692A pdb=" N LYS B 866 " --> pdb=" O VAL B 859 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL B 859 " --> pdb=" O LYS B 866 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG B 868 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL B 857 " --> pdb=" O ARG B 868 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU B 870 " --> pdb=" O GLU B 855 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 723 through 724 Processing sheet with id=AD2, first strand: chain 'B' and resid 992 through 993 removed outlier: 6.893A pdb=" N ILE B 758 " --> pdb=" O ALA B 894 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N VAL B 896 " --> pdb=" O ILE B 758 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE B 760 " --> pdb=" O VAL B 896 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N VAL B 913 " --> pdb=" O HIS B 741 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR B 743 " --> pdb=" O VAL B 913 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ILE B 915 " --> pdb=" O THR B 743 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ALA B 745 " --> pdb=" O ILE B 915 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N PHE B1009 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1084 through 1087 removed outlier: 4.288A pdb=" N VAL B1084 " --> pdb=" O ILE B1118 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1095 through 1096 Processing sheet with id=AD5, first strand: chain 'C' and resid 5 through 13 removed outlier: 3.614A pdb=" N ILE C 188 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AD7, first strand: chain 'C' and resid 37 through 43 removed outlier: 3.595A pdb=" N ILE C 37 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU C 140 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASN C 43 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR C 138 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 93 through 94 Processing sheet with id=AD9, first strand: chain 'C' and resid 233 through 234 removed outlier: 6.553A pdb=" N LYS C 233 " --> pdb=" O TYR C 244 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 35 through 40 removed outlier: 6.243A pdb=" N ILE E 83 " --> pdb=" O PHE E 95 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 113 through 115 removed outlier: 6.605A pdb=" N MET E 142 " --> pdb=" O ILE E 181 " (cutoff:3.500A) 1169 hydrogen bonds defined for protein. 3237 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 17.33 Time building geometry restraints manager: 8.16 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: 8246 1.34 - 1.46: 6249 1.46 - 1.58: 12540 1.58 - 1.71: 65 1.71 - 1.83: 197 Bond restraints: 27297 Sorted by residual: bond pdb=" CG1 ILE E 106 " pdb=" CD1 ILE E 106 " ideal model delta sigma weight residual 1.513 1.426 0.087 3.90e-02 6.57e+02 4.93e+00 bond pdb=" CG1 ILE B 722 " pdb=" CD1 ILE B 722 " ideal model delta sigma weight residual 1.513 1.435 0.078 3.90e-02 6.57e+02 4.01e+00 bond pdb=" CB VAL E 114 " pdb=" CG1 VAL E 114 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.42e+00 bond pdb=" N ASN B 62 " pdb=" CA ASN B 62 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.12e+00 bond pdb=" CG1 ILE J 23 " pdb=" CD1 ILE J 23 " ideal model delta sigma weight residual 1.513 1.448 0.065 3.90e-02 6.57e+02 2.78e+00 ... (remaining 27292 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 36432 2.49 - 4.98: 556 4.98 - 7.48: 39 7.48 - 9.97: 4 9.97 - 12.46: 4 Bond angle restraints: 37035 Sorted by residual: angle pdb=" CA PHE A 938 " pdb=" CB PHE A 938 " pdb=" CG PHE A 938 " ideal model delta sigma weight residual 113.80 117.81 -4.01 1.00e+00 1.00e+00 1.61e+01 angle pdb=" C ASP A1152 " pdb=" N ILE A1153 " pdb=" CA ILE A1153 " ideal model delta sigma weight residual 122.97 119.19 3.78 9.80e-01 1.04e+00 1.49e+01 angle pdb=" C ASN B 61 " pdb=" N ASN B 62 " pdb=" CA ASN B 62 " ideal model delta sigma weight residual 121.54 128.75 -7.21 1.91e+00 2.74e-01 1.42e+01 angle pdb=" C ILE A 458 " pdb=" N GLN A 459 " pdb=" CA GLN A 459 " ideal model delta sigma weight residual 120.82 126.45 -5.63 1.50e+00 4.44e-01 1.41e+01 angle pdb=" C THR A1013 " pdb=" N ASP A1014 " pdb=" CA ASP A1014 " ideal model delta sigma weight residual 126.45 132.89 -6.44 1.77e+00 3.19e-01 1.32e+01 ... (remaining 37030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 14817 17.58 - 35.16: 1375 35.16 - 52.74: 271 52.74 - 70.32: 64 70.32 - 87.90: 18 Dihedral angle restraints: 16545 sinusoidal: 7036 harmonic: 9509 Sorted by residual: dihedral pdb=" CA LYS A 148 " pdb=" C LYS A 148 " pdb=" N VAL A 149 " pdb=" CA VAL A 149 " ideal model delta harmonic sigma weight residual -180.00 -141.68 -38.32 0 5.00e+00 4.00e-02 5.87e+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 -149.07 -30.93 0 5.00e+00 4.00e-02 3.83e+01 dihedral pdb=" CA ILE S 56 " pdb=" C ILE S 56 " pdb=" N GLY S 57 " pdb=" CA GLY S 57 " ideal model delta harmonic sigma weight residual 180.00 153.70 26.30 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 16542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3490 0.068 - 0.137: 655 0.137 - 0.205: 57 0.205 - 0.274: 13 0.274 - 0.342: 2 Chirality restraints: 4217 Sorted by residual: chirality pdb=" CB ILE B 568 " pdb=" CA ILE B 568 " pdb=" CG1 ILE B 568 " pdb=" CG2 ILE B 568 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CA GLU A 100 " pdb=" N GLU A 100 " pdb=" C GLU A 100 " pdb=" CB GLU A 100 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CB VAL S 132 " pdb=" CA VAL S 132 " pdb=" CG1 VAL S 132 " pdb=" CG2 VAL S 132 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 4214 not shown) Planarity restraints: 4569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 163 " 0.017 2.00e-02 2.50e+03 3.37e-02 1.13e+01 pdb=" C SER A 163 " -0.058 2.00e-02 2.50e+03 pdb=" O SER A 163 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU A 164 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 938 " 0.021 2.00e-02 2.50e+03 2.10e-02 7.75e+00 pdb=" CG PHE A 938 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE A 938 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 938 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 938 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 938 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 938 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 152 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.98e+00 pdb=" C VAL A 152 " -0.046 2.00e-02 2.50e+03 pdb=" O VAL A 152 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN A 153 " 0.015 2.00e-02 2.50e+03 ... (remaining 4566 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 289 2.64 - 3.21: 22099 3.21 - 3.77: 41553 3.77 - 4.34: 61315 4.34 - 4.90: 98383 Nonbonded interactions: 223639 Sorted by model distance: nonbonded pdb=" OD1 ASP A 419 " pdb="MG MG A1301 " model vdw 2.078 2.170 nonbonded pdb=" OD1 ASP A 417 " pdb="MG MG A1301 " model vdw 2.082 2.170 nonbonded pdb=" O3' G P 30 " pdb="MG MG A1301 " model vdw 2.208 2.170 nonbonded pdb=" O VAL A 619 " pdb=" OH TYR S 144 " model vdw 2.247 3.040 nonbonded pdb=" OH TYR B 38 " pdb=" O PRO B 131 " model vdw 2.267 3.040 ... (remaining 223634 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: 1.610 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: 0.030 Extract box with map and model: 1.210 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 82.740 Find NCS groups from input model: 0.750 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:13.910 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 : 0.007 0.417 27313 Z= 0.268 Angle : 0.870 30.769 37056 Z= 0.437 Chirality : 0.053 0.342 4217 Planarity : 0.006 0.063 4569 Dihedral : 14.323 87.899 10403 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.14 % Allowed : 4.28 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.12), residues: 3191 helix: -2.17 (0.11), residues: 1183 sheet: -1.37 (0.21), residues: 472 loop : -1.77 (0.14), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 131 HIS 0.009 0.001 HIS B 429 PHE 0.049 0.002 PHE A 938 TYR 0.033 0.002 TYR B1015 ARG 0.007 0.001 ARG F 76 Details of bonding type rmsd hydrogen bonds : bond 0.14755 ( 1164) hydrogen bonds : angle 6.69792 ( 3313) metal coordination : bond 0.15426 ( 16) metal coordination : angle 17.58081 ( 21) covalent geometry : bond 0.00551 (27297) covalent geometry : angle 0.76274 (37035) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 444 time to evaluate : 2.923 Fit side-chains revert: symmetry clash REVERT: A 13 ASP cc_start: 0.8417 (p0) cc_final: 0.8069 (p0) REVERT: A 175 LYS cc_start: 0.7392 (ptmt) cc_final: 0.7089 (ptmm) REVERT: A 238 GLN cc_start: 0.7041 (tt0) cc_final: 0.6763 (tp-100) REVERT: A 460 ASP cc_start: 0.8036 (m-30) cc_final: 0.7683 (m-30) REVERT: A 600 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6766 (mm-30) REVERT: A 807 MET cc_start: 0.8646 (mtt) cc_final: 0.8383 (mtm) REVERT: A 1218 LYS cc_start: 0.8193 (ptpp) cc_final: 0.7937 (mmmt) REVERT: B 386 MET cc_start: 0.6384 (mtp) cc_final: 0.6073 (mtp) REVERT: B 1047 ARG cc_start: 0.7915 (mpp-170) cc_final: 0.7700 (mtm-85) REVERT: G 47 LYS cc_start: 0.6697 (mttm) cc_final: 0.6400 (tmtt) outliers start: 4 outliers final: 2 residues processed: 447 average time/residue: 1.4829 time to fit residues: 761.2391 Evaluate side-chains 312 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 310 time to evaluate : 3.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 878 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 2.9990 chunk 243 optimal weight: 0.5980 chunk 135 optimal weight: 10.0000 chunk 83 optimal weight: 0.6980 chunk 164 optimal weight: 0.6980 chunk 129 optimal weight: 4.9990 chunk 251 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 187 optimal weight: 0.8980 chunk 291 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 107 ASN A 232 ASN A 412 GLN A 459 GLN A 513 ASN A 651 GLN A 660 ASN A 685 GLN A 894 ASN A 941 GLN A 962 ASN A 994 ASN A1023 ASN A1116 GLN A1222 ASN A1233 ASN A1239 HIS B 169 ASN B 298 GLN B 357 HIS B 657 GLN B 693 GLN B 740 GLN B 754 GLN B 778 HIS B1040 GLN B1122 HIS C 129 GLN E 65 ASN F 119 GLN F 140 ASN ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 ASN J 37 ASN ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN S 55 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.143670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.110131 restraints weight = 31187.372| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.47 r_work: 0.3029 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27313 Z= 0.133 Angle : 0.549 14.772 37056 Z= 0.285 Chirality : 0.043 0.198 4217 Planarity : 0.004 0.046 4569 Dihedral : 10.084 73.176 3932 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.36 % Allowed : 10.98 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.31 (0.14), residues: 3191 helix: -0.30 (0.14), residues: 1198 sheet: -0.96 (0.22), residues: 467 loop : -1.22 (0.15), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 365 HIS 0.004 0.001 HIS B 429 PHE 0.035 0.001 PHE A 938 TYR 0.015 0.001 TYR B1015 ARG 0.007 0.000 ARG E 51 Details of bonding type rmsd hydrogen bonds : bond 0.04208 ( 1164) hydrogen bonds : angle 4.89347 ( 3313) metal coordination : bond 0.00993 ( 16) metal coordination : angle 6.51468 ( 21) covalent geometry : bond 0.00304 (27297) covalent geometry : angle 0.52671 (37035) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 334 time to evaluate : 3.173 Fit side-chains revert: symmetry clash REVERT: A 13 ASP cc_start: 0.8452 (p0) cc_final: 0.7885 (p0) REVERT: A 16 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8052 (mt-10) REVERT: A 175 LYS cc_start: 0.7488 (ptmt) cc_final: 0.7153 (ptmm) REVERT: A 238 GLN cc_start: 0.7058 (tt0) cc_final: 0.6562 (tp-100) REVERT: A 264 TYR cc_start: 0.7135 (t80) cc_final: 0.6794 (p90) REVERT: A 644 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8091 (mm-30) REVERT: A 807 MET cc_start: 0.8987 (mtt) cc_final: 0.8723 (mtm) REVERT: A 898 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8336 (tp) REVERT: A 1031 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7744 (mt-10) REVERT: A 1218 LYS cc_start: 0.8210 (ptpp) cc_final: 0.7686 (mmmt) REVERT: B 72 ASN cc_start: 0.7965 (m110) cc_final: 0.7322 (t0) REVERT: B 386 MET cc_start: 0.6269 (mtp) cc_final: 0.5945 (mtp) REVERT: B 980 LEU cc_start: 0.8078 (mt) cc_final: 0.7832 (mp) REVERT: B 1047 ARG cc_start: 0.8512 (mpp-170) cc_final: 0.8230 (mtm-85) REVERT: B 1100 ILE cc_start: 0.8353 (mm) cc_final: 0.8042 (tp) REVERT: C 239 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.5961 (mt-10) REVERT: C 247 GLU cc_start: 0.7667 (mp0) cc_final: 0.7455 (mp0) REVERT: E 40 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7203 (mm-30) REVERT: E 160 LYS cc_start: 0.8200 (mmtt) cc_final: 0.7995 (tptt) REVERT: G 28 ARG cc_start: 0.7851 (ttm110) cc_final: 0.7510 (ttp-110) REVERT: G 47 LYS cc_start: 0.6861 (mttm) cc_final: 0.6413 (tmtt) REVERT: G 49 GLU cc_start: 0.7479 (tp30) cc_final: 0.7130 (tp30) outliers start: 40 outliers final: 14 residues processed: 353 average time/residue: 1.5550 time to fit residues: 632.0627 Evaluate side-chains 313 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 296 time to evaluate : 3.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 651 SER Chi-restraints excluded: chain B residue 899 GLU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain E residue 126 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 17 optimal weight: 2.9990 chunk 242 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 277 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 281 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 289 optimal weight: 0.0030 chunk 175 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 651 GLN A 957 GLN A1116 GLN B 159 ASN B 295 HIS B 298 GLN C 171 ASN ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.144162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.111263 restraints weight = 30957.141| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.48 r_work: 0.3047 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27313 Z= 0.120 Angle : 0.505 10.774 37056 Z= 0.264 Chirality : 0.043 0.177 4217 Planarity : 0.004 0.041 4569 Dihedral : 9.875 73.128 3930 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.90 % Allowed : 12.10 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 3191 helix: 0.51 (0.15), residues: 1201 sheet: -0.71 (0.23), residues: 466 loop : -0.94 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 365 HIS 0.004 0.001 HIS C 275 PHE 0.033 0.001 PHE A 938 TYR 0.016 0.001 TYR S 78 ARG 0.010 0.000 ARG E 51 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 1164) hydrogen bonds : angle 4.56880 ( 3313) metal coordination : bond 0.00763 ( 16) metal coordination : angle 4.94919 ( 21) covalent geometry : bond 0.00275 (27297) covalent geometry : angle 0.49090 (37035) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 322 time to evaluate : 3.567 Fit side-chains REVERT: A 135 CYS cc_start: 0.0794 (OUTLIER) cc_final: 0.0296 (m) REVERT: A 175 LYS cc_start: 0.7460 (ptmt) cc_final: 0.7062 (ptmm) REVERT: A 238 GLN cc_start: 0.7046 (tt0) cc_final: 0.6512 (tp-100) REVERT: A 264 TYR cc_start: 0.7105 (t80) cc_final: 0.6806 (p90) REVERT: A 644 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8030 (mm-30) REVERT: A 807 MET cc_start: 0.8904 (mtt) cc_final: 0.8675 (mtm) REVERT: A 898 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8338 (tp) REVERT: A 940 GLN cc_start: 0.8179 (tm-30) cc_final: 0.7529 (mm110) REVERT: A 1031 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7676 (mt-10) REVERT: A 1059 PHE cc_start: 0.8015 (m-80) cc_final: 0.7657 (m-80) REVERT: A 1218 LYS cc_start: 0.8207 (ptpp) cc_final: 0.7651 (mmmt) REVERT: B 72 ASN cc_start: 0.7949 (m110) cc_final: 0.7234 (t0) REVERT: B 386 MET cc_start: 0.6296 (mtp) cc_final: 0.5891 (mtp) REVERT: B 504 ASP cc_start: 0.7834 (t0) cc_final: 0.7598 (t70) REVERT: B 518 LYS cc_start: 0.8322 (ttpp) cc_final: 0.7925 (tttt) REVERT: B 1047 ARG cc_start: 0.8468 (mpp-170) cc_final: 0.8135 (mtm-85) REVERT: B 1100 ILE cc_start: 0.8340 (mm) cc_final: 0.8063 (tp) REVERT: C 187 PHE cc_start: 0.9247 (OUTLIER) cc_final: 0.8373 (p90) REVERT: C 239 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.5980 (mt-10) REVERT: C 247 GLU cc_start: 0.7703 (mp0) cc_final: 0.7420 (mp0) REVERT: C 270 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7619 (ttt90) REVERT: E 160 LYS cc_start: 0.8175 (mmtt) cc_final: 0.7967 (tptt) REVERT: G 28 ARG cc_start: 0.7671 (ttm110) cc_final: 0.7199 (ttp-110) REVERT: G 60 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7429 (mt-10) REVERT: J 25 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8731 (mmtt) REVERT: J 59 LEU cc_start: 0.9217 (mp) cc_final: 0.8973 (mm) outliers start: 56 outliers final: 24 residues processed: 352 average time/residue: 1.4490 time to fit residues: 590.9159 Evaluate side-chains 325 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 294 time to evaluate : 3.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 651 SER Chi-restraints excluded: chain B residue 899 GLU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain J residue 25 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 265 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 204 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 274 optimal weight: 8.9990 chunk 164 optimal weight: 0.5980 chunk 99 optimal weight: 5.9990 chunk 262 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 GLN B 298 GLN B 431 HIS ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN S 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.141431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.108534 restraints weight = 31286.086| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.47 r_work: 0.3003 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 27313 Z= 0.216 Angle : 0.569 12.500 37056 Z= 0.298 Chirality : 0.046 0.198 4217 Planarity : 0.004 0.043 4569 Dihedral : 9.930 72.749 3930 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.38 % Allowed : 13.25 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.15), residues: 3191 helix: 0.66 (0.15), residues: 1193 sheet: -0.65 (0.24), residues: 460 loop : -0.80 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 365 HIS 0.008 0.001 HIS B 429 PHE 0.036 0.002 PHE A 938 TYR 0.018 0.002 TYR S 78 ARG 0.011 0.001 ARG E 51 Details of bonding type rmsd hydrogen bonds : bond 0.04394 ( 1164) hydrogen bonds : angle 4.68956 ( 3313) metal coordination : bond 0.00910 ( 16) metal coordination : angle 4.97211 ( 21) covalent geometry : bond 0.00523 (27297) covalent geometry : angle 0.55719 (37035) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 298 time to evaluate : 3.504 Fit side-chains REVERT: A 135 CYS cc_start: 0.1095 (OUTLIER) cc_final: 0.0312 (m) REVERT: A 175 LYS cc_start: 0.7534 (ptmt) cc_final: 0.7079 (ptmm) REVERT: A 238 GLN cc_start: 0.7189 (tt0) cc_final: 0.6614 (tp-100) REVERT: A 246 GLU cc_start: 0.8035 (tt0) cc_final: 0.7646 (mt-10) REVERT: A 264 TYR cc_start: 0.7015 (t80) cc_final: 0.6812 (p90) REVERT: A 807 MET cc_start: 0.8971 (mtt) cc_final: 0.8700 (mtm) REVERT: A 851 GLU cc_start: 0.8058 (pm20) cc_final: 0.7746 (mm-30) REVERT: A 898 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8406 (tp) REVERT: A 1031 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7759 (mt-10) REVERT: A 1218 LYS cc_start: 0.8273 (ptpp) cc_final: 0.7682 (mmmt) REVERT: B 72 ASN cc_start: 0.7923 (m110) cc_final: 0.7253 (t0) REVERT: B 383 ASN cc_start: 0.7654 (OUTLIER) cc_final: 0.7410 (t0) REVERT: B 386 MET cc_start: 0.6373 (mtp) cc_final: 0.6044 (mtp) REVERT: B 504 ASP cc_start: 0.7888 (t0) cc_final: 0.7657 (t70) REVERT: B 1047 ARG cc_start: 0.8462 (mpp-170) cc_final: 0.8122 (mtm-85) REVERT: B 1100 ILE cc_start: 0.8388 (mm) cc_final: 0.8103 (tp) REVERT: C 187 PHE cc_start: 0.9265 (OUTLIER) cc_final: 0.8432 (p90) REVERT: C 239 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6154 (mt-10) REVERT: C 247 GLU cc_start: 0.7638 (mp0) cc_final: 0.7342 (mp0) REVERT: C 270 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7600 (ttt90) REVERT: F 81 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.7962 (mt-10) REVERT: F 122 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: G 28 ARG cc_start: 0.7680 (ttm110) cc_final: 0.7278 (ttp-110) REVERT: G 49 GLU cc_start: 0.7626 (tp30) cc_final: 0.7254 (tp30) outliers start: 70 outliers final: 32 residues processed: 339 average time/residue: 1.4887 time to fit residues: 586.2316 Evaluate side-chains 323 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 282 time to evaluate : 3.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 651 SER Chi-restraints excluded: chain B residue 899 GLU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1161 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 122 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 120 optimal weight: 6.9990 chunk 127 optimal weight: 0.6980 chunk 174 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 228 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 212 optimal weight: 0.7980 chunk 305 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 chunk 241 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 GLN A 651 GLN A1116 GLN B 298 GLN C 171 ASN ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.142550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.109644 restraints weight = 31229.757| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.50 r_work: 0.3010 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 27313 Z= 0.155 Angle : 0.530 11.278 37056 Z= 0.277 Chirality : 0.044 0.188 4217 Planarity : 0.004 0.045 4569 Dihedral : 9.862 72.876 3930 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.62 % Allowed : 13.52 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.16 (0.15), residues: 3191 helix: 0.90 (0.15), residues: 1196 sheet: -0.56 (0.24), residues: 460 loop : -0.71 (0.15), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 365 HIS 0.006 0.001 HIS B 429 PHE 0.034 0.002 PHE A 938 TYR 0.020 0.001 TYR S 78 ARG 0.012 0.000 ARG E 51 Details of bonding type rmsd hydrogen bonds : bond 0.03968 ( 1164) hydrogen bonds : angle 4.56593 ( 3313) metal coordination : bond 0.00735 ( 16) metal coordination : angle 4.57168 ( 21) covalent geometry : bond 0.00370 (27297) covalent geometry : angle 0.51856 (37035) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 303 time to evaluate : 5.036 Fit side-chains revert: symmetry clash REVERT: A 135 CYS cc_start: 0.1456 (OUTLIER) cc_final: 0.0622 (m) REVERT: A 175 LYS cc_start: 0.7689 (ptmt) cc_final: 0.7237 (ptmm) REVERT: A 238 GLN cc_start: 0.7062 (tt0) cc_final: 0.6480 (tp-100) REVERT: A 246 GLU cc_start: 0.8032 (tt0) cc_final: 0.7475 (mt-10) REVERT: A 264 TYR cc_start: 0.7020 (t80) cc_final: 0.6816 (p90) REVERT: A 807 MET cc_start: 0.8939 (mtt) cc_final: 0.8680 (mtm) REVERT: A 851 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7719 (mm-30) REVERT: A 898 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8332 (tp) REVERT: A 940 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7540 (mm110) REVERT: A 1031 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7774 (mt-10) REVERT: A 1218 LYS cc_start: 0.8265 (ptpp) cc_final: 0.7662 (mmmt) REVERT: B 72 ASN cc_start: 0.7927 (m110) cc_final: 0.7235 (t0) REVERT: B 383 ASN cc_start: 0.7668 (OUTLIER) cc_final: 0.7357 (t0) REVERT: B 504 ASP cc_start: 0.7897 (t0) cc_final: 0.7676 (t70) REVERT: B 1047 ARG cc_start: 0.8456 (mpp-170) cc_final: 0.8126 (mtm-85) REVERT: B 1100 ILE cc_start: 0.8357 (mm) cc_final: 0.8114 (tp) REVERT: C 134 LYS cc_start: 0.7525 (mttt) cc_final: 0.7318 (ptpt) REVERT: C 187 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.8432 (p90) REVERT: C 239 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6131 (mt-10) REVERT: C 247 GLU cc_start: 0.7613 (mp0) cc_final: 0.7320 (mp0) REVERT: C 270 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7594 (ttt90) REVERT: E 18 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7729 (tp30) REVERT: F 122 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7240 (mp0) REVERT: G 28 ARG cc_start: 0.7632 (ttm110) cc_final: 0.7257 (ttp-110) REVERT: G 49 GLU cc_start: 0.7623 (tp30) cc_final: 0.7276 (tp30) REVERT: J 25 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8773 (mmtt) REVERT: S 120 TYR cc_start: 0.8718 (m-80) cc_final: 0.8518 (m-80) outliers start: 77 outliers final: 38 residues processed: 352 average time/residue: 2.1029 time to fit residues: 856.5268 Evaluate side-chains 338 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 289 time to evaluate : 5.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 851 GLU Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 651 SER Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 899 GLU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1161 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain J residue 25 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 4 optimal weight: 3.9990 chunk 249 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 chunk 60 optimal weight: 0.3980 chunk 193 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 GLN B 298 GLN B 958 ASN ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.138417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.104962 restraints weight = 31267.083| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.49 r_work: 0.2981 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 27313 Z= 0.238 Angle : 0.595 12.773 37056 Z= 0.310 Chirality : 0.047 0.203 4217 Planarity : 0.004 0.045 4569 Dihedral : 9.948 72.487 3930 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.68 % Allowed : 14.24 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.21 (0.15), residues: 3191 helix: 0.80 (0.15), residues: 1195 sheet: -0.56 (0.24), residues: 444 loop : -0.70 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 809 HIS 0.008 0.001 HIS B 429 PHE 0.037 0.002 PHE A 938 TYR 0.020 0.002 TYR S 78 ARG 0.013 0.001 ARG E 51 Details of bonding type rmsd hydrogen bonds : bond 0.04592 ( 1164) hydrogen bonds : angle 4.71401 ( 3313) metal coordination : bond 0.00927 ( 16) metal coordination : angle 4.73137 ( 21) covalent geometry : bond 0.00581 (27297) covalent geometry : angle 0.58394 (37035) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 291 time to evaluate : 8.022 Fit side-chains revert: symmetry clash REVERT: A 13 ASP cc_start: 0.8576 (p0) cc_final: 0.8118 (p0) REVERT: A 135 CYS cc_start: 0.1754 (OUTLIER) cc_final: 0.0779 (m) REVERT: A 175 LYS cc_start: 0.7712 (ptmt) cc_final: 0.7201 (ptmm) REVERT: A 238 GLN cc_start: 0.7218 (tt0) cc_final: 0.6611 (tp-100) REVERT: A 246 GLU cc_start: 0.8048 (tt0) cc_final: 0.7526 (mt-10) REVERT: A 807 MET cc_start: 0.8953 (mtt) cc_final: 0.8656 (mtm) REVERT: A 851 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7724 (mm-30) REVERT: A 898 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8445 (tp) REVERT: A 973 ASN cc_start: 0.8093 (m-40) cc_final: 0.7795 (m110) REVERT: A 1031 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7786 (mt-10) REVERT: A 1160 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8745 (ttp80) REVERT: A 1218 LYS cc_start: 0.8364 (ptpp) cc_final: 0.7732 (mmmt) REVERT: B 160 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7489 (mmmt) REVERT: B 504 ASP cc_start: 0.7947 (t0) cc_final: 0.7725 (t70) REVERT: B 814 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7699 (mt-10) REVERT: B 1043 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7847 (tm-30) REVERT: B 1047 ARG cc_start: 0.8462 (mpp-170) cc_final: 0.8119 (mtm-85) REVERT: C 130 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: C 187 PHE cc_start: 0.9293 (OUTLIER) cc_final: 0.8460 (p90) REVERT: C 239 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6137 (mt-10) REVERT: C 247 GLU cc_start: 0.7507 (mp0) cc_final: 0.7109 (mp0) REVERT: C 270 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7790 (ttt90) REVERT: F 122 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7314 (mp0) REVERT: G 28 ARG cc_start: 0.7748 (ttm110) cc_final: 0.7384 (ttp-110) REVERT: G 49 GLU cc_start: 0.7691 (tp30) cc_final: 0.7199 (tp30) outliers start: 79 outliers final: 42 residues processed: 342 average time/residue: 1.5306 time to fit residues: 608.3932 Evaluate side-chains 337 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 283 time to evaluate : 3.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 851 GLU Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1160 ARG Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 651 SER Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain B residue 899 GLU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1161 SER Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain S residue 40 LEU Chi-restraints excluded: chain S residue 118 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 51.862 > 50: distance: 79 - 86: 15.633 distance: 86 - 87: 18.772 distance: 87 - 88: 9.438 distance: 87 - 90: 15.647 distance: 88 - 89: 16.933 distance: 88 - 95: 26.596 distance: 90 - 91: 27.100 distance: 91 - 92: 18.034 distance: 92 - 93: 7.777 distance: 93 - 94: 6.733 distance: 95 - 96: 32.406 distance: 96 - 97: 16.677 distance: 97 - 98: 7.839 distance: 97 - 99: 7.942 distance: 99 - 100: 17.468 distance: 100 - 101: 6.504 distance: 100 - 103: 4.350 distance: 101 - 102: 12.888 distance: 101 - 109: 28.912 distance: 103 - 104: 5.123 distance: 104 - 105: 5.088 distance: 104 - 106: 4.881 distance: 105 - 107: 10.445 distance: 106 - 108: 9.363 distance: 107 - 108: 5.556 distance: 109 - 110: 8.581 distance: 110 - 111: 23.285 distance: 110 - 113: 21.839 distance: 111 - 112: 15.886 distance: 111 - 117: 20.021 distance: 113 - 114: 14.811 distance: 114 - 115: 17.653 distance: 114 - 116: 13.054 distance: 117 - 118: 26.318 distance: 118 - 119: 26.411 distance: 118 - 121: 12.730 distance: 119 - 120: 36.991 distance: 119 - 126: 6.751 distance: 121 - 122: 14.509 distance: 122 - 123: 22.512 distance: 123 - 124: 21.442 distance: 124 - 125: 7.026 distance: 126 - 127: 17.250 distance: 127 - 128: 8.453 distance: 127 - 130: 17.187 distance: 128 - 129: 13.578 distance: 128 - 137: 10.942 distance: 130 - 131: 14.897 distance: 131 - 132: 15.534 distance: 131 - 133: 9.815 distance: 132 - 134: 15.893 distance: 133 - 135: 9.344 distance: 134 - 136: 18.102 distance: 135 - 136: 18.360 distance: 137 - 138: 6.431 distance: 137 - 143: 19.729 distance: 138 - 139: 12.335 distance: 138 - 141: 23.760 distance: 139 - 144: 4.715 distance: 141 - 142: 20.942 distance: 142 - 143: 39.788 distance: 144 - 145: 5.787 distance: 145 - 146: 20.539 distance: 145 - 148: 17.713 distance: 146 - 147: 9.800 distance: 146 - 151: 43.393 distance: 148 - 149: 20.972 distance: 148 - 150: 14.083 distance: 151 - 152: 22.264 distance: 152 - 153: 9.244 distance: 152 - 155: 18.800 distance: 153 - 159: 25.503 distance: 155 - 156: 10.033 distance: 156 - 157: 16.408 distance: 156 - 158: 19.944 distance: 159 - 160: 17.045 distance: 160 - 161: 6.855 distance: 160 - 163: 18.562 distance: 161 - 162: 11.455 distance: 161 - 170: 6.929 distance: 163 - 164: 6.228 distance: 164 - 165: 8.628 distance: 165 - 167: 4.192 distance: 166 - 168: 4.486 distance: 167 - 169: 5.520 distance: 168 - 169: 8.940