Starting phenix.real_space_refine on Mon Sep 14 00:37:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rid_4889/09_2026/6rid_4889.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rid_4889/09_2026/6rid_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_4889/09_2026/6rid_4889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rid_4889/09_2026/6rid_4889.map" model { file = "/net/cci-nas-00/data/ceres_data/6rid_4889/09_2026/6rid_4889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rid_4889/09_2026/6rid_4889.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6rid_4889/09_2026/6rid_4889.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rid_4889/09_2026/6rid_4889.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.14s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'RNAv2': 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: 4.91, per 1000 atoms: 0.18 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: 2.08 Conformation dependent library (CDL) restraints added in 1.0 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: 3.25 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: 5.89 Time building geometry restraints manager: 2.73 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=" C3' DC T 33 " pdb=" C2' DC T 33 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C1' DC T 27 " pdb=" N1 DC T 27 " ideal model delta sigma weight residual 1.468 1.506 -0.038 1.40e-02 5.10e+03 7.45e+00 bond pdb=" C3' DT N 29 " pdb=" C2' DT N 29 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.41e+00 bond pdb=" C3' DC T 22 " pdb=" C2' DC T 22 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.01e+00 bond pdb=" C1' DT T 30 " pdb=" N1 DT T 30 " ideal model delta sigma weight residual 1.468 1.504 -0.036 1.40e-02 5.10e+03 6.71e+00 ... (remaining 27292 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 36413 2.49 - 4.98: 575 4.98 - 7.48: 39 7.48 - 9.97: 4 9.97 - 12.46: 4 Bond angle restraints: 37035 Sorted by residual: angle pdb=" O4' DC T 27 " pdb=" C4' DC T 27 " pdb=" C3' DC T 27 " ideal model delta sigma weight residual 106.00 102.35 3.65 6.00e-01 2.78e+00 3.71e+01 angle pdb=" C4' DC T 27 " pdb=" C3' DC T 27 " pdb=" C2' DC T 27 " ideal model delta sigma weight residual 103.10 99.10 4.00 9.00e-01 1.23e+00 1.98e+01 angle pdb=" N3 DT T 21 " pdb=" C4 DT T 21 " pdb=" O4 DT T 21 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT N 27 " pdb=" C4 DT N 27 " pdb=" O4 DT N 27 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" O4 DT N 27 " pdb=" C4 DT N 27 " pdb=" C5 DT N 27 " ideal model delta sigma weight residual 124.90 122.05 2.85 7.00e-01 2.04e+00 1.66e+01 ... (remaining 37030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 14794 17.58 - 35.16: 1374 35.16 - 52.74: 272 52.74 - 70.32: 50 70.32 - 87.90: 17 Dihedral angle restraints: 16507 sinusoidal: 6998 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=" O5' U P 24 " pdb=" C5' U P 24 " pdb=" C4' U P 24 " pdb=" C3' U P 24 " ideal model delta sinusoidal sigma weight residual 180.00 140.62 39.38 3 6.40e+00 2.44e-02 3.83e+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 ... (remaining 16504 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3464 0.068 - 0.137: 671 0.137 - 0.205: 60 0.205 - 0.274: 20 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: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 28.670 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 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= 0.290 Angle : 0.878 30.769 37056 Z= 0.455 Chirality : 0.055 0.342 4217 Planarity : 0.006 0.063 4569 Dihedral : 14.161 87.899 10365 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 3.54 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.007 0.001 ARG F 76 TYR 0.033 0.002 TYR B1015 PHE 0.049 0.002 PHE A 938 TRP 0.024 0.002 TRP A 131 HIS 0.009 0.001 HIS B 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.26 (27297) covalent geometry : angle 0.77175 / 0.45 (37035) hydrogen bonds : bond 0.14755 / 10.05 ( 1164) hydrogen bonds : angle 6.69792 / 4.67 ( 3313) metal coordination : bond 0.15426 / 12.23 ( 16) metal coordination : angle 17.58081 / 11.66 ( 21) *********************** 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 : 1.040 Fit side-chains revert: symmetry clash REVERT: A 13 ASP cc_start: 0.8418 (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: 0.6743 time to fit residues: 347.5261 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 : 0.977 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.4980 chunk 215 optimal weight: 0.0050 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.0980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.0970 chunk 298 optimal weight: 0.8980 overall best weight: 0.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN A 107 ASN A 232 ASN A 412 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 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: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.144978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.112115 restraints weight = 31374.885| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.46 r_work: 0.3053 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 27313 Z= 0.111 Angle : 0.563 15.122 37056 Z= 0.290 Chirality : 0.043 0.226 4217 Planarity : 0.004 0.048 4569 Dihedral : 9.415 59.092 3894 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.43 % Allowed : 10.64 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.14), residues: 3191 helix: -0.35 (0.14), residues: 1207 sheet: -0.96 (0.22), residues: 467 loop : -1.33 (0.15), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 51 TYR 0.015 0.001 TYR B1015 PHE 0.031 0.001 PHE A 938 TRP 0.015 0.001 TRP A 365 HIS 0.003 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (27297) covalent geometry : angle 0.53771 / 0.29 (37035) hydrogen bonds : bond 0.04161 / 2.75 ( 1164) hydrogen bonds : angle 5.01435 / 3.52 ( 3313) metal coordination : bond 0.01127 / 0.89 ( 16) metal coordination : angle 7.00726 / 4.51 ( 21) *********************** 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 387 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 345 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 13 ASP cc_start: 0.8594 (p0) cc_final: 0.8127 (p0) REVERT: A 16 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8095 (mt-10) REVERT: A 175 LYS cc_start: 0.7435 (ptmt) cc_final: 0.7084 (ptmm) REVERT: A 238 GLN cc_start: 0.6986 (tt0) cc_final: 0.6513 (tp-100) REVERT: A 600 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7259 (mm-30) REVERT: A 644 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8045 (mm-30) REVERT: A 807 MET cc_start: 0.8969 (mtt) cc_final: 0.8704 (mtm) REVERT: A 898 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8302 (tp) REVERT: A 1218 LYS cc_start: 0.8180 (ptpp) cc_final: 0.7636 (mmmt) REVERT: B 72 ASN cc_start: 0.7953 (m110) cc_final: 0.7293 (t0) REVERT: B 386 MET cc_start: 0.6244 (mtp) cc_final: 0.5842 (mtp) REVERT: B 980 LEU cc_start: 0.8073 (mt) cc_final: 0.7858 (mp) REVERT: B 1047 ARG cc_start: 0.8485 (mpp-170) cc_final: 0.8163 (mtm-85) REVERT: B 1100 ILE cc_start: 0.8342 (mm) cc_final: 0.7984 (tp) REVERT: C 239 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6103 (mt-10) REVERT: E 40 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7036 (mm-30) REVERT: E 160 LYS cc_start: 0.8298 (mmtt) cc_final: 0.8097 (tptt) REVERT: G 28 ARG cc_start: 0.7808 (ttm110) cc_final: 0.7480 (ttp-110) REVERT: G 47 LYS cc_start: 0.6749 (mttm) cc_final: 0.6359 (tmtt) REVERT: G 49 GLU cc_start: 0.7460 (tp30) cc_final: 0.7096 (tp30) REVERT: J 59 LEU cc_start: 0.9174 (mp) cc_final: 0.8933 (mm) REVERT: S 120 TYR cc_start: 0.8664 (m-80) cc_final: 0.8446 (m-80) outliers start: 42 outliers final: 16 residues processed: 369 average time/residue: 0.6365 time to fit residues: 272.0607 Evaluate side-chains 321 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 303 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 245 ILE 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 B residue 56 LEU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 899 GLU 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 11 optimal weight: 9.9990 chunk 87 optimal weight: 0.7980 chunk 134 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 201 optimal weight: 0.4980 chunk 5 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 196 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 651 GLN A 957 GLN A1116 GLN B 159 ASN B 298 GLN B 357 HIS C 171 ASN F 112 ASN ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN S 62 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.144334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.111584 restraints weight = 31332.726| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.52 r_work: 0.3044 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27313 Z= 0.133 Angle : 0.535 12.644 37056 Z= 0.278 Chirality : 0.044 0.229 4217 Planarity : 0.004 0.042 4569 Dihedral : 9.231 59.436 3892 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.90 % Allowed : 12.16 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.14), residues: 3191 helix: 0.35 (0.15), residues: 1205 sheet: -0.79 (0.23), residues: 467 loop : -1.04 (0.15), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 51 TYR 0.014 0.001 TYR B1015 PHE 0.035 0.001 PHE A 938 TRP 0.012 0.001 TRP A 365 HIS 0.004 0.001 HIS B 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (27297) covalent geometry : angle 0.51871 / 0.28 (37035) hydrogen bonds : bond 0.04035 / 2.65 ( 1164) hydrogen bonds : angle 4.75352 / 3.34 ( 3313) metal coordination : bond 0.00833 / 0.63 ( 16) metal coordination : angle 5.53804 / 3.63 ( 21) *********************** 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 365 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 309 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 13 ASP cc_start: 0.8449 (p0) cc_final: 0.7643 (p0) REVERT: A 16 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7778 (mt-10) REVERT: A 135 CYS cc_start: 0.0593 (OUTLIER) cc_final: 0.0157 (m) REVERT: A 175 LYS cc_start: 0.7417 (ptmt) cc_final: 0.7077 (ptmm) REVERT: A 238 GLN cc_start: 0.7018 (tt0) cc_final: 0.6505 (tp-100) REVERT: A 264 TYR cc_start: 0.7079 (t80) cc_final: 0.6796 (p90) REVERT: A 644 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8061 (mm-30) REVERT: A 807 MET cc_start: 0.8953 (mtt) cc_final: 0.8690 (mtm) REVERT: A 898 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8351 (tp) REVERT: A 1031 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7721 (mt-10) REVERT: A 1218 LYS cc_start: 0.8264 (ptpp) cc_final: 0.7742 (mmmt) REVERT: B 72 ASN cc_start: 0.7921 (m110) cc_final: 0.7228 (t0) REVERT: B 234 VAL cc_start: 0.9171 (OUTLIER) cc_final: 0.8969 (t) REVERT: B 386 MET cc_start: 0.6265 (mtp) cc_final: 0.5937 (mtp) REVERT: B 980 LEU cc_start: 0.8062 (mt) cc_final: 0.7831 (mp) REVERT: B 1047 ARG cc_start: 0.8491 (mpp-170) cc_final: 0.8159 (mtm-85) REVERT: B 1100 ILE cc_start: 0.8339 (mm) cc_final: 0.8007 (tp) REVERT: C 239 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.5960 (mt-10) REVERT: C 270 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7616 (ttt90) REVERT: E 160 LYS cc_start: 0.8188 (mmtt) cc_final: 0.7983 (tptt) REVERT: G 28 ARG cc_start: 0.7723 (ttm110) cc_final: 0.7260 (ttp-110) REVERT: G 47 LYS cc_start: 0.6862 (mttm) cc_final: 0.6368 (tmtt) REVERT: G 49 GLU cc_start: 0.7488 (tp30) cc_final: 0.7127 (tp30) REVERT: J 25 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8723 (mmtt) REVERT: J 59 LEU cc_start: 0.9196 (mp) cc_final: 0.8949 (mm) REVERT: S 89 ARG cc_start: 0.8897 (ttt-90) cc_final: 0.8684 (ttt-90) outliers start: 56 outliers final: 24 residues processed: 339 average time/residue: 0.6418 time to fit residues: 252.2433 Evaluate side-chains 332 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 301 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 415 ASP 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 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 162 SER Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 899 GLU 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 126 SER Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain F residue 139 VAL 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 145 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 317 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 292 optimal weight: 3.9990 chunk 273 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 130 optimal weight: 0.0170 overall best weight: 1.7224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 651 GLN B 298 GLN B 431 HIS F 112 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.141645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.108293 restraints weight = 31365.350| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.43 r_work: 0.3002 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1519 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= 0.222 Angle : 0.589 12.702 37056 Z= 0.306 Chirality : 0.046 0.233 4217 Planarity : 0.004 0.042 4569 Dihedral : 9.257 59.580 3892 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.34 % Allowed : 12.74 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.14), residues: 3191 helix: 0.54 (0.15), residues: 1200 sheet: -0.69 (0.23), residues: 468 loop : -0.90 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 51 TYR 0.019 0.002 TYR E 8 PHE 0.038 0.002 PHE A 938 TRP 0.011 0.002 TRP A 365 HIS 0.009 0.001 HIS B 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.22 (27297) covalent geometry : angle 0.57677 / 0.31 (37035) hydrogen bonds : bond 0.04478 / 2.93 ( 1164) hydrogen bonds : angle 4.76208 / 3.35 ( 3313) metal coordination : bond 0.00921 / 0.71 ( 16) metal coordination : angle 5.01103 / 3.19 ( 21) *********************** 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 370 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 301 time to evaluate : 1.123 Fit side-chains REVERT: A 135 CYS cc_start: 0.0911 (OUTLIER) cc_final: 0.0223 (m) REVERT: A 175 LYS cc_start: 0.7508 (ptmt) cc_final: 0.7074 (ptmm) REVERT: A 238 GLN cc_start: 0.7157 (tt0) cc_final: 0.6607 (tp-100) REVERT: A 246 GLU cc_start: 0.8095 (tt0) cc_final: 0.7432 (mt-10) REVERT: A 644 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8041 (mm-30) REVERT: A 807 MET cc_start: 0.8940 (mtt) cc_final: 0.8667 (mtm) REVERT: A 898 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8475 (tp) REVERT: A 1031 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7785 (mt-10) REVERT: A 1218 LYS cc_start: 0.8335 (ptpp) cc_final: 0.7754 (mmmt) REVERT: B 72 ASN cc_start: 0.7932 (m110) cc_final: 0.7262 (t0) REVERT: B 234 VAL cc_start: 0.9177 (OUTLIER) cc_final: 0.8975 (t) REVERT: B 386 MET cc_start: 0.6410 (mtp) cc_final: 0.6069 (mtp) REVERT: B 980 LEU cc_start: 0.8178 (mt) cc_final: 0.7938 (mp) REVERT: B 1047 ARG cc_start: 0.8472 (mpp-170) cc_final: 0.8129 (mtm-85) REVERT: B 1100 ILE cc_start: 0.8326 (mm) cc_final: 0.7992 (tp) REVERT: C 187 PHE cc_start: 0.9282 (OUTLIER) cc_final: 0.8445 (p90) REVERT: C 239 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6099 (mt-10) REVERT: C 270 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7811 (ttt90) REVERT: F 81 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8011 (mt-10) REVERT: F 112 ASN cc_start: 0.9017 (OUTLIER) cc_final: 0.8788 (p0) REVERT: G 28 ARG cc_start: 0.7620 (ttm110) cc_final: 0.7216 (ttp-110) REVERT: S 89 ARG cc_start: 0.8913 (ttt-90) cc_final: 0.8683 (ttt-90) outliers start: 69 outliers final: 35 residues processed: 336 average time/residue: 0.7042 time to fit residues: 274.3871 Evaluate side-chains 333 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 289 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 MET 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 343 ASN 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 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 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 234 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 612 ASP Chi-restraints excluded: chain B residue 651 SER Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 899 GLU Chi-restraints excluded: chain B residue 1027 THR 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 136 THR 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 112 ASN Chi-restraints excluded: chain F residue 139 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 250 optimal weight: 0.0870 chunk 276 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 253 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 208 optimal weight: 1.9990 chunk 199 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 137 optimal weight: 0.7980 chunk 304 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 651 GLN B 298 GLN C 171 ASN F 112 ASN ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 ASN ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN S 62 ASN S 73 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.143729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.111114 restraints weight = 31186.818| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.48 r_work: 0.3030 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1634 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= 0.116 Angle : 0.517 10.835 37056 Z= 0.270 Chirality : 0.043 0.227 4217 Planarity : 0.003 0.040 4569 Dihedral : 9.181 59.847 3892 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.04 % Allowed : 13.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.15), residues: 3191 helix: 0.87 (0.15), residues: 1200 sheet: -0.58 (0.23), residues: 467 loop : -0.76 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 51 TYR 0.020 0.001 TYR S 78 PHE 0.029 0.001 PHE A 938 TRP 0.013 0.001 TRP A 365 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (27297) covalent geometry : angle 0.50509 / 0.27 (37035) hydrogen bonds : bond 0.03773 / 2.47 ( 1164) hydrogen bonds : angle 4.57986 / 3.22 ( 3313) metal coordination : bond 0.00668 / 0.52 ( 16) metal coordination : angle 4.59773 / 3.00 ( 21) *********************** 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 373 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 313 time to evaluate : 1.048 Fit side-chains REVERT: A 135 CYS cc_start: 0.0966 (OUTLIER) cc_final: 0.0448 (m) REVERT: A 175 LYS cc_start: 0.7450 (ptmt) cc_final: 0.7043 (ptmm) REVERT: A 238 GLN cc_start: 0.7080 (tt0) cc_final: 0.6525 (tp-100) REVERT: A 246 GLU cc_start: 0.8091 (tt0) cc_final: 0.7464 (mt-10) REVERT: A 644 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8047 (mm-30) REVERT: A 807 MET cc_start: 0.8889 (mtt) cc_final: 0.8627 (mtm) REVERT: A 898 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8348 (tp) REVERT: A 940 GLN cc_start: 0.8202 (tm-30) cc_final: 0.7583 (mm110) REVERT: A 1031 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: A 1218 LYS cc_start: 0.8273 (ptpp) cc_final: 0.7721 (mmmt) REVERT: B 72 ASN cc_start: 0.7938 (m110) cc_final: 0.7290 (t0) REVERT: B 234 VAL cc_start: 0.9171 (OUTLIER) cc_final: 0.8964 (t) REVERT: B 386 MET cc_start: 0.6490 (mtp) cc_final: 0.6081 (mtp) REVERT: B 1047 ARG cc_start: 0.8466 (mpp-170) cc_final: 0.8139 (mtm-85) REVERT: B 1100 ILE cc_start: 0.8354 (mm) cc_final: 0.8075 (tp) REVERT: C 130 GLU cc_start: 0.8025 (tt0) cc_final: 0.7822 (tm-30) REVERT: C 187 PHE cc_start: 0.9259 (OUTLIER) cc_final: 0.8428 (p90) REVERT: C 239 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6053 (mt-10) REVERT: C 270 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7629 (ttt90) REVERT: F 81 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.7943 (mt-10) REVERT: G 28 ARG cc_start: 0.7642 (ttm110) cc_final: 0.7267 (ttp-110) REVERT: G 49 GLU cc_start: 0.7532 (tp30) cc_final: 0.7136 (tp30) REVERT: J 25 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8777 (mmtt) REVERT: J 59 LEU cc_start: 0.9230 (mp) cc_final: 0.8992 (mm) outliers start: 60 outliers final: 28 residues processed: 346 average time/residue: 0.6926 time to fit residues: 278.1811 Evaluate side-chains 328 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 291 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 517 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 798 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 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 234 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 677 VAL 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 193 MET 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 182 SER Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 112 ASN 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 55 optimal weight: 1.9990 chunk 89 optimal weight: 0.1980 chunk 132 optimal weight: 0.8980 chunk 216 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 307 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 302 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 651 GLN B 298 GLN F 112 ASN ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 ASN ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.143965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.110922 restraints weight = 31168.359| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.43 r_work: 0.3052 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27313 Z= 0.119 Angle : 0.514 10.472 37056 Z= 0.268 Chirality : 0.043 0.216 4217 Planarity : 0.003 0.044 4569 Dihedral : 9.163 58.929 3892 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.11 % Allowed : 14.07 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.15), residues: 3191 helix: 1.01 (0.15), residues: 1206 sheet: -0.52 (0.23), residues: 457 loop : -0.65 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 51 TYR 0.021 0.001 TYR S 78 PHE 0.031 0.001 PHE A 938 TRP 0.012 0.001 TRP A 365 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (27297) covalent geometry : angle 0.50253 / 0.27 (37035) hydrogen bonds : bond 0.03694 / 2.41 ( 1164) hydrogen bonds : angle 4.50288 / 3.17 ( 3313) metal coordination : bond 0.00653 / 0.51 ( 16) metal coordination : angle 4.49202 / 2.94 ( 21) *********************** 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 360 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 298 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: A 135 CYS cc_start: 0.0993 (OUTLIER) cc_final: 0.0463 (m) REVERT: A 175 LYS cc_start: 0.7555 (ptmt) cc_final: 0.7132 (ptmm) REVERT: A 238 GLN cc_start: 0.7042 (tt0) cc_final: 0.6475 (tp-100) REVERT: A 246 GLU cc_start: 0.7916 (tt0) cc_final: 0.7404 (mt-10) REVERT: A 644 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8031 (mm-30) REVERT: A 807 MET cc_start: 0.8867 (mtt) cc_final: 0.8615 (mtm) REVERT: A 898 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8336 (tp) REVERT: A 940 GLN cc_start: 0.8179 (tm-30) cc_final: 0.7541 (mm110) REVERT: A 1031 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7654 (mt-10) REVERT: A 1218 LYS cc_start: 0.8237 (ptpp) cc_final: 0.7658 (mmmt) REVERT: B 72 ASN cc_start: 0.7918 (m110) cc_final: 0.7250 (t0) REVERT: B 234 VAL cc_start: 0.9122 (OUTLIER) cc_final: 0.8921 (t) REVERT: B 386 MET cc_start: 0.6353 (mtp) cc_final: 0.5961 (mtp) REVERT: B 1047 ARG cc_start: 0.8429 (mpp-170) cc_final: 0.8111 (mtm-85) REVERT: B 1100 ILE cc_start: 0.8374 (mm) cc_final: 0.8105 (tp) REVERT: C 130 GLU cc_start: 0.8013 (tt0) cc_final: 0.7796 (tm-30) REVERT: C 134 LYS cc_start: 0.7554 (mptt) cc_final: 0.7345 (ptpt) REVERT: C 187 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.8428 (p90) REVERT: C 239 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6084 (mt-10) REVERT: C 270 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7588 (ttt90) REVERT: G 28 ARG cc_start: 0.7551 (ttm110) cc_final: 0.7196 (ttp-110) REVERT: G 49 GLU cc_start: 0.7572 (tp30) cc_final: 0.7202 (tp30) REVERT: J 25 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8775 (mmtt) REVERT: J 59 LEU cc_start: 0.9227 (mp) cc_final: 0.8987 (mm) outliers start: 62 outliers final: 35 residues processed: 334 average time/residue: 0.7034 time to fit residues: 271.6410 Evaluate side-chains 336 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 293 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 155 LEU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 517 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 798 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 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 234 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 369 LEU 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 C residue 175 THR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain J residue 25 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 216 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 193 optimal weight: 3.9990 chunk 254 optimal weight: 0.0470 chunk 307 optimal weight: 0.7980 chunk 234 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 HIS A 459 GLN A 651 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 = 0.3633 r_free = 0.3633 target = 0.144303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.111662 restraints weight = 30956.920| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.47 r_work: 0.3039 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27313 Z= 0.115 Angle : 0.504 9.913 37056 Z= 0.263 Chirality : 0.043 0.209 4217 Planarity : 0.003 0.047 4569 Dihedral : 9.113 59.606 3892 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.97 % Allowed : 14.78 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.15), residues: 3191 helix: 1.13 (0.15), residues: 1208 sheet: -0.44 (0.23), residues: 459 loop : -0.57 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 51 TYR 0.022 0.001 TYR S 78 PHE 0.030 0.001 PHE A 938 TRP 0.012 0.001 TRP A 365 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (27297) covalent geometry : angle 0.49428 / 0.26 (37035) hydrogen bonds : bond 0.03586 / 2.35 ( 1164) hydrogen bonds : angle 4.43136 / 3.12 ( 3313) metal coordination : bond 0.00616 / 0.48 ( 16) metal coordination : angle 4.17642 / 2.73 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 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 362 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 304 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: A 135 CYS cc_start: 0.1058 (OUTLIER) cc_final: 0.0443 (m) REVERT: A 175 LYS cc_start: 0.7522 (ptmt) cc_final: 0.7100 (ptmm) REVERT: A 238 GLN cc_start: 0.7079 (tt0) cc_final: 0.6544 (tp-100) REVERT: A 246 GLU cc_start: 0.7911 (tt0) cc_final: 0.7439 (mt-10) REVERT: A 644 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8062 (mm-30) REVERT: A 807 MET cc_start: 0.8865 (mtt) cc_final: 0.8623 (mtm) REVERT: A 898 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8342 (tp) REVERT: A 940 GLN cc_start: 0.8206 (tm-30) cc_final: 0.7595 (mm110) REVERT: A 1031 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7754 (mt-10) REVERT: A 1218 LYS cc_start: 0.8184 (ptpp) cc_final: 0.7649 (mmmt) REVERT: B 72 ASN cc_start: 0.7937 (m110) cc_final: 0.7272 (t0) REVERT: B 234 VAL cc_start: 0.9132 (OUTLIER) cc_final: 0.8922 (t) REVERT: B 256 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8741 (tpt) REVERT: B 386 MET cc_start: 0.6383 (mtp) cc_final: 0.5977 (mtp) REVERT: B 1047 ARG cc_start: 0.8437 (mpp-170) cc_final: 0.8139 (mtm-85) REVERT: B 1100 ILE cc_start: 0.8370 (mm) cc_final: 0.8134 (tp) REVERT: C 130 GLU cc_start: 0.7990 (tt0) cc_final: 0.7706 (tm-30) REVERT: C 187 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.8442 (p90) REVERT: C 270 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7585 (ttt90) REVERT: F 81 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.7948 (mt-10) REVERT: F 122 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: G 28 ARG cc_start: 0.7575 (ttm110) cc_final: 0.7211 (ttp-110) REVERT: G 49 GLU cc_start: 0.7580 (tp30) cc_final: 0.7213 (tp30) REVERT: J 25 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8790 (mmtt) REVERT: J 59 LEU cc_start: 0.9234 (mp) cc_final: 0.8993 (mm) outliers start: 58 outliers final: 32 residues processed: 334 average time/residue: 0.7129 time to fit residues: 275.2383 Evaluate side-chains 336 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 294 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 473 ASP Chi-restraints excluded: chain A residue 517 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 798 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 1025 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 234 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 369 LEU 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 C residue 175 THR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 270 ARG 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 Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain J residue 25 LYS Chi-restraints excluded: chain S residue 40 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 138 optimal weight: 4.9990 chunk 237 optimal weight: 4.9990 chunk 258 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 306 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 297 optimal weight: 4.9990 chunk 307 optimal weight: 0.9980 chunk 251 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3581 r_free = 0.3581 target = 0.139987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.106392 restraints weight = 31268.910| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.48 r_work: 0.2991 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 27313 Z= 0.221 Angle : 0.589 12.055 37056 Z= 0.306 Chirality : 0.047 0.212 4217 Planarity : 0.004 0.045 4569 Dihedral : 9.202 59.312 3892 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.04 % Allowed : 15.22 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.15), residues: 3191 helix: 0.95 (0.15), residues: 1200 sheet: -0.50 (0.24), residues: 455 loop : -0.63 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 51 TYR 0.021 0.002 TYR S 78 PHE 0.038 0.002 PHE A 938 TRP 0.010 0.002 TRP A 809 HIS 0.007 0.001 HIS B 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.22 (27297) covalent geometry : angle 0.58018 / 0.31 (37035) hydrogen bonds : bond 0.04382 / 2.87 ( 1164) hydrogen bonds : angle 4.61865 / 3.25 ( 3313) metal coordination : bond 0.00848 / 0.65 ( 16) metal coordination : angle 4.36027 / 2.72 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 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 354 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 294 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: A 13 ASP cc_start: 0.8549 (p0) cc_final: 0.8099 (p0) REVERT: A 135 CYS cc_start: 0.1767 (OUTLIER) cc_final: 0.0815 (m) REVERT: A 175 LYS cc_start: 0.7561 (ptmt) cc_final: 0.7103 (ptmm) REVERT: A 238 GLN cc_start: 0.7209 (tt0) cc_final: 0.6635 (tp-100) REVERT: A 246 GLU cc_start: 0.8048 (tt0) cc_final: 0.7585 (mt-10) REVERT: A 644 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8043 (mm-30) REVERT: A 807 MET cc_start: 0.8915 (mtt) cc_final: 0.8643 (mtm) REVERT: A 898 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8493 (tp) REVERT: A 1031 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7819 (mt-10) REVERT: A 1218 LYS cc_start: 0.8284 (ptpp) cc_final: 0.7726 (mmmt) REVERT: B 383 ASN cc_start: 0.7566 (OUTLIER) cc_final: 0.7211 (t0) REVERT: B 386 MET cc_start: 0.6506 (mtp) cc_final: 0.6092 (mtp) REVERT: B 1043 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7875 (tm-30) REVERT: B 1047 ARG cc_start: 0.8452 (mpp-170) cc_final: 0.8119 (mtm-85) REVERT: B 1100 ILE cc_start: 0.8364 (mm) cc_final: 0.8115 (tp) REVERT: C 130 GLU cc_start: 0.7998 (tt0) cc_final: 0.7684 (tm-30) REVERT: C 187 PHE cc_start: 0.9278 (OUTLIER) cc_final: 0.8446 (p90) REVERT: C 270 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7808 (ttt90) REVERT: F 122 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: G 28 ARG cc_start: 0.7616 (ttm110) cc_final: 0.7303 (ttp-110) REVERT: G 49 GLU cc_start: 0.7679 (tp30) cc_final: 0.7374 (tp30) REVERT: J 25 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8748 (mmtt) outliers start: 60 outliers final: 35 residues processed: 326 average time/residue: 0.6943 time to fit residues: 261.7444 Evaluate side-chains 331 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 288 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 1031 GLU Chi-restraints excluded: chain A residue 1099 SER 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 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 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 F residue 139 VAL Chi-restraints excluded: chain J residue 25 LYS Chi-restraints excluded: chain S residue 40 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 25 optimal weight: 0.8980 chunk 174 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 273 optimal weight: 4.9990 chunk 270 optimal weight: 1.9990 chunk 306 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 315 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.140268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.106750 restraints weight = 31182.636| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.47 r_work: 0.2998 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 27313 Z= 0.195 Angle : 0.566 11.756 37056 Z= 0.295 Chirality : 0.046 0.223 4217 Planarity : 0.004 0.047 4569 Dihedral : 9.202 58.997 3892 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.77 % Allowed : 15.53 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.15), residues: 3191 helix: 0.96 (0.15), residues: 1199 sheet: -0.47 (0.24), residues: 455 loop : -0.62 (0.15), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 51 TYR 0.022 0.002 TYR S 78 PHE 0.036 0.002 PHE A 938 TRP 0.011 0.001 TRP A 365 HIS 0.006 0.001 HIS B 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 (27297) covalent geometry : angle 0.55656 / 0.29 (37035) hydrogen bonds : bond 0.04216 / 2.76 ( 1164) hydrogen bonds : angle 4.60130 / 3.24 ( 3313) metal coordination : bond 0.00786 / 0.59 ( 16) metal coordination : angle 4.29124 / 2.67 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 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 345 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 293 time to evaluate : 1.149 Fit side-chains revert: symmetry clash REVERT: A 13 ASP cc_start: 0.8553 (p0) cc_final: 0.8109 (p0) REVERT: A 135 CYS cc_start: 0.2387 (OUTLIER) cc_final: 0.1564 (m) REVERT: A 175 LYS cc_start: 0.7638 (ptmt) cc_final: 0.7188 (ptmm) REVERT: A 238 GLN cc_start: 0.7181 (tt0) cc_final: 0.6586 (tp-100) REVERT: A 246 GLU cc_start: 0.8050 (tt0) cc_final: 0.7574 (mt-10) REVERT: A 644 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8051 (mm-30) REVERT: A 807 MET cc_start: 0.8900 (mtt) cc_final: 0.8630 (mtm) REVERT: A 851 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7782 (mm-30) REVERT: A 898 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8393 (tp) REVERT: A 973 ASN cc_start: 0.8060 (m-40) cc_final: 0.7758 (m110) REVERT: A 1031 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7844 (mt-10) REVERT: A 1218 LYS cc_start: 0.8272 (ptpp) cc_final: 0.7703 (mmmt) REVERT: B 72 ASN cc_start: 0.7971 (m110) cc_final: 0.7293 (t0) REVERT: B 383 ASN cc_start: 0.7552 (OUTLIER) cc_final: 0.7182 (t0) REVERT: B 386 MET cc_start: 0.6498 (mtp) cc_final: 0.6099 (mtp) REVERT: B 1047 ARG cc_start: 0.8465 (mpp-170) cc_final: 0.8130 (mtm-85) REVERT: B 1100 ILE cc_start: 0.8351 (mm) cc_final: 0.8113 (tp) REVERT: C 130 GLU cc_start: 0.7955 (tt0) cc_final: 0.7632 (tm-30) REVERT: C 134 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7845 (ptpt) REVERT: C 187 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.8477 (p90) REVERT: C 270 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7738 (ttt90) REVERT: F 122 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7322 (mp0) REVERT: G 28 ARG cc_start: 0.7606 (ttm110) cc_final: 0.7269 (ttp-110) REVERT: G 49 GLU cc_start: 0.7656 (tp30) cc_final: 0.7174 (tp30) REVERT: J 25 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8756 (mmtt) outliers start: 52 outliers final: 35 residues processed: 324 average time/residue: 0.6883 time to fit residues: 258.9026 Evaluate side-chains 333 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 288 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 370 VAL Chi-restraints excluded: chain A residue 473 ASP 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 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 1099 SER Chi-restraints excluded: chain A residue 1183 ASP 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 C residue 134 LYS Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 270 ARG 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 Chi-restraints excluded: chain S residue 40 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 231 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 156 optimal weight: 0.9980 chunk 226 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 chunk 294 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 651 GLN B 298 GLN ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3584 r_free = 0.3584 target = 0.140270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.106806 restraints weight = 31069.615| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.48 r_work: 0.2989 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 27313 Z= 0.203 Angle : 0.577 12.025 37056 Z= 0.300 Chirality : 0.046 0.223 4217 Planarity : 0.004 0.046 4569 Dihedral : 9.226 59.720 3892 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.77 % Allowed : 15.70 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.15), residues: 3191 helix: 0.94 (0.15), residues: 1201 sheet: -0.47 (0.24), residues: 455 loop : -0.61 (0.15), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 51 TYR 0.022 0.002 TYR S 78 PHE 0.036 0.002 PHE A 938 TRP 0.011 0.001 TRP A 809 HIS 0.006 0.001 HIS B 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.20 (27297) covalent geometry : angle 0.56799 / 0.30 (37035) hydrogen bonds : bond 0.04294 / 2.81 ( 1164) hydrogen bonds : angle 4.62481 / 3.25 ( 3313) metal coordination : bond 0.00797 / 0.60 ( 16) metal coordination : angle 4.27262 / 2.64 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 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 347 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 295 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: A 13 ASP cc_start: 0.8548 (p0) cc_final: 0.8113 (p0) REVERT: A 135 CYS cc_start: 0.2455 (OUTLIER) cc_final: 0.1602 (m) REVERT: A 175 LYS cc_start: 0.7661 (ptmt) cc_final: 0.7189 (ptmm) REVERT: A 238 GLN cc_start: 0.7188 (tt0) cc_final: 0.6580 (tp-100) REVERT: A 246 GLU cc_start: 0.8055 (tt0) cc_final: 0.7576 (mt-10) REVERT: A 644 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8095 (mm-30) REVERT: A 807 MET cc_start: 0.8902 (mtt) cc_final: 0.8636 (mtm) REVERT: A 851 GLU cc_start: 0.8029 (pm20) cc_final: 0.7765 (mm-30) REVERT: A 898 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8443 (tp) REVERT: A 973 ASN cc_start: 0.8075 (m-40) cc_final: 0.7763 (m110) REVERT: A 1031 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7873 (mt-10) REVERT: A 1218 LYS cc_start: 0.8296 (ptpp) cc_final: 0.7702 (mmmt) REVERT: B 72 ASN cc_start: 0.7963 (m110) cc_final: 0.7278 (t0) REVERT: B 298 GLN cc_start: 0.6955 (tt0) cc_final: 0.6531 (tp40) REVERT: B 386 MET cc_start: 0.6494 (mtp) cc_final: 0.6146 (mtp) REVERT: B 1047 ARG cc_start: 0.8464 (mpp-170) cc_final: 0.8129 (mtm-85) REVERT: B 1100 ILE cc_start: 0.8376 (mm) cc_final: 0.8152 (tp) REVERT: C 130 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7593 (tm-30) REVERT: C 134 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7907 (ptpt) REVERT: C 187 PHE cc_start: 0.9277 (OUTLIER) cc_final: 0.8478 (p90) REVERT: C 270 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7802 (ttt90) REVERT: F 122 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7346 (mp0) REVERT: G 28 ARG cc_start: 0.7654 (ttm110) cc_final: 0.7331 (ttp-110) REVERT: G 38 ARG cc_start: 0.6068 (mtt90) cc_final: 0.5772 (mtt90) REVERT: G 49 GLU cc_start: 0.7606 (tp30) cc_final: 0.7078 (tp30) REVERT: J 25 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8745 (mmtt) REVERT: S 101 LYS cc_start: 0.6948 (mttt) cc_final: 0.6606 (pptt) outliers start: 52 outliers final: 36 residues processed: 327 average time/residue: 0.7112 time to fit residues: 269.8259 Evaluate side-chains 335 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 291 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 370 VAL Chi-restraints excluded: chain A residue 473 ASP 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 798 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 1025 LEU Chi-restraints excluded: chain A residue 1099 SER Chi-restraints excluded: chain A residue 1183 ASP 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 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 C residue 130 GLU Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 270 ARG 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 Chi-restraints excluded: chain S residue 40 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 135 optimal weight: 3.9990 chunk 195 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 226 optimal weight: 1.9990 chunk 196 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 316 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 299 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 651 GLN ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.141262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.108052 restraints weight = 31014.597| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.45 r_work: 0.3019 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27313 Z= 0.170 Angle : 0.552 11.565 37056 Z= 0.288 Chirality : 0.045 0.223 4217 Planarity : 0.004 0.046 4569 Dihedral : 9.205 59.727 3892 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.70 % Allowed : 15.90 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.15), residues: 3191 helix: 1.03 (0.15), residues: 1203 sheet: -0.49 (0.24), residues: 460 loop : -0.58 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 51 TYR 0.023 0.002 TYR S 78 PHE 0.034 0.002 PHE A 938 TRP 0.012 0.001 TRP A 365 HIS 0.005 0.001 HIS B 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (27297) covalent geometry : angle 0.54357 / 0.29 (37035) hydrogen bonds : bond 0.04081 / 2.67 ( 1164) hydrogen bonds : angle 4.56827 / 3.21 ( 3313) metal coordination : bond 0.00713 / 0.54 ( 16) metal coordination : angle 4.14386 / 2.56 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8999.88 seconds wall clock time: 154 minutes 21.58 seconds (9261.58 seconds total)