Starting phenix.real_space_refine on Mon Sep 14 12:33:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6omf_20090/09_2026/6omf_20090.cif Found real_map, /net/cci-nas-00/data/ceres_data/6omf_20090/09_2026/6omf_20090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6omf_20090/09_2026/6omf_20090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6omf_20090/09_2026/6omf_20090.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6omf_20090/09_2026/6omf_20090.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6omf_20090/09_2026/6omf_20090.cif" model { file = "/net/cci-nas-00/data/ceres_data/6omf_20090/09_2026/6omf_20090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6omf_20090/09_2026/6omf_20090.cif" } resolution = 3.26 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= 0.001 sd= 0.097 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 91 5.49 5 Mg 1 5.21 5 S 113 5.16 5 C 18704 2.51 5 N 5356 2.21 5 O 5984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s 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: 30251 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1806 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain: "B" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1714 Classifications: {'peptide': 223} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain breaks: 1 Chain: "C" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1281} Chain: "D" Number of atoms: 10382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10382 Classifications: {'peptide': 1336} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1279} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 2244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2244 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 270} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "J" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1024 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 7, 'TRANS': 119} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "T" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 876 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain breaks: 1 Chain: "N" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1008 Classifications: {'DNA': 49} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 48} Chain breaks: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14536 SG CYS D 70 76.782 56.932 39.310 1.00130.61 S ATOM 14550 SG CYS D 72 75.342 53.700 39.036 1.00135.78 S ATOM 14658 SG CYS D 85 75.580 55.675 35.979 1.00130.37 S ATOM 14682 SG CYS D 88 72.765 56.876 39.407 1.00132.90 S ATOM 20370 SG CYS D 814 113.580 111.847 46.036 1.00123.43 S ATOM 20935 SG CYS D 888 111.052 109.530 48.012 1.00119.80 S ATOM 20986 SG CYS D 895 114.938 108.672 48.811 1.00114.70 S ATOM 21007 SG CYS D 898 113.371 111.890 49.704 1.00114.60 S Time building chain proxies: 5.23, per 1000 atoms: 0.17 Number of scatterers: 30251 At special positions: 0 Unit cell: (176.8, 183.3, 145.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 113 16.00 P 91 15.00 Mg 1 11.99 O 5984 8.00 N 5356 7.00 C 18704 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: 2.41 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " Number of angles added : 12 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6690 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 54 sheets defined 38.5% alpha, 14.9% beta 38 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 3.47 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.719A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.955A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'B' and resid 34 through 49 removed outlier: 3.523A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.981A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.591A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 39 removed outlier: 3.545A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.811A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 removed outlier: 3.757A pdb=" N PHE C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.604A pdb=" N ARG C 247 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.653A pdb=" N ILE C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 removed outlier: 3.563A pdb=" N ALA C 293 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 290 through 294' Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 4.251A pdb=" N ALA C 381 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU C 382 " --> pdb=" O ARG C 378 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 481 removed outlier: 3.752A pdb=" N ARG C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.540A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 528 Processing helix chain 'C' and resid 607 through 612 Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 703 through 711 removed outlier: 4.462A pdb=" N ALA C 707 " --> pdb=" O GLY C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 826 Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.636A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 942 through 979 Processing helix chain 'C' and resid 987 through 992 Processing helix chain 'C' and resid 996 through 1000 removed outlier: 3.692A pdb=" N LEU C1000 " --> pdb=" O TRP C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1007 through 1038 removed outlier: 4.179A pdb=" N GLN C1013 " --> pdb=" O ASN C1009 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU C1026 " --> pdb=" O LYS C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.180A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.816A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.844A pdb=" N LEU C1151 " --> pdb=" O ARG C1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 Processing helix chain 'C' and resid 1167 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1281 Processing helix chain 'C' and resid 1284 through 1293 Processing helix chain 'C' and resid 1297 through 1309 removed outlier: 4.218A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS C1303 " --> pdb=" O ASN C1299 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1331 removed outlier: 3.559A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 33 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.913A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG D 98 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.600A pdb=" N SER D 119 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 194 through 208 Processing helix chain 'D' and resid 210 through 230 Processing helix chain 'D' and resid 233 through 236 removed outlier: 3.732A pdb=" N TRP D 236 " --> pdb=" O LYS D 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 233 through 236' Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 264 through 285 removed outlier: 3.567A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 307 removed outlier: 3.524A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU D 301 " --> pdb=" O ARG D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 removed outlier: 3.561A pdb=" N ILE D 331 " --> pdb=" O ALA D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 377 Processing helix chain 'D' and resid 377 through 386 Processing helix chain 'D' and resid 393 through 404 removed outlier: 3.585A pdb=" N ALA D 397 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 416 removed outlier: 3.531A pdb=" N LEU D 412 " --> pdb=" O VAL D 408 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP D 413 " --> pdb=" O TRP D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 removed outlier: 3.596A pdb=" N LEU D 478 " --> pdb=" O LEU D 474 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG D 481 " --> pdb=" O GLN D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 531 through 539 Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 598 through 603 removed outlier: 3.529A pdb=" N SER D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 612 Processing helix chain 'D' and resid 614 through 634 removed outlier: 3.831A pdb=" N PHE D 620 " --> pdb=" O PRO D 616 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP D 622 " --> pdb=" O VAL D 618 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN D 623 " --> pdb=" O ILE D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.852A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 removed outlier: 3.597A pdb=" N VAL D 661 " --> pdb=" O ALA D 657 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA D 662 " --> pdb=" O GLU D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 702 removed outlier: 3.858A pdb=" N ASN D 680 " --> pdb=" O GLY D 676 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP D 691 " --> pdb=" O ALA D 687 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 694 " --> pdb=" O ASN D 690 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP D 699 " --> pdb=" O LYS D 695 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASN D 700 " --> pdb=" O ALA D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 775 Processing helix chain 'D' and resid 776 through 804 removed outlier: 3.546A pdb=" N GLY D 782 " --> pdb=" O GLY D 778 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA D 784 " --> pdb=" O ARG D 780 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 Processing helix chain 'D' and resid 865 through 876 removed outlier: 4.184A pdb=" N LEU D 871 " --> pdb=" O GLN D 867 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 872 " --> pdb=" O TRP D 868 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 900 removed outlier: 3.601A pdb=" N GLY D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 896 through 900' Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.907A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER D 922 " --> pdb=" O ILE D 918 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE D 923 " --> pdb=" O ALA D 919 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 930 removed outlier: 3.701A pdb=" N LEU D 930 " --> pdb=" O GLY D 927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1145 removed outlier: 3.689A pdb=" N VAL D1141 " --> pdb=" O GLY D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1225 Processing helix chain 'D' and resid 1225 through 1242 removed outlier: 3.567A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG D1231 " --> pdb=" O HIS D1227 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL D1234 " --> pdb=" O THR D1230 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 removed outlier: 3.883A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1281 through 1295 removed outlier: 3.578A pdb=" N ASN D1289 " --> pdb=" O VAL D1285 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG D1290 " --> pdb=" O LYS D1286 " (cutoff:3.500A) Processing helix chain 'D' and resid 1318 through 1324 removed outlier: 3.524A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.839A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR D1333 " --> pdb=" O THR D1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 1347 through 1354 Processing helix chain 'D' and resid 1361 through 1373 removed outlier: 4.549A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS D1366 " --> pdb=" O GLY D1362 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 32 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 77 Processing helix chain 'F' and resid 56 through 65 Processing helix chain 'F' and resid 72 through 84 Processing helix chain 'F' and resid 87 through 98 removed outlier: 3.563A pdb=" N ARG F 91 " --> pdb=" O ASP F 87 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN F 98 " --> pdb=" O MET F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 109 removed outlier: 4.028A pdb=" N ARG F 108 " --> pdb=" O LYS F 104 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR F 109 " --> pdb=" O ILE F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 133 removed outlier: 3.543A pdb=" N GLY F 126 " --> pdb=" O GLU F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 161 removed outlier: 3.925A pdb=" N TYR F 145 " --> pdb=" O ARG F 141 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TRP F 148 " --> pdb=" O THR F 144 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TRP F 149 " --> pdb=" O TYR F 145 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA F 157 " --> pdb=" O THR F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 190 removed outlier: 4.421A pdb=" N HIS F 187 " --> pdb=" O ARG F 183 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS F 188 " --> pdb=" O GLU F 184 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU F 189 " --> pdb=" O LEU F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 203 Processing helix chain 'F' and resid 205 through 215 Processing helix chain 'F' and resid 233 through 238 removed outlier: 3.719A pdb=" N ILE F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 266 removed outlier: 3.670A pdb=" N ASP F 253 " --> pdb=" O THR F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 279 removed outlier: 3.520A pdb=" N VAL F 273 " --> pdb=" O LYS F 269 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE F 278 " --> pdb=" O LEU F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 295 Processing helix chain 'F' and resid 298 through 320 removed outlier: 3.558A pdb=" N GLN F 320 " --> pdb=" O ILE F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 329 Processing helix chain 'J' and resid 10 through 20 removed outlier: 3.820A pdb=" N LYS J 14 " --> pdb=" O SER J 10 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY J 20 " --> pdb=" O PHE J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 114 Processing helix chain 'J' and resid 123 through 127 removed outlier: 3.968A pdb=" N ASP J 126 " --> pdb=" O ASP J 123 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 3.991A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.946A pdb=" N TYR A 177 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.559A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.575A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 15 through 16 removed outlier: 3.526A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR B 27 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET B 205 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 15 through 16 removed outlier: 3.526A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR B 27 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET B 205 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 99 through 101 removed outlier: 6.642A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY B 151 " --> pdb=" O MET B 51 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N MET B 51 " --> pdb=" O GLY B 151 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 99 through 101 Processing sheet with id=AB1, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AB2, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AB3, first strand: chain 'B' and resid 109 through 111 removed outlier: 7.070A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.426A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 59 through 60 removed outlier: 7.144A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET C 124 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 143 through 145 Processing sheet with id=AB7, first strand: chain 'C' and resid 147 through 148 removed outlier: 6.347A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AB9, first strand: chain 'C' and resid 230 through 231 Processing sheet with id=AC1, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.833A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AC3, first strand: chain 'C' and resid 599 through 606 removed outlier: 5.267A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 616 through 617 removed outlier: 3.623A pdb=" N PHE C 645 " --> pdb=" O VAL C 634 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS C 636 " --> pdb=" O SER C 643 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.664A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.804A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC8, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC9, first strand: chain 'C' and resid 816 through 819 removed outlier: 6.947A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA C1067 " --> pdb=" O LEU C1233 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 816 through 819 removed outlier: 6.947A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA C1067 " --> pdb=" O LEU C1233 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 846 through 847 removed outlier: 3.870A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASP C 842 " --> pdb=" O VAL C1046 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL C1046 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.804A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 887 through 889 Processing sheet with id=AD5, first strand: chain 'C' and resid 1087 through 1088 Processing sheet with id=AD6, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 5.921A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 7.510A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AD9, first strand: chain 'C' and resid 1335 through 1340 Processing sheet with id=AE1, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.165A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.397A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.174A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AE3, first strand: chain 'D' and resid 254 through 255 removed outlier: 3.545A pdb=" N ARG D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AE5, first strand: chain 'D' and resid 553 through 556 removed outlier: 3.728A pdb=" N GLU D 554 " --> pdb=" O LYS D 566 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AE7, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE8, first strand: chain 'D' and resid 821 through 822 Processing sheet with id=AE9, first strand: chain 'D' and resid 949 through 951 removed outlier: 3.501A pdb=" N ILE D 950 " --> pdb=" O ALA D1018 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 991 through 996 removed outlier: 4.366A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AF3, first strand: chain 'D' and resid 1025 through 1026 Processing sheet with id=AF4, first strand: chain 'D' and resid 1087 through 1088 removed outlier: 4.361A pdb=" N ILE D1080 " --> pdb=" O VAL D1088 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 1046 through 1048 removed outlier: 3.696A pdb=" N VAL D1107 " --> pdb=" O LEU D1059 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 1189 through 1191 removed outlier: 6.529A pdb=" N LYS D1172 " --> pdb=" O GLU D1168 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLU D1168 " --> pdb=" O LYS D1172 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ARG D1174 " --> pdb=" O GLY D1166 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 1266 through 1268 removed outlier: 6.808A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 34 through 41 removed outlier: 6.502A pdb=" N PHE J 34 " --> pdb=" O LEU J 60 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU J 60 " --> pdb=" O PHE J 34 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ASP J 36 " --> pdb=" O MET J 58 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N MET J 58 " --> pdb=" O ASP J 36 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU J 38 " --> pdb=" O TRP J 56 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N TRP J 56 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE J 53 " --> pdb=" O PHE J 76 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 34 through 41 removed outlier: 6.502A pdb=" N PHE J 34 " --> pdb=" O LEU J 60 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU J 60 " --> pdb=" O PHE J 34 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ASP J 36 " --> pdb=" O MET J 58 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N MET J 58 " --> pdb=" O ASP J 36 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU J 38 " --> pdb=" O TRP J 56 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N TRP J 56 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU J 59 " --> pdb=" O ARG J 70 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG J 70 " --> pdb=" O GLU J 59 " (cutoff:3.500A) 1092 hydrogen bonds defined for protein. 3102 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 94 hydrogen bonds 188 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 7.04 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 5073 1.27 - 1.40: 7169 1.40 - 1.53: 17919 1.53 - 1.67: 547 1.67 - 1.80: 196 Bond restraints: 30904 Sorted by residual: bond pdb=" CA GLN D 300 " pdb=" C GLN D 300 " ideal model delta sigma weight residual 1.523 1.371 0.152 1.34e-02 5.57e+03 1.29e+02 bond pdb=" CA ALA D 305 " pdb=" C ALA D 305 " ideal model delta sigma weight residual 1.521 1.432 0.088 9.90e-03 1.02e+04 7.97e+01 bond pdb=" C ALA D 302 " pdb=" O ALA D 302 " ideal model delta sigma weight residual 1.237 1.134 0.103 1.19e-02 7.06e+03 7.47e+01 bond pdb=" CA ALA D 302 " pdb=" CB ALA D 302 " ideal model delta sigma weight residual 1.528 1.397 0.131 1.59e-02 3.96e+03 6.80e+01 bond pdb=" C ASP D 304 " pdb=" O ASP D 304 " ideal model delta sigma weight residual 1.235 1.133 0.103 1.26e-02 6.30e+03 6.65e+01 ... (remaining 30899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 41424 3.14 - 6.27: 628 6.27 - 9.41: 75 9.41 - 12.54: 8 12.54 - 15.68: 6 Bond angle restraints: 42141 Sorted by residual: angle pdb=" N ALA D 305 " pdb=" CA ALA D 305 " pdb=" C ALA D 305 " ideal model delta sigma weight residual 112.93 102.82 10.11 1.33e+00 5.65e-01 5.78e+01 angle pdb=" N GLU D 301 " pdb=" CA GLU D 301 " pdb=" C GLU D 301 " ideal model delta sigma weight residual 113.88 105.30 8.58 1.23e+00 6.61e-01 4.87e+01 angle pdb=" C LEU D 903 " pdb=" N ALA D 904 " pdb=" CA ALA D 904 " ideal model delta sigma weight residual 121.54 134.35 -12.81 1.91e+00 2.74e-01 4.50e+01 angle pdb=" C GLN D 300 " pdb=" CA GLN D 300 " pdb=" CB GLN D 300 " ideal model delta sigma weight residual 110.42 97.69 12.73 1.99e+00 2.53e-01 4.09e+01 angle pdb=" N VAL D1240 " pdb=" CA VAL D1240 " pdb=" C VAL D1240 " ideal model delta sigma weight residual 111.90 106.91 4.99 8.10e-01 1.52e+00 3.79e+01 ... (remaining 42136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 17666 35.79 - 71.58: 1026 71.58 - 107.36: 45 107.36 - 143.15: 2 143.15 - 178.94: 4 Dihedral angle restraints: 18743 sinusoidal: 8351 harmonic: 10392 Sorted by residual: dihedral pdb=" CA GLN D1326 " pdb=" C GLN D1326 " pdb=" N GLU D1327 " pdb=" CA GLU D1327 " ideal model delta harmonic sigma weight residual -180.00 -136.00 -44.00 0 5.00e+00 4.00e-02 7.74e+01 dihedral pdb=" CA GLU A 7 " pdb=" C GLU A 7 " pdb=" N PHE A 8 " pdb=" CA PHE A 8 " ideal model delta harmonic sigma weight residual 180.00 144.40 35.60 0 5.00e+00 4.00e-02 5.07e+01 dihedral pdb=" CA ASP C 485 " pdb=" C ASP C 485 " pdb=" N THR C 486 " pdb=" CA THR C 486 " ideal model delta harmonic sigma weight residual -180.00 -145.60 -34.40 0 5.00e+00 4.00e-02 4.73e+01 ... (remaining 18740 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 4283 0.092 - 0.185: 488 0.185 - 0.277: 22 0.277 - 0.369: 2 0.369 - 0.462: 2 Chirality restraints: 4797 Sorted by residual: chirality pdb=" CA ASP D 304 " pdb=" N ASP D 304 " pdb=" C ASP D 304 " pdb=" CB ASP D 304 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.33e+00 chirality pdb=" CA GLU D 301 " pdb=" N GLU D 301 " pdb=" C GLU D 301 " pdb=" CB GLU D 301 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" CB VAL D1027 " pdb=" CA VAL D1027 " pdb=" CG1 VAL D1027 " pdb=" CG2 VAL D1027 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 4794 not shown) Planarity restraints: 5196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 485 " 0.016 2.00e-02 2.50e+03 3.35e-02 1.13e+01 pdb=" C ASP C 485 " -0.058 2.00e-02 2.50e+03 pdb=" O ASP C 485 " 0.022 2.00e-02 2.50e+03 pdb=" N THR C 486 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D1326 " 0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C GLN D1326 " -0.057 2.00e-02 2.50e+03 pdb=" O GLN D1326 " 0.022 2.00e-02 2.50e+03 pdb=" N GLU D1327 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 749 " -0.050 5.00e-02 4.00e+02 7.48e-02 8.95e+00 pdb=" N PRO D 750 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO D 750 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 750 " -0.041 5.00e-02 4.00e+02 ... (remaining 5193 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 173 2.42 - 3.04: 17570 3.04 - 3.66: 48373 3.66 - 4.28: 70542 4.28 - 4.90: 114774 Nonbonded interactions: 251432 Sorted by model distance: nonbonded pdb=" O ASP A 233 " pdb=" OE1 GLU A 235 " model vdw 1.800 3.040 nonbonded pdb=" O LEU D 299 " pdb=" N ALA D 302 " model vdw 1.853 3.120 nonbonded pdb=" NE2 GLN D 300 " pdb=" OD2 ASP D 304 " model vdw 1.854 3.120 nonbonded pdb=" O GLN D 300 " pdb=" NE2 GLN D 300 " model vdw 1.896 3.120 nonbonded pdb=" O LEU D 299 " pdb=" N GLU D 301 " model vdw 2.040 3.120 ... (remaining 251427 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 158 or resid 167 through 233)) selection = (chain 'B' and resid 5 through 233) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.530 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 31.200 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 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 : 0.012 0.184 30912 Z= 0.603 Angle : 1.071 25.481 42153 Z= 0.632 Chirality : 0.059 0.462 4797 Planarity : 0.007 0.075 5196 Dihedral : 19.649 178.938 12053 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.20 % Favored : 92.63 % Rotamer: Outliers : 12.34 % Allowed : 13.94 % Favored : 73.72 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -4.28 (0.11), residues: 3596 helix: -2.83 (0.10), residues: 1302 sheet: -3.09 (0.21), residues: 465 loop : -2.75 (0.12), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 28 TYR 0.026 0.003 TYR C1251 PHE 0.027 0.003 PHE D 57 TRP 0.012 0.002 TRP C 807 HIS 0.018 0.002 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.01173 / 0.60 (30904) covalent geometry : angle 1.05169 / 0.63 (42141) hydrogen bonds : bond 0.19124 / 13.14 ( 1170) hydrogen bonds : angle 8.27950 / 5.81 ( 3290) metal coordination : bond 0.11636 / 5.62 ( 8) metal coordination : angle 12.18525 / 6.78 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 379 poor density : 519 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7724 (tp40) REVERT: A 145 LYS cc_start: 0.8283 (tttt) cc_final: 0.7776 (tttp) REVERT: A 199 ASP cc_start: 0.7516 (m-30) cc_final: 0.7079 (m-30) REVERT: A 212 ASP cc_start: 0.6370 (OUTLIER) cc_final: 0.5939 (t0) REVERT: A 215 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6703 (mm-30) REVERT: A 223 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7660 (mt) REVERT: B 10 LYS cc_start: 0.8373 (mttp) cc_final: 0.7986 (mppt) REVERT: B 25 LYS cc_start: 0.7423 (tttt) cc_final: 0.7119 (ttmm) REVERT: B 68 TYR cc_start: 0.8324 (p90) cc_final: 0.8026 (p90) REVERT: B 125 LYS cc_start: 0.7579 (tttt) cc_final: 0.7318 (ttpt) REVERT: B 145 LYS cc_start: 0.8037 (tttt) cc_final: 0.7607 (tttp) REVERT: B 147 GLN cc_start: 0.6350 (tt0) cc_final: 0.6105 (mt0) REVERT: B 200 LYS cc_start: 0.7856 (tttt) cc_final: 0.7186 (ttpp) REVERT: B 205 MET cc_start: 0.7568 (ttp) cc_final: 0.7019 (ttt) REVERT: C 36 GLN cc_start: 0.7529 (tt0) cc_final: 0.7203 (tt0) REVERT: C 60 GLN cc_start: 0.6214 (OUTLIER) cc_final: 0.5885 (mt0) REVERT: C 62 TYR cc_start: 0.8226 (OUTLIER) cc_final: 0.7771 (m-80) REVERT: C 118 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7910 (mtmm) REVERT: C 130 MET cc_start: 0.8416 (ttm) cc_final: 0.8138 (ttp) REVERT: C 161 LYS cc_start: 0.8584 (mttt) cc_final: 0.8050 (pttm) REVERT: C 203 LYS cc_start: 0.8365 (mtmt) cc_final: 0.7846 (mttt) REVERT: C 237 LEU cc_start: 0.6440 (mp) cc_final: 0.6232 (mp) REVERT: C 241 LEU cc_start: 0.8862 (tp) cc_final: 0.8009 (pp) REVERT: C 244 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8785 (pm20) REVERT: C 246 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7095 (tp) REVERT: C 295 LYS cc_start: 0.6415 (mmtt) cc_final: 0.6076 (mmmt) REVERT: C 297 VAL cc_start: 0.8003 (OUTLIER) cc_final: 0.7672 (p) REVERT: C 315 MET cc_start: 0.8724 (ttm) cc_final: 0.8124 (ttm) REVERT: C 334 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7657 (pt0) REVERT: C 407 ARG cc_start: 0.7728 (ttp80) cc_final: 0.7494 (ttp80) REVERT: C 412 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7584 (mm-30) REVERT: C 441 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7945 (mm-30) REVERT: C 446 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.7939 (m-30) REVERT: C 504 GLU cc_start: 0.8656 (tt0) cc_final: 0.8155 (tm-30) REVERT: C 538 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.6916 (pp) REVERT: C 546 GLU cc_start: 0.7466 (mt-10) cc_final: 0.6873 (mp0) REVERT: C 568 ASN cc_start: 0.7980 (OUTLIER) cc_final: 0.7567 (p0) REVERT: C 681 MET cc_start: 0.6567 (mtt) cc_final: 0.6107 (mtt) REVERT: C 737 ASN cc_start: 0.6328 (m-40) cc_final: 0.6036 (m110) REVERT: C 805 MET cc_start: 0.8476 (ptm) cc_final: 0.8250 (ptt) REVERT: C 814 ASP cc_start: 0.8232 (m-30) cc_final: 0.7987 (m-30) REVERT: C 1023 HIS cc_start: 0.7991 (t70) cc_final: 0.7489 (t70) REVERT: C 1073 LYS cc_start: 0.8425 (pttt) cc_final: 0.8113 (pttp) REVERT: C 1137 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6758 (mt-10) REVERT: C 1142 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.6634 (ttm110) REVERT: D 140 TYR cc_start: 0.8545 (m-80) cc_final: 0.7862 (m-10) REVERT: D 155 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7060 (tt0) REVERT: D 200 GLN cc_start: 0.8444 (mm-40) cc_final: 0.7938 (tm-30) REVERT: D 322 ARG cc_start: 0.8494 (mtp85) cc_final: 0.8031 (ptt90) REVERT: D 399 LYS cc_start: 0.7702 (mtpt) cc_final: 0.7443 (mttp) REVERT: D 422 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8022 (mp) REVERT: D 425 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.6566 (ttp-110) REVERT: D 458 ASN cc_start: 0.9184 (t0) cc_final: 0.8714 (t0) REVERT: D 466 MET cc_start: 0.8463 (mtp) cc_final: 0.8055 (mtm) REVERT: D 484 MET cc_start: 0.8658 (mtp) cc_final: 0.8365 (mtp) REVERT: D 508 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6767 (tp) REVERT: D 599 LYS cc_start: 0.7588 (mppt) cc_final: 0.7306 (mppt) REVERT: D 610 ARG cc_start: 0.7835 (mmt-90) cc_final: 0.7443 (mtm110) REVERT: D 612 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8074 (mt) REVERT: D 665 GLN cc_start: 0.8075 (tp-100) cc_final: 0.7817 (mm-40) REVERT: D 708 ASN cc_start: 0.8079 (OUTLIER) cc_final: 0.7665 (p0) REVERT: D 731 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.8099 (tpt-90) REVERT: D 798 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7114 (ttp80) REVERT: D 918 ILE cc_start: 0.7337 (OUTLIER) cc_final: 0.6847 (pt) REVERT: D 1025 MET cc_start: 0.7455 (tpt) cc_final: 0.7176 (tpt) REVERT: D 1149 ARG cc_start: 0.8381 (mmm160) cc_final: 0.7671 (tpp-160) REVERT: D 1172 LYS cc_start: 0.6957 (mmtm) cc_final: 0.6114 (mmpt) REVERT: D 1174 ARG cc_start: 0.6729 (mtt-85) cc_final: 0.6472 (mtt-85) REVERT: D 1317 GLU cc_start: 0.5460 (tm-30) cc_final: 0.5194 (tm-30) REVERT: D 1345 ARG cc_start: 0.8217 (mtp85) cc_final: 0.7950 (ttm-80) REVERT: E 55 GLU cc_start: 0.7163 (tt0) cc_final: 0.6661 (tt0) REVERT: E 62 GLN cc_start: 0.8387 (tp-100) cc_final: 0.8019 (tp-100) REVERT: E 70 GLN cc_start: 0.8462 (tt0) cc_final: 0.8257 (tt0) REVERT: F 59 GLN cc_start: 0.6995 (mp10) cc_final: 0.6657 (mp10) REVERT: F 64 GLU cc_start: 0.8392 (tp30) cc_final: 0.8145 (tp30) REVERT: F 67 TYR cc_start: 0.7692 (m-80) cc_final: 0.7138 (m-10) REVERT: F 92 ARG cc_start: 0.7986 (ttm110) cc_final: 0.7660 (ttt-90) REVERT: F 96 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7667 (mt-10) REVERT: F 216 ASN cc_start: 0.8090 (t0) cc_final: 0.7874 (t0) REVERT: F 224 THR cc_start: 0.7675 (OUTLIER) cc_final: 0.7274 (p) REVERT: F 240 ASP cc_start: 0.7843 (t0) cc_final: 0.7148 (t0) REVERT: F 243 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.7076 (tt0) REVERT: F 256 LYS cc_start: 0.7907 (mttt) cc_final: 0.7658 (mmtm) REVERT: F 269 LYS cc_start: 0.8583 (tppt) cc_final: 0.8333 (tppt) REVERT: J 11 ARG cc_start: 0.8715 (mtt180) cc_final: 0.8467 (ptp-170) REVERT: J 24 ARG cc_start: 0.7517 (mmt90) cc_final: 0.7267 (tpp80) REVERT: J 37 CYS cc_start: 0.7998 (t) cc_final: 0.7701 (t) REVERT: J 54 TRP cc_start: 0.8217 (m100) cc_final: 0.7913 (m100) REVERT: J 56 TRP cc_start: 0.6753 (p-90) cc_final: 0.5118 (p-90) REVERT: J 72 GLN cc_start: 0.7433 (mt0) cc_final: 0.7010 (mt0) REVERT: J 101 ARG cc_start: 0.7835 (ttm110) cc_final: 0.7336 (mtt90) outliers start: 379 outliers final: 188 residues processed: 845 average time/residue: 0.2078 time to fit residues: 276.6637 Evaluate side-chains 576 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 362 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 446 ASP Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 759 SER Chi-restraints excluded: chain C residue 770 CYS Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1022 LYS Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1137 GLU Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1142 ARG Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1247 SER Chi-restraints excluded: chain C residue 1250 SER Chi-restraints excluded: chain C residue 1252 SER Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain C residue 1341 ASP Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 425 ARG Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 731 ARG Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 798 ARG Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 875 ASN Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 992 LYS Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1028 ILE Chi-restraints excluded: chain D residue 1111 ASP Chi-restraints excluded: chain D residue 1135 THR Chi-restraints excluded: chain D residue 1164 SER Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1219 ASP Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1268 ASN Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 267 ASN Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 58 MET Chi-restraints excluded: chain J residue 71 TYR Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 104 HIS Chi-restraints excluded: chain J residue 129 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN B 84 ASN B 186 ASN C 69 GLN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN C 258 ASN C 276 GLN C 510 GLN C 513 GLN C 649 GLN C 856 ASN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS C1220 GLN C1324 ASN D 157 GLN D 294 ASN D 340 GLN D 365 GLN D 720 ASN D 771 GLN D 817 HIS D 954 ASN D1019 ASN D1126 GLN D1195 GLN D1235 ASN D1289 ASN E 31 GLN F 160 ASN F 170 HIS ** F 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 320 GLN J 63 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.150322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.098468 restraints weight = 43620.174| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.09 r_work: 0.3172 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30912 Z= 0.167 Angle : 0.701 13.863 42153 Z= 0.371 Chirality : 0.047 0.327 4797 Planarity : 0.005 0.056 5196 Dihedral : 19.215 173.279 5355 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.23 % Favored : 93.72 % Rotamer: Outliers : 7.16 % Allowed : 18.04 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.02 (0.12), residues: 3596 helix: -1.27 (0.13), residues: 1328 sheet: -2.96 (0.21), residues: 432 loop : -2.31 (0.13), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 81 TYR 0.022 0.001 TYR A 177 PHE 0.027 0.002 PHE D 988 TRP 0.012 0.001 TRP C 997 HIS 0.013 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (30904) covalent geometry : angle 0.69321 / 0.37 (42141) hydrogen bonds : bond 0.04922 / 3.44 ( 1170) hydrogen bonds : angle 5.63636 / 3.83 ( 3290) metal coordination : bond 0.01342 / 0.61 ( 8) metal coordination : angle 6.31222 / 3.78 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 419 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8235 (mm-40) cc_final: 0.8021 (tp40) REVERT: A 120 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.7953 (p0) REVERT: A 145 LYS cc_start: 0.8659 (tttt) cc_final: 0.8234 (tttm) REVERT: A 182 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.8044 (mtm110) REVERT: A 212 ASP cc_start: 0.6828 (OUTLIER) cc_final: 0.6349 (t0) REVERT: A 223 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7838 (mt) REVERT: B 10 LYS cc_start: 0.8647 (mttp) cc_final: 0.8132 (mppt) REVERT: B 51 MET cc_start: 0.7712 (ttt) cc_final: 0.7133 (ttp) REVERT: B 71 LYS cc_start: 0.6111 (tppt) cc_final: 0.5766 (tppt) REVERT: B 125 LYS cc_start: 0.7544 (tttt) cc_final: 0.7066 (tppt) REVERT: B 145 LYS cc_start: 0.7626 (tttt) cc_final: 0.7340 (tttt) REVERT: B 200 LYS cc_start: 0.8155 (tttt) cc_final: 0.7766 (ttpp) REVERT: C 31 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.6534 (mm110) REVERT: C 36 GLN cc_start: 0.7738 (tt0) cc_final: 0.7399 (tt0) REVERT: C 130 MET cc_start: 0.8753 (ttm) cc_final: 0.8439 (ttp) REVERT: C 161 LYS cc_start: 0.8521 (mttt) cc_final: 0.8044 (pttm) REVERT: C 189 ASP cc_start: 0.7941 (m-30) cc_final: 0.7544 (m-30) REVERT: C 203 LYS cc_start: 0.8605 (mtmt) cc_final: 0.8380 (mttm) REVERT: C 241 LEU cc_start: 0.8862 (tp) cc_final: 0.8075 (pp) REVERT: C 244 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8909 (pm20) REVERT: C 246 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7111 (tp) REVERT: C 315 MET cc_start: 0.8811 (ttm) cc_final: 0.8403 (ttm) REVERT: C 334 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7555 (pt0) REVERT: C 369 MET cc_start: 0.8726 (ttp) cc_final: 0.8059 (tmm) REVERT: C 424 ASP cc_start: 0.7774 (m-30) cc_final: 0.7449 (m-30) REVERT: C 446 ASP cc_start: 0.8371 (m-30) cc_final: 0.8055 (m-30) REVERT: C 456 VAL cc_start: 0.8162 (t) cc_final: 0.7959 (t) REVERT: C 459 MET cc_start: 0.8292 (mtp) cc_final: 0.8091 (mtp) REVERT: C 504 GLU cc_start: 0.8661 (tt0) cc_final: 0.8397 (tm-30) REVERT: C 510 GLN cc_start: 0.8044 (tp40) cc_final: 0.7759 (tp-100) REVERT: C 516 ASP cc_start: 0.7270 (p0) cc_final: 0.7060 (p0) REVERT: C 538 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.7040 (pp) REVERT: C 542 ARG cc_start: 0.8283 (mtt180) cc_final: 0.7282 (ptp-170) REVERT: C 546 GLU cc_start: 0.7710 (mt-10) cc_final: 0.6988 (mp0) REVERT: C 704 MET cc_start: 0.7849 (mmm) cc_final: 0.7078 (tpp) REVERT: C 737 ASN cc_start: 0.6620 (m-40) cc_final: 0.6365 (m110) REVERT: C 788 SER cc_start: 0.8344 (OUTLIER) cc_final: 0.7970 (p) REVERT: C 805 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8379 (ptp) REVERT: C 814 ASP cc_start: 0.8762 (m-30) cc_final: 0.8509 (m-30) REVERT: C 1023 HIS cc_start: 0.7716 (t70) cc_final: 0.7256 (t70) REVERT: C 1073 LYS cc_start: 0.8554 (pttt) cc_final: 0.8321 (pttp) REVERT: C 1085 MET cc_start: 0.8620 (mmt) cc_final: 0.8153 (mmt) REVERT: C 1157 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.6900 (pp30) REVERT: C 1174 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7287 (mt-10) REVERT: D 29 MET cc_start: 0.7129 (ttm) cc_final: 0.6850 (ttm) REVERT: D 39 LYS cc_start: 0.8854 (mtmt) cc_final: 0.8615 (mtmm) REVERT: D 140 TYR cc_start: 0.8758 (m-80) cc_final: 0.8403 (m-10) REVERT: D 200 GLN cc_start: 0.8451 (mm-40) cc_final: 0.7937 (tm-30) REVERT: D 304 ASP cc_start: 0.7933 (m-30) cc_final: 0.7711 (m-30) REVERT: D 322 ARG cc_start: 0.8677 (mtp85) cc_final: 0.8100 (ptt90) REVERT: D 399 LYS cc_start: 0.7809 (mtpt) cc_final: 0.7403 (mttp) REVERT: D 422 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8082 (mp) REVERT: D 458 ASN cc_start: 0.9148 (t0) cc_final: 0.8820 (t0) REVERT: D 484 MET cc_start: 0.9198 (mtp) cc_final: 0.8936 (mtp) REVERT: D 578 ILE cc_start: 0.8263 (mt) cc_final: 0.8037 (mt) REVERT: D 610 ARG cc_start: 0.8138 (mmt-90) cc_final: 0.7524 (mtm110) REVERT: D 747 MET cc_start: 0.8172 (mmt) cc_final: 0.7891 (mmt) REVERT: D 765 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8118 (mt-10) REVERT: D 905 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6548 (mpt180) REVERT: D 918 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7259 (pt) REVERT: D 954 ASN cc_start: 0.6899 (OUTLIER) cc_final: 0.6657 (t0) REVERT: D 992 LYS cc_start: 0.6078 (OUTLIER) cc_final: 0.5521 (pttm) REVERT: D 1149 ARG cc_start: 0.8467 (mmm160) cc_final: 0.7764 (tpp-160) REVERT: D 1172 LYS cc_start: 0.7073 (mmtm) cc_final: 0.5678 (mmpt) REVERT: D 1174 ARG cc_start: 0.6763 (mtt-85) cc_final: 0.6547 (mtt-85) REVERT: D 1262 ARG cc_start: 0.7226 (mtp180) cc_final: 0.6867 (mtp-110) REVERT: D 1284 ARG cc_start: 0.8293 (ttp80) cc_final: 0.8082 (mtp180) REVERT: D 1345 ARG cc_start: 0.8609 (mtp85) cc_final: 0.8339 (ttm110) REVERT: D 1368 ASP cc_start: 0.6843 (OUTLIER) cc_final: 0.5781 (m-30) REVERT: E 3 ARG cc_start: 0.8020 (tpp-160) cc_final: 0.7410 (tpt170) REVERT: E 62 GLN cc_start: 0.8509 (tp-100) cc_final: 0.8141 (tp-100) REVERT: E 76 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8583 (mm-30) REVERT: F 64 GLU cc_start: 0.8480 (tp30) cc_final: 0.8238 (tp30) REVERT: F 67 TYR cc_start: 0.7619 (m-80) cc_final: 0.7089 (m-10) REVERT: F 92 ARG cc_start: 0.7800 (ttm110) cc_final: 0.7441 (ttt-90) REVERT: F 96 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7990 (mt-10) REVERT: F 216 ASN cc_start: 0.8200 (t0) cc_final: 0.7964 (t0) REVERT: F 240 ASP cc_start: 0.8133 (t0) cc_final: 0.7065 (t0) REVERT: F 269 LYS cc_start: 0.8561 (tppt) cc_final: 0.8209 (tppt) REVERT: J 37 CYS cc_start: 0.7991 (t) cc_final: 0.7624 (t) REVERT: J 56 TRP cc_start: 0.6564 (p-90) cc_final: 0.5152 (p-90) REVERT: J 67 PHE cc_start: 0.8021 (m-80) cc_final: 0.7544 (m-80) REVERT: J 76 PHE cc_start: 0.8414 (t80) cc_final: 0.8041 (t80) REVERT: J 82 TRP cc_start: 0.6826 (m100) cc_final: 0.6504 (m100) REVERT: J 101 ARG cc_start: 0.7854 (ttm110) cc_final: 0.7500 (mtt90) outliers start: 220 outliers final: 143 residues processed: 604 average time/residue: 0.2056 time to fit residues: 197.6931 Evaluate side-chains 509 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 348 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1022 LYS Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1109 ILE Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1247 SER Chi-restraints excluded: chain C residue 1252 SER Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 954 ASN Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 992 LYS Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1028 ILE Chi-restraints excluded: chain D residue 1135 THR Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1223 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1268 ASN Chi-restraints excluded: chain D residue 1291 GLU Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 267 ASN Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 58 MET Chi-restraints excluded: chain J residue 71 TYR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 104 HIS Chi-restraints excluded: chain J residue 129 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 110 optimal weight: 3.9990 chunk 70 optimal weight: 0.0060 chunk 247 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 264 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 217 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 chunk 274 optimal weight: 9.9990 chunk 292 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 117 HIS C 31 GLN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS C 856 ASN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 HIS D 910 ASN D1326 GLN F 251 GLN ** F 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.150550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.098715 restraints weight = 43696.910| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.15 r_work: 0.3168 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30912 Z= 0.152 Angle : 0.639 11.021 42153 Z= 0.336 Chirality : 0.045 0.344 4797 Planarity : 0.004 0.048 5196 Dihedral : 18.594 172.177 5206 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.48 % Favored : 93.49 % Rotamer: Outliers : 5.93 % Allowed : 19.18 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.34 (0.13), residues: 3596 helix: -0.50 (0.14), residues: 1330 sheet: -2.66 (0.21), residues: 436 loop : -2.07 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 81 TYR 0.022 0.001 TYR A 177 PHE 0.018 0.001 PHE D 172 TRP 0.028 0.002 TRP J 57 HIS 0.011 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (30904) covalent geometry : angle 0.63297 / 0.34 (42141) hydrogen bonds : bond 0.04105 / 2.85 ( 1170) hydrogen bonds : angle 5.08218 / 3.45 ( 3290) metal coordination : bond 0.00870 / 0.43 ( 8) metal coordination : angle 5.13053 / 3.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 379 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7485 (ttpt) REVERT: A 145 LYS cc_start: 0.8749 (tttt) cc_final: 0.8216 (tttm) REVERT: A 212 ASP cc_start: 0.6888 (OUTLIER) cc_final: 0.6407 (t0) REVERT: A 223 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7892 (mt) REVERT: B 10 LYS cc_start: 0.8626 (mttp) cc_final: 0.8125 (mppt) REVERT: B 71 LYS cc_start: 0.6583 (tppt) cc_final: 0.6316 (tppt) REVERT: B 125 LYS cc_start: 0.7566 (tttt) cc_final: 0.7197 (tptm) REVERT: B 145 LYS cc_start: 0.7615 (tttt) cc_final: 0.7315 (tttp) REVERT: B 147 GLN cc_start: 0.6549 (tt0) cc_final: 0.5969 (mt0) REVERT: B 200 LYS cc_start: 0.8180 (tttt) cc_final: 0.7582 (tttp) REVERT: C 36 GLN cc_start: 0.7691 (tt0) cc_final: 0.7331 (tt0) REVERT: C 130 MET cc_start: 0.8791 (ttm) cc_final: 0.8489 (ttp) REVERT: C 241 LEU cc_start: 0.8879 (tp) cc_final: 0.8088 (pp) REVERT: C 246 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7191 (tp) REVERT: C 315 MET cc_start: 0.8841 (ttm) cc_final: 0.8486 (ttm) REVERT: C 369 MET cc_start: 0.8747 (ttp) cc_final: 0.8167 (tmm) REVERT: C 446 ASP cc_start: 0.8386 (m-30) cc_final: 0.8146 (m-30) REVERT: C 456 VAL cc_start: 0.8091 (t) cc_final: 0.7866 (t) REVERT: C 504 GLU cc_start: 0.8695 (tt0) cc_final: 0.8470 (tm-30) REVERT: C 510 GLN cc_start: 0.8007 (tp40) cc_final: 0.7702 (tp-100) REVERT: C 538 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.7046 (pp) REVERT: C 546 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7104 (mp0) REVERT: C 641 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6696 (mm-30) REVERT: C 704 MET cc_start: 0.7986 (mmm) cc_final: 0.7214 (tpp) REVERT: C 737 ASN cc_start: 0.6696 (m-40) cc_final: 0.6418 (m110) REVERT: C 788 SER cc_start: 0.8388 (OUTLIER) cc_final: 0.7972 (p) REVERT: C 805 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8317 (ptp) REVERT: C 1073 LYS cc_start: 0.8644 (pttt) cc_final: 0.8439 (pttp) REVERT: C 1085 MET cc_start: 0.8581 (mmt) cc_final: 0.8300 (mmt) REVERT: C 1157 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.6896 (pp30) REVERT: C 1174 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7281 (mt-10) REVERT: C 1290 MET cc_start: 0.8628 (ttm) cc_final: 0.8177 (ttm) REVERT: C 1321 GLU cc_start: 0.8243 (tp30) cc_final: 0.8041 (tp30) REVERT: D 29 MET cc_start: 0.7026 (ttm) cc_final: 0.6799 (ttm) REVERT: D 39 LYS cc_start: 0.8857 (mtmt) cc_final: 0.8604 (mtmm) REVERT: D 140 TYR cc_start: 0.8707 (m-80) cc_final: 0.8394 (m-10) REVERT: D 200 GLN cc_start: 0.8431 (mm-40) cc_final: 0.7934 (tm-30) REVERT: D 304 ASP cc_start: 0.7884 (m-30) cc_final: 0.7585 (m-30) REVERT: D 322 ARG cc_start: 0.8651 (mtp85) cc_final: 0.8079 (ptt90) REVERT: D 395 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7815 (tptt) REVERT: D 422 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8050 (mp) REVERT: D 458 ASN cc_start: 0.9120 (t0) cc_final: 0.8796 (t0) REVERT: D 484 MET cc_start: 0.9216 (mtp) cc_final: 0.8932 (mtp) REVERT: D 525 MET cc_start: 0.8551 (ptp) cc_final: 0.8324 (ptm) REVERT: D 610 ARG cc_start: 0.8163 (mmt-90) cc_final: 0.7526 (mtm110) REVERT: D 747 MET cc_start: 0.8111 (mmt) cc_final: 0.7906 (mmt) REVERT: D 765 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8196 (mt-10) REVERT: D 905 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.6523 (mpt180) REVERT: D 918 ILE cc_start: 0.7618 (OUTLIER) cc_final: 0.7141 (pt) REVERT: D 983 LYS cc_start: 0.8651 (mmmm) cc_final: 0.8410 (mmmm) REVERT: D 984 LEU cc_start: 0.6067 (tp) cc_final: 0.5817 (tp) REVERT: D 1149 ARG cc_start: 0.8487 (mmm160) cc_final: 0.7795 (tpp-160) REVERT: D 1172 LYS cc_start: 0.7162 (mmtm) cc_final: 0.5987 (mmpt) REVERT: D 1174 ARG cc_start: 0.6589 (mtt-85) cc_final: 0.6357 (mtt-85) REVERT: D 1189 MET cc_start: 0.7727 (ptm) cc_final: 0.7514 (ptp) REVERT: D 1262 ARG cc_start: 0.7262 (mtp180) cc_final: 0.6595 (mtm110) REVERT: D 1345 ARG cc_start: 0.8868 (mtp85) cc_final: 0.8617 (ttm-80) REVERT: D 1368 ASP cc_start: 0.6806 (OUTLIER) cc_final: 0.5650 (m-30) REVERT: E 3 ARG cc_start: 0.7987 (tpp-160) cc_final: 0.7734 (tpt170) REVERT: F 64 GLU cc_start: 0.8381 (tp30) cc_final: 0.8129 (tp30) REVERT: F 67 TYR cc_start: 0.7840 (m-80) cc_final: 0.7247 (m-10) REVERT: F 92 ARG cc_start: 0.7617 (ttm110) cc_final: 0.7213 (ttt-90) REVERT: F 96 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7762 (mt-10) REVERT: F 216 ASN cc_start: 0.8180 (t0) cc_final: 0.7964 (t0) REVERT: F 240 ASP cc_start: 0.8131 (t0) cc_final: 0.7035 (t0) REVERT: F 269 LYS cc_start: 0.8578 (tppt) cc_final: 0.8275 (tppt) REVERT: J 37 CYS cc_start: 0.7969 (t) cc_final: 0.7599 (t) REVERT: J 56 TRP cc_start: 0.6639 (p-90) cc_final: 0.5676 (p-90) REVERT: J 57 TRP cc_start: 0.7847 (p-90) cc_final: 0.7491 (p-90) REVERT: J 67 PHE cc_start: 0.7984 (m-80) cc_final: 0.7582 (m-80) REVERT: J 76 PHE cc_start: 0.8433 (t80) cc_final: 0.8159 (t80) REVERT: J 101 ARG cc_start: 0.7934 (ttm110) cc_final: 0.7568 (mtt90) outliers start: 182 outliers final: 135 residues processed: 528 average time/residue: 0.2017 time to fit residues: 170.2900 Evaluate side-chains 500 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 351 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 898 GLU Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1022 LYS Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1109 ILE Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1252 SER Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1028 ILE Chi-restraints excluded: chain D residue 1135 THR Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1223 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 71 TYR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 104 HIS Chi-restraints excluded: chain J residue 129 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 3 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 chunk 346 optimal weight: 0.0010 chunk 211 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 246 optimal weight: 4.9990 chunk 222 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN C 628 HIS C 684 ASN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 GLN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 954 ASN F 170 HIS ** F 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.151140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.100426 restraints weight = 43662.273| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 3.17 r_work: 0.3187 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30912 Z= 0.132 Angle : 0.611 11.918 42153 Z= 0.320 Chirality : 0.044 0.340 4797 Planarity : 0.004 0.070 5196 Dihedral : 18.254 172.088 5150 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.92 % Favored : 94.05 % Rotamer: Outliers : 5.44 % Allowed : 20.68 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.95 (0.13), residues: 3596 helix: -0.07 (0.14), residues: 1326 sheet: -2.50 (0.22), residues: 420 loop : -1.93 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 200 TYR 0.021 0.001 TYR A 177 PHE 0.020 0.001 PHE C 385 TRP 0.038 0.001 TRP C 997 HIS 0.008 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (30904) covalent geometry : angle 0.60709 / 0.32 (42141) hydrogen bonds : bond 0.03692 / 2.57 ( 1170) hydrogen bonds : angle 4.75953 / 3.23 ( 3290) metal coordination : bond 0.00646 / 0.29 ( 8) metal coordination : angle 4.37222 / 2.63 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 371 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.5921 (OUTLIER) cc_final: 0.5643 (pm20) REVERT: A 8 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7103 (m-10) REVERT: A 25 LYS cc_start: 0.7678 (ttpt) cc_final: 0.7360 (ttmm) REVERT: A 145 LYS cc_start: 0.8824 (tttt) cc_final: 0.8390 (tttp) REVERT: A 212 ASP cc_start: 0.6980 (OUTLIER) cc_final: 0.6499 (t0) REVERT: A 223 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7917 (mt) REVERT: B 10 LYS cc_start: 0.8676 (mttp) cc_final: 0.8332 (mtmm) REVERT: B 125 LYS cc_start: 0.7440 (tttt) cc_final: 0.7081 (tptm) REVERT: B 145 LYS cc_start: 0.7540 (tttt) cc_final: 0.7243 (tttp) REVERT: B 147 GLN cc_start: 0.6369 (tt0) cc_final: 0.5763 (mt0) REVERT: B 200 LYS cc_start: 0.8213 (tttt) cc_final: 0.7748 (tttp) REVERT: C 36 GLN cc_start: 0.7667 (tt0) cc_final: 0.7300 (tt0) REVERT: C 130 MET cc_start: 0.8771 (ttm) cc_final: 0.8452 (ttp) REVERT: C 161 LYS cc_start: 0.8653 (mttt) cc_final: 0.8079 (pttm) REVERT: C 200 ARG cc_start: 0.7277 (mmm160) cc_final: 0.7010 (mmm160) REVERT: C 223 LEU cc_start: 0.8528 (mt) cc_final: 0.8306 (tp) REVERT: C 241 LEU cc_start: 0.9017 (tp) cc_final: 0.8317 (pp) REVERT: C 315 MET cc_start: 0.8879 (ttm) cc_final: 0.8534 (ttm) REVERT: C 424 ASP cc_start: 0.7798 (m-30) cc_final: 0.7289 (m-30) REVERT: C 446 ASP cc_start: 0.8402 (m-30) cc_final: 0.8183 (m-30) REVERT: C 456 VAL cc_start: 0.8116 (t) cc_final: 0.7896 (t) REVERT: C 504 GLU cc_start: 0.8637 (tt0) cc_final: 0.8428 (tm-30) REVERT: C 510 GLN cc_start: 0.8105 (tp40) cc_final: 0.7798 (tp-100) REVERT: C 513 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8181 (mt0) REVERT: C 538 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7109 (pp) REVERT: C 546 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7171 (mp0) REVERT: C 641 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6713 (mm-30) REVERT: C 645 PHE cc_start: 0.7829 (m-80) cc_final: 0.6878 (m-80) REVERT: C 704 MET cc_start: 0.7993 (mmm) cc_final: 0.7207 (tpp) REVERT: C 737 ASN cc_start: 0.6672 (m-40) cc_final: 0.6416 (m110) REVERT: C 788 SER cc_start: 0.8454 (OUTLIER) cc_final: 0.7963 (p) REVERT: C 805 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8338 (ptp) REVERT: C 1073 LYS cc_start: 0.8696 (pttt) cc_final: 0.8445 (pttp) REVERT: C 1085 MET cc_start: 0.8553 (mmp) cc_final: 0.8338 (mmt) REVERT: C 1157 GLN cc_start: 0.7399 (OUTLIER) cc_final: 0.6834 (pp30) REVERT: C 1174 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7333 (mt-10) REVERT: C 1211 ARG cc_start: 0.7859 (mtp85) cc_final: 0.7643 (mtp85) REVERT: C 1296 ASP cc_start: 0.8903 (t0) cc_final: 0.8495 (t0) REVERT: C 1321 GLU cc_start: 0.8168 (tp30) cc_final: 0.7635 (tp30) REVERT: D 29 MET cc_start: 0.7026 (ttm) cc_final: 0.6810 (ttm) REVERT: D 39 LYS cc_start: 0.8897 (mtmt) cc_final: 0.8629 (mtmm) REVERT: D 140 TYR cc_start: 0.8730 (m-80) cc_final: 0.8389 (m-10) REVERT: D 200 GLN cc_start: 0.8414 (mm-40) cc_final: 0.7919 (tm-30) REVERT: D 304 ASP cc_start: 0.7987 (m-30) cc_final: 0.7676 (m-30) REVERT: D 322 ARG cc_start: 0.8662 (mtp85) cc_final: 0.8129 (ptt90) REVERT: D 395 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7818 (tptt) REVERT: D 441 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7788 (mm) REVERT: D 458 ASN cc_start: 0.9016 (t0) cc_final: 0.8741 (t0) REVERT: D 484 MET cc_start: 0.9261 (mtp) cc_final: 0.9000 (mtp) REVERT: D 525 MET cc_start: 0.8514 (ptp) cc_final: 0.8303 (ptm) REVERT: D 610 ARG cc_start: 0.8187 (mmt-90) cc_final: 0.7512 (mtm110) REVERT: D 765 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8239 (mt-10) REVERT: D 785 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7379 (t70) REVERT: D 788 LEU cc_start: 0.8183 (mm) cc_final: 0.7916 (mp) REVERT: D 918 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7191 (pt) REVERT: D 983 LYS cc_start: 0.8712 (mmmm) cc_final: 0.8353 (mmmm) REVERT: D 1149 ARG cc_start: 0.8505 (mmm160) cc_final: 0.7816 (tpp-160) REVERT: D 1172 LYS cc_start: 0.7200 (mmtm) cc_final: 0.5933 (mmpt) REVERT: D 1174 ARG cc_start: 0.6538 (mtt-85) cc_final: 0.6267 (mtt-85) REVERT: D 1260 MET cc_start: 0.8857 (mtp) cc_final: 0.8616 (mtm) REVERT: D 1262 ARG cc_start: 0.7185 (mtp180) cc_final: 0.6619 (mtm110) REVERT: D 1291 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8153 (tm-30) REVERT: D 1345 ARG cc_start: 0.8941 (mtp85) cc_final: 0.8553 (ttm-80) REVERT: D 1368 ASP cc_start: 0.6920 (OUTLIER) cc_final: 0.5674 (m-30) REVERT: E 43 ASN cc_start: 0.8621 (m-40) cc_final: 0.8046 (t0) REVERT: F 53 ARG cc_start: 0.6963 (mtt-85) cc_final: 0.6614 (mtp180) REVERT: F 64 GLU cc_start: 0.8477 (tp30) cc_final: 0.8269 (tp30) REVERT: F 67 TYR cc_start: 0.7820 (m-80) cc_final: 0.7252 (m-10) REVERT: F 90 SER cc_start: 0.8427 (OUTLIER) cc_final: 0.8173 (p) REVERT: F 92 ARG cc_start: 0.7577 (ttm110) cc_final: 0.7359 (ttt-90) REVERT: F 111 ASN cc_start: 0.8079 (t0) cc_final: 0.7835 (t0) REVERT: F 151 ARG cc_start: 0.6438 (OUTLIER) cc_final: 0.5877 (ttp80) REVERT: F 207 ASP cc_start: 0.7908 (p0) cc_final: 0.7700 (t0) REVERT: F 240 ASP cc_start: 0.8162 (t0) cc_final: 0.7064 (t0) REVERT: F 269 LYS cc_start: 0.8570 (tppt) cc_final: 0.8272 (tppt) REVERT: J 24 ARG cc_start: 0.7757 (mmt90) cc_final: 0.7414 (mmt90) REVERT: J 37 CYS cc_start: 0.7988 (t) cc_final: 0.7617 (t) REVERT: J 56 TRP cc_start: 0.6551 (p-90) cc_final: 0.5589 (p-90) REVERT: J 57 TRP cc_start: 0.7949 (p-90) cc_final: 0.7569 (p-90) REVERT: J 67 PHE cc_start: 0.7962 (m-80) cc_final: 0.7616 (m-80) REVERT: J 76 PHE cc_start: 0.8347 (t80) cc_final: 0.8113 (t80) REVERT: J 101 ARG cc_start: 0.7990 (ttm110) cc_final: 0.7577 (mtt90) outliers start: 167 outliers final: 120 residues processed: 502 average time/residue: 0.1981 time to fit residues: 158.5975 Evaluate side-chains 485 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 348 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 898 GLU Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1247 SER Chi-restraints excluded: chain C residue 1250 SER Chi-restraints excluded: chain C residue 1252 SER Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1028 ILE Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1223 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 151 ARG Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 71 TYR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 129 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 28 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 131 optimal weight: 0.0770 chunk 147 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 242 optimal weight: 1.9990 chunk 360 optimal weight: 40.0000 chunk 339 optimal weight: 10.0000 chunk 259 optimal weight: 4.9990 chunk 219 optimal weight: 0.9980 chunk 346 optimal weight: 8.9990 overall best weight: 2.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 46 GLN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 HIS ** F 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.148102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.096448 restraints weight = 44102.163| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.13 r_work: 0.3128 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 30912 Z= 0.230 Angle : 0.666 9.824 42153 Z= 0.345 Chirality : 0.046 0.342 4797 Planarity : 0.004 0.078 5196 Dihedral : 18.105 174.659 5109 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.01 % Favored : 92.96 % Rotamer: Outliers : 6.19 % Allowed : 20.51 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.95 (0.13), residues: 3596 helix: -0.09 (0.14), residues: 1333 sheet: -2.47 (0.23), residues: 427 loop : -1.93 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 200 TYR 0.023 0.002 TYR A 177 PHE 0.018 0.002 PHE D 437 TRP 0.049 0.002 TRP C 997 HIS 0.009 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.23 (30904) covalent geometry : angle 0.66174 / 0.34 (42141) hydrogen bonds : bond 0.03994 / 2.75 ( 1170) hydrogen bonds : angle 4.76311 / 3.23 ( 3290) metal coordination : bond 0.01334 / 0.62 ( 8) metal coordination : angle 4.55376 / 2.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 359 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.7441 (m-10) REVERT: A 25 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7646 (ttpt) REVERT: A 122 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6966 (mt-10) REVERT: A 145 LYS cc_start: 0.8843 (tttt) cc_final: 0.8361 (tttp) REVERT: A 212 ASP cc_start: 0.7102 (OUTLIER) cc_final: 0.6613 (t70) REVERT: A 223 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.8091 (mt) REVERT: B 10 LYS cc_start: 0.8767 (mttp) cc_final: 0.8454 (mtmm) REVERT: B 125 LYS cc_start: 0.7588 (tttt) cc_final: 0.7204 (tptm) REVERT: B 145 LYS cc_start: 0.7705 (tttt) cc_final: 0.7405 (tttp) REVERT: B 147 GLN cc_start: 0.6450 (tt0) cc_final: 0.5849 (mt0) REVERT: B 200 LYS cc_start: 0.8228 (tttt) cc_final: 0.7736 (tttp) REVERT: B 205 MET cc_start: 0.8246 (ttp) cc_final: 0.7949 (ttp) REVERT: C 36 GLN cc_start: 0.7726 (tt0) cc_final: 0.7362 (tt0) REVERT: C 124 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8113 (ptm) REVERT: C 130 MET cc_start: 0.8946 (ttm) cc_final: 0.8512 (ttm) REVERT: C 161 LYS cc_start: 0.8703 (mttt) cc_final: 0.8082 (pttm) REVERT: C 200 ARG cc_start: 0.7199 (mmm160) cc_final: 0.6911 (mmm160) REVERT: C 223 LEU cc_start: 0.8557 (mt) cc_final: 0.8335 (tp) REVERT: C 239 MET cc_start: 0.5702 (mtm) cc_final: 0.5496 (mtp) REVERT: C 241 LEU cc_start: 0.9033 (tp) cc_final: 0.8257 (pp) REVERT: C 246 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7496 (tp) REVERT: C 315 MET cc_start: 0.8900 (ttm) cc_final: 0.8558 (ttm) REVERT: C 424 ASP cc_start: 0.7841 (m-30) cc_final: 0.7219 (m-30) REVERT: C 446 ASP cc_start: 0.8464 (m-30) cc_final: 0.8211 (m-30) REVERT: C 510 GLN cc_start: 0.8158 (tp40) cc_final: 0.7871 (tp40) REVERT: C 516 ASP cc_start: 0.7288 (p0) cc_final: 0.6966 (p0) REVERT: C 538 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7059 (pp) REVERT: C 542 ARG cc_start: 0.8308 (mtt180) cc_final: 0.7234 (ptp-170) REVERT: C 546 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7208 (mp0) REVERT: C 637 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.6925 (ptt-90) REVERT: C 641 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6860 (mm-30) REVERT: C 704 MET cc_start: 0.8142 (mmm) cc_final: 0.7369 (tpp) REVERT: C 737 ASN cc_start: 0.6774 (m-40) cc_final: 0.6573 (m110) REVERT: C 805 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8392 (ptm) REVERT: C 1073 LYS cc_start: 0.8781 (pttt) cc_final: 0.8539 (pttp) REVERT: C 1085 MET cc_start: 0.8683 (mmp) cc_final: 0.8399 (mmt) REVERT: C 1157 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.7016 (pp30) REVERT: C 1174 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7355 (mt-10) REVERT: C 1211 ARG cc_start: 0.7927 (mtp85) cc_final: 0.7710 (mtp85) REVERT: C 1290 MET cc_start: 0.8816 (ttm) cc_final: 0.8442 (ttm) REVERT: C 1321 GLU cc_start: 0.8222 (tp30) cc_final: 0.7967 (tp30) REVERT: C 1340 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7257 (pt0) REVERT: D 29 MET cc_start: 0.7292 (ttm) cc_final: 0.7034 (ttm) REVERT: D 39 LYS cc_start: 0.8930 (mtmt) cc_final: 0.8678 (mtmm) REVERT: D 140 TYR cc_start: 0.8679 (m-80) cc_final: 0.8212 (m-10) REVERT: D 200 GLN cc_start: 0.8443 (mm-40) cc_final: 0.7949 (tm-30) REVERT: D 304 ASP cc_start: 0.7997 (m-30) cc_final: 0.7716 (m-30) REVERT: D 322 ARG cc_start: 0.8725 (mtp85) cc_final: 0.8368 (ptt90) REVERT: D 372 MET cc_start: 0.7708 (mtp) cc_final: 0.7452 (mtm) REVERT: D 375 GLU cc_start: 0.8283 (tp30) cc_final: 0.8042 (tp30) REVERT: D 395 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7947 (tptt) REVERT: D 422 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8109 (mp) REVERT: D 484 MET cc_start: 0.9304 (mtp) cc_final: 0.9028 (mtp) REVERT: D 610 ARG cc_start: 0.8236 (mmt-90) cc_final: 0.7580 (mtm110) REVERT: D 765 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8197 (mt-10) REVERT: D 905 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6847 (mpt180) REVERT: D 918 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7301 (pt) REVERT: D 981 GLU cc_start: 0.7514 (tt0) cc_final: 0.7295 (tt0) REVERT: D 983 LYS cc_start: 0.8712 (mmmm) cc_final: 0.8427 (mmmm) REVERT: D 1149 ARG cc_start: 0.8533 (mmm160) cc_final: 0.7793 (tpp-160) REVERT: D 1172 LYS cc_start: 0.7456 (mmtm) cc_final: 0.6326 (mmpt) REVERT: D 1260 MET cc_start: 0.8901 (mtp) cc_final: 0.8652 (mtm) REVERT: D 1291 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8188 (tm-30) REVERT: D 1345 ARG cc_start: 0.8949 (mtp85) cc_final: 0.8638 (ttm-80) REVERT: D 1368 ASP cc_start: 0.6866 (OUTLIER) cc_final: 0.5580 (m-30) REVERT: E 43 ASN cc_start: 0.8774 (m-40) cc_final: 0.8336 (t0) REVERT: F 53 ARG cc_start: 0.7077 (mtt-85) cc_final: 0.6772 (mtp180) REVERT: F 64 GLU cc_start: 0.8583 (tp30) cc_final: 0.8205 (tp30) REVERT: F 67 TYR cc_start: 0.7827 (m-80) cc_final: 0.7279 (m-10) REVERT: F 92 ARG cc_start: 0.7980 (ttm110) cc_final: 0.7531 (ttt-90) REVERT: F 111 ASN cc_start: 0.8115 (t0) cc_final: 0.7870 (t0) REVERT: F 151 ARG cc_start: 0.6557 (OUTLIER) cc_final: 0.6121 (ttp80) REVERT: F 240 ASP cc_start: 0.8130 (t0) cc_final: 0.7141 (t0) REVERT: F 269 LYS cc_start: 0.8616 (tppt) cc_final: 0.8333 (tppt) REVERT: J 24 ARG cc_start: 0.7849 (mmt90) cc_final: 0.7462 (mmt90) REVERT: J 37 CYS cc_start: 0.7934 (t) cc_final: 0.7583 (t) REVERT: J 51 ARG cc_start: 0.7037 (mtt180) cc_final: 0.6502 (mtt-85) REVERT: J 56 TRP cc_start: 0.6633 (p-90) cc_final: 0.5649 (p-90) REVERT: J 57 TRP cc_start: 0.7980 (p-90) cc_final: 0.7568 (p-90) REVERT: J 67 PHE cc_start: 0.8026 (m-80) cc_final: 0.7649 (m-80) REVERT: J 76 PHE cc_start: 0.8263 (t80) cc_final: 0.8026 (t80) REVERT: J 97 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7799 (pp20) REVERT: J 101 ARG cc_start: 0.8006 (ttm110) cc_final: 0.7653 (mtt90) REVERT: J 103 PHE cc_start: 0.8150 (t80) cc_final: 0.7836 (t80) outliers start: 190 outliers final: 142 residues processed: 511 average time/residue: 0.1941 time to fit residues: 158.1331 Evaluate side-chains 498 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 336 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 898 GLU Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1247 SER Chi-restraints excluded: chain C residue 1250 SER Chi-restraints excluded: chain C residue 1252 SER Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1340 GLU Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1028 ILE Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1223 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 151 ARG Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 71 TYR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 341 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 217 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 312 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 260 optimal weight: 9.9990 chunk 348 optimal weight: 30.0000 chunk 228 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 230 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 897 HIS F 170 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.149722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.098408 restraints weight = 43722.580| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 3.10 r_work: 0.3165 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30912 Z= 0.148 Angle : 0.616 10.325 42153 Z= 0.319 Chirality : 0.044 0.341 4797 Planarity : 0.004 0.046 5196 Dihedral : 17.915 177.839 5101 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.84 % Favored : 94.13 % Rotamer: Outliers : 5.34 % Allowed : 21.85 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.71 (0.14), residues: 3596 helix: 0.20 (0.14), residues: 1323 sheet: -2.33 (0.24), residues: 413 loop : -1.86 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1262 TYR 0.021 0.001 TYR A 177 PHE 0.018 0.001 PHE D 172 TRP 0.052 0.001 TRP C 997 HIS 0.011 0.001 HIS J 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (30904) covalent geometry : angle 0.61144 / 0.32 (42141) hydrogen bonds : bond 0.03638 / 2.51 ( 1170) hydrogen bonds : angle 4.56676 / 3.09 ( 3290) metal coordination : bond 0.00721 / 0.33 ( 8) metal coordination : angle 4.34076 / 2.61 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 361 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7899 (ttpt) cc_final: 0.7453 (ttmm) REVERT: A 122 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6940 (mt-10) REVERT: A 145 LYS cc_start: 0.8922 (tttt) cc_final: 0.8500 (tttp) REVERT: A 212 ASP cc_start: 0.7022 (OUTLIER) cc_final: 0.6557 (t70) REVERT: B 10 LYS cc_start: 0.8735 (mttp) cc_final: 0.8411 (mtmm) REVERT: B 38 THR cc_start: 0.7851 (OUTLIER) cc_final: 0.7039 (m) REVERT: B 51 MET cc_start: 0.7982 (ttp) cc_final: 0.7726 (ttm) REVERT: B 125 LYS cc_start: 0.7534 (tttt) cc_final: 0.7163 (tptm) REVERT: B 200 LYS cc_start: 0.8214 (tttt) cc_final: 0.7706 (tttp) REVERT: C 36 GLN cc_start: 0.7639 (tt0) cc_final: 0.7325 (tt0) REVERT: C 96 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8177 (pp) REVERT: C 130 MET cc_start: 0.8865 (ttm) cc_final: 0.8532 (ttp) REVERT: C 161 LYS cc_start: 0.8686 (mttt) cc_final: 0.8047 (pttm) REVERT: C 315 MET cc_start: 0.8942 (ttm) cc_final: 0.8596 (ttm) REVERT: C 424 ASP cc_start: 0.7835 (m-30) cc_final: 0.7163 (m-30) REVERT: C 510 GLN cc_start: 0.8192 (tp40) cc_final: 0.7862 (tp40) REVERT: C 516 ASP cc_start: 0.7292 (p0) cc_final: 0.6972 (p0) REVERT: C 538 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7120 (pp) REVERT: C 546 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7251 (mp0) REVERT: C 549 ASP cc_start: 0.8902 (OUTLIER) cc_final: 0.8673 (t0) REVERT: C 637 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.6985 (ptt-90) REVERT: C 641 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6850 (mm-30) REVERT: C 645 PHE cc_start: 0.7822 (m-80) cc_final: 0.7112 (m-80) REVERT: C 737 ASN cc_start: 0.6780 (m-40) cc_final: 0.6527 (m110) REVERT: C 805 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8393 (ptp) REVERT: C 1022 LYS cc_start: 0.5233 (OUTLIER) cc_final: 0.4992 (tmmt) REVERT: C 1073 LYS cc_start: 0.8794 (pttt) cc_final: 0.8540 (pttp) REVERT: C 1085 MET cc_start: 0.8671 (mmp) cc_final: 0.8386 (mmt) REVERT: C 1157 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.6994 (pp30) REVERT: C 1174 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7588 (mt-10) REVERT: C 1211 ARG cc_start: 0.7905 (mtp85) cc_final: 0.7669 (mtp85) REVERT: C 1290 MET cc_start: 0.8806 (ttm) cc_final: 0.8336 (ttm) REVERT: C 1321 GLU cc_start: 0.8147 (tp30) cc_final: 0.7826 (tp30) REVERT: C 1340 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7513 (pt0) REVERT: D 29 MET cc_start: 0.7138 (ttm) cc_final: 0.6885 (ttm) REVERT: D 39 LYS cc_start: 0.8890 (mtmt) cc_final: 0.8654 (mtmm) REVERT: D 200 GLN cc_start: 0.8427 (mm-40) cc_final: 0.7950 (tm-30) REVERT: D 322 ARG cc_start: 0.8744 (mtp85) cc_final: 0.8418 (ptt90) REVERT: D 372 MET cc_start: 0.7605 (mtp) cc_final: 0.7402 (mtm) REVERT: D 395 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7960 (tptt) REVERT: D 441 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7883 (mm) REVERT: D 484 MET cc_start: 0.9307 (mtp) cc_final: 0.9067 (mtp) REVERT: D 525 MET cc_start: 0.8421 (ptp) cc_final: 0.8212 (ptm) REVERT: D 610 ARG cc_start: 0.8226 (mmt-90) cc_final: 0.7561 (mtm110) REVERT: D 765 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8234 (mt-10) REVERT: D 785 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7410 (t70) REVERT: D 905 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6838 (mpt180) REVERT: D 918 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.7211 (pt) REVERT: D 981 GLU cc_start: 0.7508 (tt0) cc_final: 0.7300 (tt0) REVERT: D 983 LYS cc_start: 0.8659 (mmmm) cc_final: 0.8351 (mmmm) REVERT: D 1149 ARG cc_start: 0.8561 (mmm160) cc_final: 0.7846 (tpp-160) REVERT: D 1291 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8153 (tm-30) REVERT: D 1345 ARG cc_start: 0.8933 (mtp85) cc_final: 0.8607 (ttm-80) REVERT: D 1368 ASP cc_start: 0.6854 (OUTLIER) cc_final: 0.5583 (m-30) REVERT: E 43 ASN cc_start: 0.8808 (m-40) cc_final: 0.8353 (t0) REVERT: F 53 ARG cc_start: 0.7088 (mtt-85) cc_final: 0.6816 (mtp180) REVERT: F 64 GLU cc_start: 0.8481 (tp30) cc_final: 0.8255 (tp30) REVERT: F 67 TYR cc_start: 0.7806 (m-80) cc_final: 0.7241 (m-10) REVERT: F 92 ARG cc_start: 0.7834 (ttm110) cc_final: 0.7436 (ttt-90) REVERT: F 111 ASN cc_start: 0.8164 (t0) cc_final: 0.7770 (t0) REVERT: F 200 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8275 (tm-30) REVERT: F 240 ASP cc_start: 0.8114 (t0) cc_final: 0.7119 (t0) REVERT: F 269 LYS cc_start: 0.8539 (tppt) cc_final: 0.8270 (tppt) REVERT: J 24 ARG cc_start: 0.7869 (mmt90) cc_final: 0.7482 (mmt90) REVERT: J 37 CYS cc_start: 0.7983 (t) cc_final: 0.7665 (t) REVERT: J 56 TRP cc_start: 0.6599 (p-90) cc_final: 0.5620 (p-90) REVERT: J 57 TRP cc_start: 0.8064 (p-90) cc_final: 0.7700 (p-90) REVERT: J 67 PHE cc_start: 0.8029 (m-80) cc_final: 0.7674 (m-80) REVERT: J 76 PHE cc_start: 0.8241 (t80) cc_final: 0.7993 (t80) REVERT: J 97 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7881 (pp20) REVERT: J 101 ARG cc_start: 0.8009 (ttm110) cc_final: 0.7686 (mtt90) REVERT: J 103 PHE cc_start: 0.8127 (t80) cc_final: 0.7805 (t80) outliers start: 164 outliers final: 120 residues processed: 492 average time/residue: 0.1963 time to fit residues: 153.5630 Evaluate side-chains 476 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 337 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 898 GLU Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1005 GLU Chi-restraints excluded: chain C residue 1022 LYS Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1250 SER Chi-restraints excluded: chain C residue 1252 SER Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1340 GLU Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1028 ILE Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1223 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 71 TYR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 284 optimal weight: 7.9990 chunk 192 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 275 optimal weight: 4.9990 chunk 29 optimal weight: 20.0000 chunk 142 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 285 optimal weight: 8.9990 chunk 224 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 897 HIS F 170 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.147894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.096605 restraints weight = 44085.919| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 3.13 r_work: 0.3135 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 30912 Z= 0.224 Angle : 0.654 9.785 42153 Z= 0.337 Chirality : 0.045 0.342 4797 Planarity : 0.004 0.047 5196 Dihedral : 17.890 178.474 5091 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.01 % Favored : 92.96 % Rotamer: Outliers : 5.99 % Allowed : 21.95 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.73 (0.14), residues: 3596 helix: 0.15 (0.14), residues: 1327 sheet: -2.33 (0.23), residues: 425 loop : -1.86 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1262 TYR 0.021 0.002 TYR A 177 PHE 0.018 0.002 PHE D 437 TRP 0.053 0.002 TRP C 997 HIS 0.027 0.001 HIS D 897 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.22 (30904) covalent geometry : angle 0.64833 / 0.34 (42141) hydrogen bonds : bond 0.03816 / 2.63 ( 1170) hydrogen bonds : angle 4.61228 / 3.13 ( 3290) metal coordination : bond 0.01151 / 0.47 ( 8) metal coordination : angle 5.05585 / 2.87 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 346 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.7840 (mtm180) cc_final: 0.7485 (mtm180) REVERT: A 25 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7394 (ttmm) REVERT: A 122 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6981 (mt-10) REVERT: A 145 LYS cc_start: 0.8894 (tttt) cc_final: 0.8443 (tttp) REVERT: A 212 ASP cc_start: 0.7086 (OUTLIER) cc_final: 0.6607 (t70) REVERT: B 10 LYS cc_start: 0.8763 (mttp) cc_final: 0.8460 (mtmm) REVERT: B 71 LYS cc_start: 0.6084 (tppt) cc_final: 0.5795 (tppt) REVERT: B 125 LYS cc_start: 0.7566 (tttt) cc_final: 0.7194 (tptm) REVERT: B 200 LYS cc_start: 0.8182 (tttt) cc_final: 0.7673 (tttp) REVERT: B 205 MET cc_start: 0.8169 (ttp) cc_final: 0.7906 (ttp) REVERT: C 36 GLN cc_start: 0.7660 (tt0) cc_final: 0.7329 (tt0) REVERT: C 96 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8133 (pp) REVERT: C 130 MET cc_start: 0.8926 (ttm) cc_final: 0.8615 (ttp) REVERT: C 161 LYS cc_start: 0.8653 (mttt) cc_final: 0.8018 (pttm) REVERT: C 241 LEU cc_start: 0.8774 (tp) cc_final: 0.7733 (pt) REVERT: C 246 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7385 (mp) REVERT: C 315 MET cc_start: 0.8944 (ttm) cc_final: 0.8608 (ttm) REVERT: C 510 GLN cc_start: 0.8164 (tp40) cc_final: 0.7873 (tp40) REVERT: C 516 ASP cc_start: 0.7326 (p0) cc_final: 0.7023 (p0) REVERT: C 538 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7096 (pp) REVERT: C 542 ARG cc_start: 0.8306 (mtt180) cc_final: 0.7172 (ptp-170) REVERT: C 546 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7406 (mp0) REVERT: C 637 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7215 (ptt-90) REVERT: C 641 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6884 (mm-30) REVERT: C 645 PHE cc_start: 0.7863 (m-80) cc_final: 0.7339 (m-80) REVERT: C 737 ASN cc_start: 0.6787 (m-40) cc_final: 0.6557 (m110) REVERT: C 805 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8398 (ptm) REVERT: C 1022 LYS cc_start: 0.5130 (OUTLIER) cc_final: 0.4874 (tmmt) REVERT: C 1073 LYS cc_start: 0.8883 (pttt) cc_final: 0.8622 (pttp) REVERT: C 1085 MET cc_start: 0.8734 (mmp) cc_final: 0.8414 (mmt) REVERT: C 1157 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7143 (pp30) REVERT: C 1174 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7664 (mt-10) REVERT: C 1211 ARG cc_start: 0.7924 (mtp85) cc_final: 0.7713 (mtp85) REVERT: C 1290 MET cc_start: 0.8859 (ttm) cc_final: 0.8538 (ttm) REVERT: C 1321 GLU cc_start: 0.8164 (tp30) cc_final: 0.7855 (tp30) REVERT: C 1340 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7623 (pt0) REVERT: D 29 MET cc_start: 0.7238 (ttm) cc_final: 0.6983 (ttm) REVERT: D 39 LYS cc_start: 0.8889 (mtmt) cc_final: 0.8640 (mtmm) REVERT: D 200 GLN cc_start: 0.8438 (mm-40) cc_final: 0.7953 (tm-30) REVERT: D 322 ARG cc_start: 0.8733 (mtp85) cc_final: 0.8413 (ptt90) REVERT: D 372 MET cc_start: 0.7671 (mtp) cc_final: 0.7425 (mtm) REVERT: D 395 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8030 (tptt) REVERT: D 484 MET cc_start: 0.9314 (mtp) cc_final: 0.9069 (mtp) REVERT: D 610 ARG cc_start: 0.8251 (mmt-90) cc_final: 0.7816 (ttp80) REVERT: D 765 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8183 (mt-10) REVERT: D 785 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7445 (t70) REVERT: D 905 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6874 (mpt180) REVERT: D 918 ILE cc_start: 0.7723 (OUTLIER) cc_final: 0.7274 (pt) REVERT: D 983 LYS cc_start: 0.8657 (mmmm) cc_final: 0.8348 (mmmm) REVERT: D 1149 ARG cc_start: 0.8564 (mmm160) cc_final: 0.7853 (tpp-160) REVERT: D 1345 ARG cc_start: 0.8934 (mtp85) cc_final: 0.8623 (ttm-80) REVERT: D 1366 HIS cc_start: 0.7649 (OUTLIER) cc_final: 0.6969 (m-70) REVERT: D 1368 ASP cc_start: 0.6949 (OUTLIER) cc_final: 0.5689 (m-30) REVERT: E 43 ASN cc_start: 0.8839 (m-40) cc_final: 0.8350 (t0) REVERT: F 53 ARG cc_start: 0.7150 (mtt-85) cc_final: 0.6927 (mtp180) REVERT: F 64 GLU cc_start: 0.8524 (tp30) cc_final: 0.8159 (tp30) REVERT: F 67 TYR cc_start: 0.7795 (m-80) cc_final: 0.7249 (m-10) REVERT: F 92 ARG cc_start: 0.7834 (ttm110) cc_final: 0.7444 (ttt-90) REVERT: F 111 ASN cc_start: 0.8167 (t0) cc_final: 0.7761 (t0) REVERT: F 200 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8296 (tm-30) REVERT: F 240 ASP cc_start: 0.8099 (t0) cc_final: 0.7238 (t0) REVERT: F 243 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6979 (tt0) REVERT: F 256 LYS cc_start: 0.7931 (mttp) cc_final: 0.7418 (mptt) REVERT: F 269 LYS cc_start: 0.8543 (tppt) cc_final: 0.8303 (tptt) REVERT: J 24 ARG cc_start: 0.7934 (mmt90) cc_final: 0.7539 (mmt90) REVERT: J 37 CYS cc_start: 0.8020 (t) cc_final: 0.7712 (t) REVERT: J 51 ARG cc_start: 0.7100 (mtt180) cc_final: 0.6584 (mtt-85) REVERT: J 56 TRP cc_start: 0.6594 (p-90) cc_final: 0.5649 (p-90) REVERT: J 57 TRP cc_start: 0.8068 (p-90) cc_final: 0.7701 (p-90) REVERT: J 67 PHE cc_start: 0.8035 (m-80) cc_final: 0.7698 (m-80) REVERT: J 76 PHE cc_start: 0.8166 (t80) cc_final: 0.7930 (t80) REVERT: J 97 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7774 (pp20) REVERT: J 101 ARG cc_start: 0.8021 (ttm110) cc_final: 0.7621 (mtt90) REVERT: J 103 PHE cc_start: 0.8079 (t80) cc_final: 0.7755 (t80) REVERT: J 131 LEU cc_start: 0.4506 (OUTLIER) cc_final: 0.4244 (mp) outliers start: 184 outliers final: 143 residues processed: 493 average time/residue: 0.1904 time to fit residues: 150.1141 Evaluate side-chains 501 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 337 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 898 GLU Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1005 GLU Chi-restraints excluded: chain C residue 1022 LYS Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1109 ILE Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1247 SER Chi-restraints excluded: chain C residue 1250 SER Chi-restraints excluded: chain C residue 1252 SER Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1340 GLU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1028 ILE Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1223 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 71 TYR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 114 MET Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 131 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 294 optimal weight: 9.9990 chunk 58 optimal weight: 0.4980 chunk 118 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 chunk 300 optimal weight: 0.6980 chunk 333 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 311 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 225 optimal weight: 0.8980 chunk 247 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 GLN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 HIS J 7 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.150801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.099639 restraints weight = 43657.038| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.09 r_work: 0.3185 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30912 Z= 0.125 Angle : 0.604 9.686 42153 Z= 0.313 Chirality : 0.043 0.339 4797 Planarity : 0.004 0.045 5196 Dihedral : 17.692 174.932 5091 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.53 % Favored : 94.44 % Rotamer: Outliers : 4.98 % Allowed : 22.89 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.46 (0.14), residues: 3596 helix: 0.47 (0.15), residues: 1312 sheet: -2.20 (0.24), residues: 414 loop : -1.75 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1262 TYR 0.020 0.001 TYR A 177 PHE 0.018 0.001 PHE F 278 TRP 0.049 0.001 TRP C 997 HIS 0.006 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (30904) covalent geometry : angle 0.60068 / 0.31 (42141) hydrogen bonds : bond 0.03484 / 2.41 ( 1170) hydrogen bonds : angle 4.41850 / 2.99 ( 3290) metal coordination : bond 0.00494 / 0.21 ( 8) metal coordination : angle 4.03450 / 2.41 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 350 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.7820 (mtm180) cc_final: 0.7504 (mtm180) REVERT: A 25 LYS cc_start: 0.7864 (ttpt) cc_final: 0.7337 (ttmm) REVERT: A 122 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6947 (mt-10) REVERT: A 127 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8205 (pt0) REVERT: A 212 ASP cc_start: 0.6997 (OUTLIER) cc_final: 0.6533 (t70) REVERT: B 10 LYS cc_start: 0.8736 (mttp) cc_final: 0.8396 (mtmm) REVERT: B 71 LYS cc_start: 0.6139 (tppt) cc_final: 0.5773 (tppt) REVERT: B 125 LYS cc_start: 0.7430 (tttt) cc_final: 0.7068 (tptm) REVERT: B 200 LYS cc_start: 0.8204 (tttt) cc_final: 0.7845 (tttp) REVERT: C 36 GLN cc_start: 0.7596 (tt0) cc_final: 0.7269 (tt0) REVERT: C 96 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7957 (pp) REVERT: C 130 MET cc_start: 0.8786 (ttm) cc_final: 0.8465 (ttp) REVERT: C 161 LYS cc_start: 0.8471 (mttt) cc_final: 0.7851 (pttm) REVERT: C 239 MET cc_start: 0.6395 (mtp) cc_final: 0.6001 (mtp) REVERT: C 241 LEU cc_start: 0.8767 (tp) cc_final: 0.7699 (pt) REVERT: C 246 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7327 (mp) REVERT: C 315 MET cc_start: 0.8988 (ttm) cc_final: 0.8649 (ttm) REVERT: C 429 MET cc_start: 0.8051 (mmm) cc_final: 0.7835 (mmm) REVERT: C 510 GLN cc_start: 0.8132 (tp40) cc_final: 0.7806 (tp40) REVERT: C 516 ASP cc_start: 0.7251 (p0) cc_final: 0.6917 (p0) REVERT: C 538 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7383 (pt) REVERT: C 542 ARG cc_start: 0.8291 (mtt180) cc_final: 0.7134 (ptp-170) REVERT: C 546 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7424 (mp0) REVERT: C 637 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7244 (ptt-90) REVERT: C 641 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.6929 (mm-30) REVERT: C 645 PHE cc_start: 0.7668 (m-80) cc_final: 0.7288 (m-80) REVERT: C 737 ASN cc_start: 0.6778 (m-40) cc_final: 0.6550 (m110) REVERT: C 834 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7892 (pt0) REVERT: C 1022 LYS cc_start: 0.5194 (OUTLIER) cc_final: 0.4951 (tmmt) REVERT: C 1073 LYS cc_start: 0.8789 (pttt) cc_final: 0.8503 (pttp) REVERT: C 1085 MET cc_start: 0.8642 (mmp) cc_final: 0.8350 (mmt) REVERT: C 1157 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.6969 (pp30) REVERT: C 1174 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7649 (mt-10) REVERT: C 1211 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7629 (mtp85) REVERT: C 1268 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7811 (mp10) REVERT: C 1290 MET cc_start: 0.8808 (ttm) cc_final: 0.8239 (ttm) REVERT: C 1340 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7495 (pt0) REVERT: D 29 MET cc_start: 0.6982 (ttm) cc_final: 0.6767 (ttm) REVERT: D 39 LYS cc_start: 0.8875 (mtmt) cc_final: 0.8630 (mtmm) REVERT: D 200 GLN cc_start: 0.8419 (mm-40) cc_final: 0.7944 (tm-30) REVERT: D 322 ARG cc_start: 0.8766 (mtp85) cc_final: 0.8434 (ptt90) REVERT: D 395 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7926 (tptt) REVERT: D 441 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7802 (mm) REVERT: D 484 MET cc_start: 0.9308 (mtp) cc_final: 0.9056 (mtp) REVERT: D 610 ARG cc_start: 0.8182 (mmt-90) cc_final: 0.7790 (ttp80) REVERT: D 765 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8269 (mt-10) REVERT: D 905 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.6973 (mpt180) REVERT: D 918 ILE cc_start: 0.7650 (OUTLIER) cc_final: 0.7227 (pt) REVERT: D 983 LYS cc_start: 0.8202 (mmmm) cc_final: 0.7772 (mppt) REVERT: D 1149 ARG cc_start: 0.8529 (mmm160) cc_final: 0.7829 (tpp-160) REVERT: D 1152 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8724 (mm-30) REVERT: D 1172 LYS cc_start: 0.7468 (mmtm) cc_final: 0.6720 (mmtp) REVERT: D 1345 ARG cc_start: 0.8918 (mtp85) cc_final: 0.8546 (ttm-80) REVERT: D 1366 HIS cc_start: 0.7684 (OUTLIER) cc_final: 0.6935 (m-70) REVERT: D 1368 ASP cc_start: 0.7030 (OUTLIER) cc_final: 0.5802 (m-30) REVERT: E 43 ASN cc_start: 0.8903 (m-40) cc_final: 0.8452 (t0) REVERT: F 64 GLU cc_start: 0.8504 (tp30) cc_final: 0.8140 (tp30) REVERT: F 67 TYR cc_start: 0.7769 (m-80) cc_final: 0.7251 (m-10) REVERT: F 92 ARG cc_start: 0.7762 (ttm110) cc_final: 0.7039 (ttt-90) REVERT: F 96 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7727 (mp0) REVERT: F 111 ASN cc_start: 0.8178 (t0) cc_final: 0.7822 (t0) REVERT: F 200 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8208 (tm-30) REVERT: F 236 ASP cc_start: 0.7915 (t0) cc_final: 0.7552 (t0) REVERT: F 240 ASP cc_start: 0.8126 (t0) cc_final: 0.7035 (t0) REVERT: F 256 LYS cc_start: 0.7878 (mttp) cc_final: 0.7465 (mptt) REVERT: F 269 LYS cc_start: 0.8564 (tppt) cc_final: 0.8342 (tptt) REVERT: J 24 ARG cc_start: 0.7919 (mmt90) cc_final: 0.7520 (mmt90) REVERT: J 37 CYS cc_start: 0.7928 (t) cc_final: 0.7604 (t) REVERT: J 51 ARG cc_start: 0.6979 (mtt180) cc_final: 0.6481 (mtt-85) REVERT: J 56 TRP cc_start: 0.6522 (p-90) cc_final: 0.5582 (p-90) REVERT: J 57 TRP cc_start: 0.7929 (p-90) cc_final: 0.7544 (p-90) REVERT: J 67 PHE cc_start: 0.8009 (m-80) cc_final: 0.7694 (m-80) REVERT: J 76 PHE cc_start: 0.8184 (t80) cc_final: 0.7961 (t80) REVERT: J 97 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7781 (pp20) REVERT: J 101 ARG cc_start: 0.8013 (ttm110) cc_final: 0.7585 (mtt-85) REVERT: J 103 PHE cc_start: 0.8038 (t80) cc_final: 0.7716 (t80) REVERT: J 131 LEU cc_start: 0.4503 (OUTLIER) cc_final: 0.4229 (mt) outliers start: 153 outliers final: 115 residues processed: 473 average time/residue: 0.1991 time to fit residues: 149.8472 Evaluate side-chains 474 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 339 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 898 GLU Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1005 GLU Chi-restraints excluded: chain C residue 1022 LYS Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1247 SER Chi-restraints excluded: chain C residue 1250 SER Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1340 GLU Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1028 ILE Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1223 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 71 TYR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 131 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 158 optimal weight: 6.9990 chunk 111 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 134 optimal weight: 9.9990 chunk 277 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 288 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.151341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.100204 restraints weight = 43795.038| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.29 r_work: 0.3171 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30912 Z= 0.124 Angle : 0.601 10.875 42153 Z= 0.311 Chirality : 0.043 0.338 4797 Planarity : 0.004 0.058 5196 Dihedral : 17.587 173.142 5081 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.09 % Favored : 93.88 % Rotamer: Outliers : 4.33 % Allowed : 23.80 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.12 % 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: 3596 helix: 0.54 (0.15), residues: 1319 sheet: -2.14 (0.24), residues: 413 loop : -1.75 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 407 TYR 0.019 0.001 TYR A 177 PHE 0.017 0.001 PHE C1221 TRP 0.050 0.001 TRP C 997 HIS 0.010 0.001 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (30904) covalent geometry : angle 0.59785 / 0.31 (42141) hydrogen bonds : bond 0.03409 / 2.35 ( 1170) hydrogen bonds : angle 4.34715 / 2.95 ( 3290) metal coordination : bond 0.00552 / 0.25 ( 8) metal coordination : angle 3.81635 / 2.25 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 343 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7881 (ttpt) cc_final: 0.7463 (ttmm) REVERT: A 212 ASP cc_start: 0.7012 (OUTLIER) cc_final: 0.6570 (t70) REVERT: B 10 LYS cc_start: 0.8703 (mttp) cc_final: 0.8391 (mtmm) REVERT: B 71 LYS cc_start: 0.6449 (tppt) cc_final: 0.6230 (tppt) REVERT: B 125 LYS cc_start: 0.7432 (tttt) cc_final: 0.7096 (tptm) REVERT: B 200 LYS cc_start: 0.8204 (tttt) cc_final: 0.7912 (tttp) REVERT: B 205 MET cc_start: 0.7940 (ttp) cc_final: 0.7671 (ttp) REVERT: C 36 GLN cc_start: 0.7600 (tt0) cc_final: 0.7273 (tt0) REVERT: C 96 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7985 (pp) REVERT: C 130 MET cc_start: 0.8780 (ttm) cc_final: 0.8466 (ttp) REVERT: C 161 LYS cc_start: 0.8427 (mttt) cc_final: 0.7851 (pttm) REVERT: C 239 MET cc_start: 0.6394 (mtp) cc_final: 0.5998 (mtp) REVERT: C 241 LEU cc_start: 0.8768 (tp) cc_final: 0.7701 (pt) REVERT: C 246 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7331 (mp) REVERT: C 315 MET cc_start: 0.8957 (ttm) cc_final: 0.8617 (ttm) REVERT: C 429 MET cc_start: 0.8168 (mmm) cc_final: 0.7943 (mmm) REVERT: C 510 GLN cc_start: 0.8070 (tp40) cc_final: 0.7749 (tp40) REVERT: C 516 ASP cc_start: 0.7155 (p0) cc_final: 0.6868 (p0) REVERT: C 538 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7390 (pt) REVERT: C 542 ARG cc_start: 0.8381 (mtt180) cc_final: 0.7358 (ptp-170) REVERT: C 546 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7435 (mp0) REVERT: C 637 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7281 (ptt-90) REVERT: C 641 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6883 (mm-30) REVERT: C 805 MET cc_start: 0.8237 (ptm) cc_final: 0.7996 (ptp) REVERT: C 997 TRP cc_start: 0.6885 (m-90) cc_final: 0.6549 (m-90) REVERT: C 1022 LYS cc_start: 0.5201 (OUTLIER) cc_final: 0.4958 (tmmt) REVERT: C 1073 LYS cc_start: 0.8803 (pttt) cc_final: 0.8498 (pttp) REVERT: C 1085 MET cc_start: 0.8654 (mmp) cc_final: 0.8383 (mmt) REVERT: C 1157 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.6915 (pp30) REVERT: C 1174 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7660 (mt-10) REVERT: C 1211 ARG cc_start: 0.7843 (mtp85) cc_final: 0.7570 (mtp85) REVERT: C 1340 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7343 (pt0) REVERT: D 29 MET cc_start: 0.7002 (ttm) cc_final: 0.6789 (ttm) REVERT: D 39 LYS cc_start: 0.8905 (mtmt) cc_final: 0.8660 (mtmm) REVERT: D 200 GLN cc_start: 0.8421 (mm-40) cc_final: 0.7943 (tm-30) REVERT: D 259 ARG cc_start: 0.7891 (ttt-90) cc_final: 0.7578 (mtp85) REVERT: D 322 ARG cc_start: 0.8765 (mtp85) cc_final: 0.8436 (ptt90) REVERT: D 363 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7300 (pt) REVERT: D 395 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7914 (tptt) REVERT: D 484 MET cc_start: 0.9320 (mtp) cc_final: 0.9067 (mtp) REVERT: D 581 MET cc_start: 0.8192 (mtt) cc_final: 0.7830 (mtt) REVERT: D 610 ARG cc_start: 0.8193 (mmt-90) cc_final: 0.7851 (ttp80) REVERT: D 765 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8314 (mt-10) REVERT: D 905 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6952 (mpt180) REVERT: D 918 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7316 (pt) REVERT: D 983 LYS cc_start: 0.8195 (mmmm) cc_final: 0.7778 (mppt) REVERT: D 1149 ARG cc_start: 0.8558 (mmm160) cc_final: 0.7867 (tpp-160) REVERT: D 1152 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8697 (mm-30) REVERT: D 1167 LYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6717 (ptmm) REVERT: D 1345 ARG cc_start: 0.8918 (mtp85) cc_final: 0.8611 (ttm-80) REVERT: D 1366 HIS cc_start: 0.7693 (OUTLIER) cc_final: 0.6961 (m-70) REVERT: D 1368 ASP cc_start: 0.7016 (OUTLIER) cc_final: 0.5773 (m-30) REVERT: E 43 ASN cc_start: 0.8930 (m-40) cc_final: 0.8476 (t0) REVERT: F 64 GLU cc_start: 0.8504 (tp30) cc_final: 0.8298 (tp30) REVERT: F 92 ARG cc_start: 0.7666 (ttm110) cc_final: 0.7293 (tmm-80) REVERT: F 111 ASN cc_start: 0.8185 (t0) cc_final: 0.7840 (t0) REVERT: F 200 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8234 (tm-30) REVERT: F 236 ASP cc_start: 0.7888 (t0) cc_final: 0.7523 (t0) REVERT: F 240 ASP cc_start: 0.8149 (t0) cc_final: 0.7050 (t0) REVERT: F 256 LYS cc_start: 0.7859 (mttp) cc_final: 0.7470 (mptt) REVERT: F 269 LYS cc_start: 0.8534 (tppt) cc_final: 0.8331 (tptt) REVERT: J 24 ARG cc_start: 0.7920 (mmt90) cc_final: 0.7519 (mmt90) REVERT: J 37 CYS cc_start: 0.7979 (t) cc_final: 0.7697 (t) REVERT: J 51 ARG cc_start: 0.6944 (mtt180) cc_final: 0.6442 (mtt-85) REVERT: J 56 TRP cc_start: 0.6509 (p-90) cc_final: 0.5579 (p-90) REVERT: J 57 TRP cc_start: 0.7924 (p-90) cc_final: 0.7533 (p-90) REVERT: J 67 PHE cc_start: 0.7995 (m-80) cc_final: 0.7692 (m-80) REVERT: J 76 PHE cc_start: 0.8183 (t80) cc_final: 0.7963 (t80) REVERT: J 97 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7795 (pp20) REVERT: J 101 ARG cc_start: 0.8015 (ttm110) cc_final: 0.7591 (mtt-85) REVERT: J 103 PHE cc_start: 0.8020 (t80) cc_final: 0.7693 (t80) REVERT: J 131 LEU cc_start: 0.4332 (OUTLIER) cc_final: 0.4018 (mt) outliers start: 133 outliers final: 111 residues processed: 450 average time/residue: 0.1993 time to fit residues: 141.9957 Evaluate side-chains 466 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 337 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 898 GLU Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1005 GLU Chi-restraints excluded: chain C residue 1022 LYS Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1250 SER Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1340 GLU Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1028 ILE Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1223 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 71 TYR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 114 MET Chi-restraints excluded: chain J residue 131 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 176 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 302 optimal weight: 10.0000 chunk 144 optimal weight: 0.1980 chunk 313 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 309 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 340 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.151832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.100785 restraints weight = 43751.510| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.20 r_work: 0.3192 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30912 Z= 0.122 Angle : 0.599 10.321 42153 Z= 0.311 Chirality : 0.043 0.341 4797 Planarity : 0.004 0.043 5196 Dihedral : 17.451 171.999 5072 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.65 % Favored : 94.33 % Rotamer: Outliers : 4.46 % Allowed : 23.64 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.30 (0.14), residues: 3596 helix: 0.61 (0.15), residues: 1323 sheet: -2.07 (0.24), residues: 414 loop : -1.69 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 407 TYR 0.019 0.001 TYR A 177 PHE 0.017 0.001 PHE D 172 TRP 0.046 0.001 TRP C 997 HIS 0.004 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (30904) covalent geometry : angle 0.59641 / 0.31 (42141) hydrogen bonds : bond 0.03338 / 2.30 ( 1170) hydrogen bonds : angle 4.27746 / 2.90 ( 3290) metal coordination : bond 0.00527 / 0.25 ( 8) metal coordination : angle 3.61513 / 2.13 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 353 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7857 (ttpt) cc_final: 0.7466 (ttmm) REVERT: A 122 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7009 (mt-10) REVERT: A 127 GLN cc_start: 0.8686 (mt0) cc_final: 0.8211 (pt0) REVERT: A 212 ASP cc_start: 0.6991 (OUTLIER) cc_final: 0.6549 (t70) REVERT: B 10 LYS cc_start: 0.8720 (mttp) cc_final: 0.8417 (mtmm) REVERT: B 38 THR cc_start: 0.7798 (OUTLIER) cc_final: 0.6916 (m) REVERT: B 125 LYS cc_start: 0.7442 (tttt) cc_final: 0.7103 (tptm) REVERT: B 200 LYS cc_start: 0.8193 (tttt) cc_final: 0.7912 (tttp) REVERT: B 205 MET cc_start: 0.7878 (ttp) cc_final: 0.7610 (ttp) REVERT: C 36 GLN cc_start: 0.7572 (tt0) cc_final: 0.7244 (tt0) REVERT: C 130 MET cc_start: 0.8756 (ttm) cc_final: 0.8424 (ttp) REVERT: C 161 LYS cc_start: 0.8394 (mttt) cc_final: 0.7828 (pttm) REVERT: C 239 MET cc_start: 0.6394 (mtp) cc_final: 0.6016 (mtp) REVERT: C 241 LEU cc_start: 0.8780 (tp) cc_final: 0.7799 (pt) REVERT: C 246 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7335 (mp) REVERT: C 315 MET cc_start: 0.8970 (ttm) cc_final: 0.8635 (ttm) REVERT: C 429 MET cc_start: 0.8163 (mmm) cc_final: 0.7935 (mmm) REVERT: C 510 GLN cc_start: 0.8096 (tp40) cc_final: 0.7769 (tp40) REVERT: C 516 ASP cc_start: 0.7075 (p0) cc_final: 0.6653 (p0) REVERT: C 538 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7361 (pt) REVERT: C 542 ARG cc_start: 0.8375 (mtt180) cc_final: 0.7399 (ptp-170) REVERT: C 546 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7471 (mp0) REVERT: C 637 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7442 (ptt-90) REVERT: C 641 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6865 (mm-30) REVERT: C 805 MET cc_start: 0.8216 (ptm) cc_final: 0.7960 (ptp) REVERT: C 1034 ARG cc_start: 0.8869 (ttm110) cc_final: 0.8660 (mmm-85) REVERT: C 1073 LYS cc_start: 0.8753 (pttt) cc_final: 0.8422 (pttp) REVERT: C 1085 MET cc_start: 0.8638 (mmp) cc_final: 0.8377 (mmt) REVERT: C 1143 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7552 (tm-30) REVERT: C 1157 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.6862 (pp30) REVERT: C 1174 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7636 (mt-10) REVERT: C 1211 ARG cc_start: 0.7803 (mtp85) cc_final: 0.7552 (mtp85) REVERT: C 1290 MET cc_start: 0.8713 (ttm) cc_final: 0.8393 (ttm) REVERT: C 1296 ASP cc_start: 0.8865 (t0) cc_final: 0.8590 (t0) REVERT: C 1340 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7325 (pt0) REVERT: D 29 MET cc_start: 0.6990 (ttm) cc_final: 0.6764 (ttm) REVERT: D 39 LYS cc_start: 0.8920 (mtmt) cc_final: 0.8666 (mtmm) REVERT: D 130 MET cc_start: 0.7973 (ttm) cc_final: 0.7758 (ttm) REVERT: D 200 GLN cc_start: 0.8422 (mm-40) cc_final: 0.7932 (tm-30) REVERT: D 259 ARG cc_start: 0.7901 (ttt-90) cc_final: 0.7590 (mtp85) REVERT: D 322 ARG cc_start: 0.8765 (mtp85) cc_final: 0.8435 (ptt90) REVERT: D 363 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7319 (pt) REVERT: D 395 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7804 (tptt) REVERT: D 484 MET cc_start: 0.9317 (mtp) cc_final: 0.9039 (mtp) REVERT: D 581 MET cc_start: 0.8154 (mtt) cc_final: 0.7868 (mtt) REVERT: D 610 ARG cc_start: 0.8200 (mmt-90) cc_final: 0.7860 (ttp80) REVERT: D 765 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8341 (mt-10) REVERT: D 905 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6967 (mpt180) REVERT: D 918 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7295 (pt) REVERT: D 983 LYS cc_start: 0.8231 (mmmm) cc_final: 0.7825 (mppt) REVERT: D 1149 ARG cc_start: 0.8560 (mmm160) cc_final: 0.7722 (tpp-160) REVERT: D 1152 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8697 (mm-30) REVERT: D 1167 LYS cc_start: 0.6703 (OUTLIER) cc_final: 0.6285 (ptmm) REVERT: D 1219 ASP cc_start: 0.8045 (m-30) cc_final: 0.7841 (m-30) REVERT: D 1345 ARG cc_start: 0.8919 (mtp85) cc_final: 0.8617 (ttm-80) REVERT: D 1366 HIS cc_start: 0.7742 (OUTLIER) cc_final: 0.6953 (m-70) REVERT: D 1368 ASP cc_start: 0.7019 (OUTLIER) cc_final: 0.5840 (m-30) REVERT: E 43 ASN cc_start: 0.8927 (m-40) cc_final: 0.8485 (t0) REVERT: F 64 GLU cc_start: 0.8655 (tp30) cc_final: 0.8269 (tp30) REVERT: F 78 TYR cc_start: 0.8487 (m-10) cc_final: 0.8283 (m-80) REVERT: F 92 ARG cc_start: 0.7766 (ttm110) cc_final: 0.7435 (ttt-90) REVERT: F 111 ASN cc_start: 0.8086 (t0) cc_final: 0.7786 (t0) REVERT: F 200 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8248 (tm-30) REVERT: F 236 ASP cc_start: 0.7846 (t0) cc_final: 0.7445 (t0) REVERT: F 240 ASP cc_start: 0.8108 (t0) cc_final: 0.7002 (t0) REVERT: F 256 LYS cc_start: 0.7819 (mttp) cc_final: 0.7440 (mptt) REVERT: F 269 LYS cc_start: 0.8525 (tppt) cc_final: 0.8307 (tptt) REVERT: J 24 ARG cc_start: 0.7791 (mmt90) cc_final: 0.7441 (mmt90) REVERT: J 37 CYS cc_start: 0.7962 (t) cc_final: 0.7648 (t) REVERT: J 51 ARG cc_start: 0.6976 (mtt180) cc_final: 0.6228 (mtt-85) REVERT: J 56 TRP cc_start: 0.6472 (p-90) cc_final: 0.5546 (p-90) REVERT: J 57 TRP cc_start: 0.7913 (p-90) cc_final: 0.7520 (p-90) REVERT: J 67 PHE cc_start: 0.7978 (m-80) cc_final: 0.7680 (m-80) REVERT: J 97 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7832 (pp20) REVERT: J 101 ARG cc_start: 0.7912 (ttm110) cc_final: 0.7485 (mtt-85) REVERT: J 103 PHE cc_start: 0.8029 (t80) cc_final: 0.7744 (t80) REVERT: J 131 LEU cc_start: 0.4285 (OUTLIER) cc_final: 0.3928 (mt) outliers start: 137 outliers final: 109 residues processed: 460 average time/residue: 0.2055 time to fit residues: 150.6975 Evaluate side-chains 470 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 343 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 898 GLU Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1109 ILE Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1247 SER Chi-restraints excluded: chain C residue 1250 SER Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1340 GLU Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1028 ILE Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1223 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 71 TYR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 114 MET Chi-restraints excluded: chain J residue 131 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 141 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 346 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 316 optimal weight: 1.9990 chunk 333 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 238 optimal weight: 1.9990 chunk 208 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** C1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.151957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.100943 restraints weight = 44055.606| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.21 r_work: 0.3194 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30912 Z= 0.121 Angle : 0.595 10.439 42153 Z= 0.308 Chirality : 0.043 0.372 4797 Planarity : 0.004 0.043 5196 Dihedral : 17.353 171.800 5066 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.59 % Favored : 94.38 % Rotamer: Outliers : 4.20 % Allowed : 23.54 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.12 % 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: -1.22 (0.14), residues: 3596 helix: 0.68 (0.15), residues: 1326 sheet: -1.98 (0.24), residues: 419 loop : -1.67 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 407 TYR 0.043 0.001 TYR F 67 PHE 0.019 0.001 PHE D 172 TRP 0.061 0.001 TRP C 997 HIS 0.006 0.001 HIS C1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (30904) covalent geometry : angle 0.59229 / 0.31 (42141) hydrogen bonds : bond 0.03286 / 2.26 ( 1170) hydrogen bonds : angle 4.22848 / 2.86 ( 3290) metal coordination : bond 0.00518 / 0.24 ( 8) metal coordination : angle 3.45811 / 2.03 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8380.14 seconds wall clock time: 143 minutes 56.55 seconds (8636.55 seconds total)