Starting phenix.real_space_refine on Fri Mar 6 11:09:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6omf_20090/03_2026/6omf_20090.cif Found real_map, /net/cci-nas-00/data/ceres_data/6omf_20090/03_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_20090/03_2026/6omf_20090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6omf_20090/03_2026/6omf_20090.map" model { file = "/net/cci-nas-00/data/ceres_data/6omf_20090/03_2026/6omf_20090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6omf_20090/03_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-dev-5986/lib/python3.9/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: 6.55, per 1000 atoms: 0.22 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: 2.54 Conformation dependent library (CDL) restraints added in 1.3 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: 4.16 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: 8.01 Time building geometry restraints manager: 3.43 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: 41448 3.14 - 6.27: 606 6.27 - 9.41: 73 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: 4308 0.092 - 0.185: 466 0.185 - 0.277: 19 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 35.390 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 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= 0.551 Angle : 1.055 25.481 42153 Z= 0.581 Chirality : 0.058 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 covalent geometry : bond 0.01167 (30904) covalent geometry : angle 1.03479 (42141) hydrogen bonds : bond 0.19124 ( 1170) hydrogen bonds : angle 8.27950 ( 3290) metal coordination : bond 0.11636 ( 8) metal coordination : angle 12.18525 ( 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 : 1.075 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 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: 0.7770 (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: 0.7946 (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: 0.7106 (ttp-170) 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: 0.5673 (mmpt) REVERT: D 1174 ARG cc_start: 0.6729 (mtt-85) cc_final: 0.6423 (mtt-85) REVERT: D 1317 GLU cc_start: 0.5460 (tm-30) cc_final: 0.5195 (tm-30) REVERT: D 1345 ARG cc_start: 0.8217 (mtp85) cc_final: 0.7951 (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: 0.6656 (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: 0.7875 (t0) REVERT: F 224 THR cc_start: 0.7675 (OUTLIER) cc_final: 0.7273 (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: 0.7077 (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: 0.5119 (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: 187 residues processed: 845 average time/residue: 0.2100 time to fit residues: 277.7643 Evaluate side-chains 575 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 362 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 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... Flipped N/Q/H residues before XYZ refinement: A 227 GLN B 84 ASN B 117 HIS B 132 HIS B 186 ASN C 46 GLN 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** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS C1220 GLN C1324 ASN 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 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: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.150561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.098694 restraints weight = 43563.821| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.09 r_work: 0.3176 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 30912 Z= 0.159 Angle : 0.663 12.278 42153 Z= 0.352 Chirality : 0.043 0.155 4797 Planarity : 0.005 0.054 5196 Dihedral : 18.888 173.713 5352 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.81 % Favored : 94.16 % Rotamer: Outliers : 6.84 % Allowed : 17.68 % Favored : 75.48 % 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: -2.91 (0.13), residues: 3596 helix: -1.14 (0.13), residues: 1331 sheet: -2.92 (0.21), residues: 437 loop : -2.28 (0.13), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1372 TYR 0.021 0.001 TYR A 177 PHE 0.022 0.002 PHE C 337 TRP 0.015 0.001 TRP C 997 HIS 0.012 0.001 HIS D 777 Details of bonding type rmsd covalent geometry : bond 0.00357 (30904) covalent geometry : angle 0.65460 (42141) hydrogen bonds : bond 0.04417 ( 1170) hydrogen bonds : angle 5.42385 ( 3290) metal coordination : bond 0.01174 ( 8) metal coordination : angle 6.24077 ( 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 627 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 417 time to evaluate : 0.892 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: 0.8289 (mm-40) cc_final: 0.8083 (tp40) REVERT: A 145 LYS cc_start: 0.8698 (tttt) cc_final: 0.8272 (tttm) REVERT: A 212 ASP cc_start: 0.6866 (OUTLIER) cc_final: 0.6403 (t0) REVERT: A 223 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7873 (mt) REVERT: B 10 LYS cc_start: 0.8653 (mttp) cc_final: 0.8132 (mppt) REVERT: B 51 MET cc_start: 0.7698 (ttt) cc_final: 0.7168 (ttp) REVERT: B 66 HIS cc_start: 0.7960 (t-90) cc_final: 0.7708 (t-90) REVERT: B 125 LYS cc_start: 0.7582 (tttt) cc_final: 0.7119 (tptm) REVERT: B 145 LYS cc_start: 0.7612 (tttt) cc_final: 0.6937 (tttt) REVERT: B 200 LYS cc_start: 0.8214 (tttt) cc_final: 0.7800 (ttpp) REVERT: C 31 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.6453 (mm110) REVERT: C 36 GLN cc_start: 0.7749 (tt0) cc_final: 0.7407 (tt0) REVERT: C 130 MET cc_start: 0.8718 (ttm) cc_final: 0.8415 (ttp) REVERT: C 189 ASP cc_start: 0.7920 (m-30) cc_final: 0.7654 (m-30) REVERT: C 241 LEU cc_start: 0.8766 (tp) cc_final: 0.7973 (pp) REVERT: C 246 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7062 (tp) REVERT: C 315 MET cc_start: 0.8781 (ttm) cc_final: 0.8382 (ttm) REVERT: C 369 MET cc_start: 0.8712 (ttp) cc_final: 0.8044 (tmm) REVERT: C 424 ASP cc_start: 0.7897 (m-30) cc_final: 0.7574 (m-30) REVERT: C 446 ASP cc_start: 0.8428 (m-30) cc_final: 0.8171 (m-30) REVERT: C 456 VAL cc_start: 0.8127 (t) cc_final: 0.7900 (t) REVERT: C 504 GLU cc_start: 0.8654 (tt0) cc_final: 0.8425 (tm-30) REVERT: C 510 GLN cc_start: 0.8030 (tp40) cc_final: 0.7788 (tp-100) REVERT: C 538 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7065 (pp) REVERT: C 542 ARG cc_start: 0.8282 (mtt180) cc_final: 0.7283 (ptp-170) REVERT: C 546 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7020 (mp0) REVERT: C 596 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8332 (p0) REVERT: C 637 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.6909 (ptt-90) REVERT: C 704 MET cc_start: 0.8029 (mmm) cc_final: 0.7253 (tpp) REVERT: C 737 ASN cc_start: 0.6660 (m-40) cc_final: 0.6352 (m110) REVERT: C 788 SER cc_start: 0.8364 (OUTLIER) cc_final: 0.7980 (p) REVERT: C 805 MET cc_start: 0.8601 (ptm) cc_final: 0.8393 (ptp) REVERT: C 814 ASP cc_start: 0.8764 (m-30) cc_final: 0.8513 (m-30) REVERT: C 1023 HIS cc_start: 0.7698 (t70) cc_final: 0.7224 (t70) REVERT: C 1073 LYS cc_start: 0.8570 (pttt) cc_final: 0.8368 (pttp) REVERT: C 1085 MET cc_start: 0.8587 (mmt) cc_final: 0.8268 (mmt) REVERT: C 1174 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7235 (mt-10) REVERT: C 1296 ASP cc_start: 0.8881 (t0) cc_final: 0.8523 (t0) REVERT: C 1321 GLU cc_start: 0.8214 (tp30) cc_final: 0.7861 (tp30) REVERT: D 29 MET cc_start: 0.7167 (ttm) cc_final: 0.6932 (ttm) REVERT: D 39 LYS cc_start: 0.8869 (mtmt) cc_final: 0.8610 (mtmm) REVERT: D 140 TYR cc_start: 0.8771 (m-80) cc_final: 0.8411 (m-10) REVERT: D 200 GLN cc_start: 0.8453 (mm-40) cc_final: 0.7944 (tm-30) REVERT: D 300 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7359 (tm-30) REVERT: D 322 ARG cc_start: 0.8636 (mtp85) cc_final: 0.8089 (ptt90) REVERT: D 399 LYS cc_start: 0.7744 (mtpt) cc_final: 0.7293 (mttp) REVERT: D 422 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8162 (mp) REVERT: D 458 ASN cc_start: 0.8994 (t0) cc_final: 0.8704 (t0) REVERT: D 484 MET cc_start: 0.9205 (mtp) cc_final: 0.8931 (mtp) REVERT: D 578 ILE cc_start: 0.8365 (mt) cc_final: 0.8124 (mt) REVERT: D 610 ARG cc_start: 0.8154 (mmt-90) cc_final: 0.7543 (mtm110) REVERT: D 747 MET cc_start: 0.8173 (mmt) cc_final: 0.7913 (mmt) REVERT: D 765 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8164 (mt-10) REVERT: D 905 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6592 (mpt180) REVERT: D 918 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7306 (pt) REVERT: D 1149 ARG cc_start: 0.8445 (mmm160) cc_final: 0.7751 (tpp-160) REVERT: D 1172 LYS cc_start: 0.6979 (mmtm) cc_final: 0.5782 (mmpt) REVERT: D 1174 ARG cc_start: 0.6743 (mtt-85) cc_final: 0.6448 (mtt-85) REVERT: D 1262 ARG cc_start: 0.7430 (mtp180) cc_final: 0.7227 (mtm110) REVERT: D 1345 ARG cc_start: 0.8704 (mtp85) cc_final: 0.8401 (ttm110) REVERT: D 1368 ASP cc_start: 0.6820 (OUTLIER) cc_final: 0.5742 (m-30) REVERT: E 3 ARG cc_start: 0.8006 (tpp-160) cc_final: 0.7428 (tpt170) REVERT: E 43 ASN cc_start: 0.8607 (m-40) cc_final: 0.8142 (t0) REVERT: E 62 GLN cc_start: 0.8391 (tp-100) cc_final: 0.8049 (tp-100) REVERT: E 76 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8507 (mm-30) REVERT: F 64 GLU cc_start: 0.8524 (tp30) cc_final: 0.8288 (tp30) REVERT: F 67 TYR cc_start: 0.7803 (m-80) cc_final: 0.7242 (m-10) REVERT: F 92 ARG cc_start: 0.7793 (ttm110) cc_final: 0.7449 (ttt-90) REVERT: F 96 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8059 (mt-10) REVERT: F 216 ASN cc_start: 0.8225 (t0) cc_final: 0.7983 (t0) REVERT: F 240 ASP cc_start: 0.8164 (t0) cc_final: 0.7132 (t0) REVERT: F 269 LYS cc_start: 0.8582 (tppt) cc_final: 0.8235 (tppt) REVERT: J 24 ARG cc_start: 0.7625 (mmt90) cc_final: 0.7357 (tpp80) REVERT: J 37 CYS cc_start: 0.8016 (t) cc_final: 0.7594 (t) REVERT: J 56 TRP cc_start: 0.6579 (p-90) cc_final: 0.5512 (p-90) REVERT: J 67 PHE cc_start: 0.8010 (m-80) cc_final: 0.7568 (m-80) REVERT: J 72 GLN cc_start: 0.7383 (mt0) cc_final: 0.7006 (mt0) REVERT: J 76 PHE cc_start: 0.8418 (t80) cc_final: 0.8161 (t80) REVERT: J 82 TRP cc_start: 0.6809 (m100) cc_final: 0.6490 (m100) REVERT: J 101 ARG cc_start: 0.7849 (ttm110) cc_final: 0.7488 (mtt90) outliers start: 210 outliers final: 138 residues processed: 592 average time/residue: 0.1957 time to fit residues: 183.7391 Evaluate side-chains 505 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 354 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 120 ASP Chi-restraints excluded: chain A residue 124 VAL 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 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 194 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 356 THR 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 596 ASP Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 644 LEU 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 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 913 VAL 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 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 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 300 GLN Chi-restraints excluded: chain D residue 363 LEU 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 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 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 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 807 LEU 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 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 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 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 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: 0.0050 chunk 247 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 264 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 217 optimal weight: 4.9990 chunk 239 optimal weight: 0.6980 chunk 274 optimal weight: 10.0000 chunk 292 optimal weight: 20.0000 chunk 69 optimal weight: 8.9990 overall best weight: 1.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS C 46 GLN ** 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 875 ASN D 954 ASN D1326 GLN F 251 GLN ** F 267 ASN ** 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 = 0.3968 r_free = 0.3968 target = 0.148239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.097321 restraints weight = 44056.766| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 3.16 r_work: 0.3142 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 30912 Z= 0.206 Angle : 0.649 9.935 42153 Z= 0.339 Chirality : 0.044 0.181 4797 Planarity : 0.004 0.055 5196 Dihedral : 18.286 172.191 5173 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.51 % Favored : 93.46 % Rotamer: Outliers : 6.22 % Allowed : 18.82 % Favored : 74.96 % 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: -2.29 (0.13), residues: 3596 helix: -0.43 (0.14), residues: 1322 sheet: -2.57 (0.22), residues: 447 loop : -2.07 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1372 TYR 0.023 0.002 TYR A 177 PHE 0.023 0.002 PHE C 186 TRP 0.028 0.001 TRP C 997 HIS 0.010 0.001 HIS D 777 Details of bonding type rmsd covalent geometry : bond 0.00482 (30904) covalent geometry : angle 0.64289 (42141) hydrogen bonds : bond 0.04037 ( 1170) hydrogen bonds : angle 4.98425 ( 3290) metal coordination : bond 0.01103 ( 8) metal coordination : angle 5.15268 ( 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 569 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 378 time to evaluate : 0.928 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: 0.7806 (OUTLIER) cc_final: 0.7591 (ttpt) REVERT: A 65 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8784 (mt) REVERT: A 93 GLN cc_start: 0.8261 (mm-40) cc_final: 0.8050 (tp40) REVERT: A 145 LYS cc_start: 0.8790 (tttt) cc_final: 0.8346 (tttp) REVERT: A 212 ASP cc_start: 0.7066 (OUTLIER) cc_final: 0.6566 (t70) REVERT: A 223 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.8073 (mt) REVERT: B 10 LYS cc_start: 0.8721 (mttp) cc_final: 0.8373 (mtmm) REVERT: B 71 LYS cc_start: 0.6254 (tppt) cc_final: 0.5849 (tppt) REVERT: B 125 LYS cc_start: 0.7575 (tttt) cc_final: 0.7210 (tptm) REVERT: B 145 LYS cc_start: 0.7672 (tttt) cc_final: 0.7360 (tttp) REVERT: B 147 GLN cc_start: 0.6752 (tt0) cc_final: 0.6062 (mt0) REVERT: B 200 LYS cc_start: 0.8278 (tttt) cc_final: 0.7809 (tttp) REVERT: C 36 GLN cc_start: 0.7722 (tt0) cc_final: 0.7351 (tt0) REVERT: C 124 MET cc_start: 0.8694 (ptm) cc_final: 0.8463 (ptm) REVERT: C 130 MET cc_start: 0.8913 (ttm) cc_final: 0.8604 (ttp) REVERT: C 161 LYS cc_start: 0.8650 (mttt) cc_final: 0.8141 (pttm) REVERT: C 189 ASP cc_start: 0.7787 (m-30) cc_final: 0.7545 (m-30) REVERT: C 241 LEU cc_start: 0.8882 (tp) cc_final: 0.8197 (pp) REVERT: C 315 MET cc_start: 0.8855 (ttm) cc_final: 0.8512 (ttm) REVERT: C 424 ASP cc_start: 0.7816 (m-30) cc_final: 0.7435 (m-30) REVERT: C 446 ASP cc_start: 0.8455 (m-30) cc_final: 0.8179 (m-30) REVERT: C 456 VAL cc_start: 0.8189 (t) cc_final: 0.7989 (t) REVERT: C 504 GLU cc_start: 0.8658 (tt0) cc_final: 0.8456 (tm-30) REVERT: C 510 GLN cc_start: 0.8212 (tp40) cc_final: 0.7907 (tp-100) REVERT: C 538 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7140 (pp) REVERT: C 546 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7195 (mp0) REVERT: C 637 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.6796 (ptt-90) REVERT: C 641 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6748 (mm-30) REVERT: C 645 PHE cc_start: 0.7902 (m-80) cc_final: 0.6802 (m-80) REVERT: C 704 MET cc_start: 0.8085 (mmm) cc_final: 0.7273 (tpp) REVERT: C 805 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8374 (ptp) REVERT: C 1073 LYS cc_start: 0.8701 (pttt) cc_final: 0.8463 (pttp) REVERT: C 1085 MET cc_start: 0.8634 (mmt) cc_final: 0.8374 (mmt) REVERT: C 1157 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7015 (pp30) REVERT: C 1160 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8223 (m-30) REVERT: C 1174 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7312 (mt-10) REVERT: D 29 MET cc_start: 0.7259 (ttm) cc_final: 0.6985 (ttm) REVERT: D 39 LYS cc_start: 0.8890 (mtmt) cc_final: 0.8644 (mtmm) REVERT: D 200 GLN cc_start: 0.8442 (mm-40) cc_final: 0.7953 (tm-30) REVERT: D 322 ARG cc_start: 0.8651 (mtp85) cc_final: 0.8120 (ptt90) REVERT: D 372 MET cc_start: 0.7878 (mtm) cc_final: 0.7637 (mtm) REVERT: D 399 LYS cc_start: 0.7796 (mtpt) cc_final: 0.7526 (mptt) REVERT: D 422 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8051 (mp) REVERT: D 458 ASN cc_start: 0.9029 (t0) cc_final: 0.8747 (t0) REVERT: D 484 MET cc_start: 0.9259 (mtp) cc_final: 0.8963 (mtp) REVERT: D 610 ARG cc_start: 0.8227 (mmt-90) cc_final: 0.7567 (mtm110) REVERT: D 765 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8206 (mt-10) REVERT: D 785 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7393 (t70) REVERT: D 918 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7241 (pt) REVERT: D 1025 MET cc_start: 0.6753 (tpt) cc_final: 0.6513 (tpt) REVERT: D 1121 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6512 (mp) REVERT: D 1149 ARG cc_start: 0.8497 (mmm160) cc_final: 0.7803 (tpp-160) REVERT: D 1172 LYS cc_start: 0.7280 (mmtm) cc_final: 0.6154 (mmpt) REVERT: D 1174 ARG cc_start: 0.6542 (mtt-85) cc_final: 0.6311 (mtt-85) REVERT: D 1260 MET cc_start: 0.8870 (mtp) cc_final: 0.8625 (mtm) REVERT: D 1345 ARG cc_start: 0.8892 (mtp85) cc_final: 0.8646 (ttm-80) REVERT: D 1368 ASP cc_start: 0.6839 (OUTLIER) cc_final: 0.5554 (m-30) REVERT: E 3 ARG cc_start: 0.8022 (tpp-160) cc_final: 0.7615 (tpt170) REVERT: E 43 ASN cc_start: 0.8700 (m-40) cc_final: 0.8266 (t0) REVERT: E 62 GLN cc_start: 0.8346 (tp-100) cc_final: 0.8062 (tp-100) REVERT: F 64 GLU cc_start: 0.8559 (tp30) cc_final: 0.8203 (tp30) REVERT: F 67 TYR cc_start: 0.7640 (m-80) cc_final: 0.7128 (m-10) REVERT: F 92 ARG cc_start: 0.7605 (ttm110) cc_final: 0.7270 (ttt-90) REVERT: F 96 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7728 (mt-10) REVERT: F 140 PHE cc_start: 0.6713 (m-80) cc_final: 0.6442 (m-80) REVERT: F 216 ASN cc_start: 0.8230 (t0) cc_final: 0.8018 (t0) REVERT: F 240 ASP cc_start: 0.8154 (t0) cc_final: 0.7199 (t0) REVERT: F 269 LYS cc_start: 0.8588 (tppt) cc_final: 0.8312 (tppt) REVERT: J 11 ARG cc_start: 0.7479 (ptp-170) cc_final: 0.7162 (mtm110) REVERT: J 24 ARG cc_start: 0.7584 (mmt90) cc_final: 0.7200 (tpp80) REVERT: J 37 CYS cc_start: 0.8022 (t) cc_final: 0.7662 (t) REVERT: J 51 ARG cc_start: 0.7001 (mpp80) cc_final: 0.6538 (mtm180) REVERT: J 56 TRP cc_start: 0.6461 (p-90) cc_final: 0.5482 (p-90) REVERT: J 67 PHE cc_start: 0.7976 (m-80) cc_final: 0.7645 (m-80) REVERT: J 76 PHE cc_start: 0.8254 (t80) cc_final: 0.7937 (t80) REVERT: J 82 TRP cc_start: 0.6417 (m100) cc_final: 0.6184 (m100) REVERT: J 101 ARG cc_start: 0.7922 (ttm110) cc_final: 0.7557 (mtt90) outliers start: 191 outliers final: 138 residues processed: 528 average time/residue: 0.1921 time to fit residues: 162.2114 Evaluate side-chains 498 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 345 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 65 LEU Chi-restraints excluded: chain A residue 70 THR 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 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 2 VAL Chi-restraints excluded: chain C residue 21 VAL 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 297 VAL Chi-restraints excluded: chain C residue 309 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 483 ASP 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 576 SER 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 994 ARG Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1022 LYS Chi-restraints excluded: chain C residue 1054 LEU 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 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 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 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 371 LYS Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 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 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 701 LEU 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 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 1121 LEU 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 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 281 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 23 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 3 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 269 optimal weight: 0.9990 chunk 346 optimal weight: 20.0000 chunk 211 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 246 optimal weight: 3.9990 chunk 222 optimal weight: 0.0970 chunk 83 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN C 628 HIS ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 GLN D 910 ASN D 954 ASN F 170 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.151180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.099631 restraints weight = 43727.834| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.07 r_work: 0.3188 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30912 Z= 0.124 Angle : 0.588 11.250 42153 Z= 0.307 Chirality : 0.042 0.229 4797 Planarity : 0.004 0.047 5196 Dihedral : 17.792 172.043 5126 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.51 % Favored : 94.47 % Rotamer: Outliers : 5.50 % Allowed : 20.22 % Favored : 74.28 % 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: -1.84 (0.14), residues: 3596 helix: 0.05 (0.14), residues: 1326 sheet: -2.41 (0.23), residues: 413 loop : -1.91 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 200 TYR 0.021 0.001 TYR A 177 PHE 0.020 0.001 PHE C 186 TRP 0.043 0.001 TRP C 997 HIS 0.009 0.001 HIS D 777 Details of bonding type rmsd covalent geometry : bond 0.00281 (30904) covalent geometry : angle 0.58418 (42141) hydrogen bonds : bond 0.03456 ( 1170) hydrogen bonds : angle 4.61244 ( 3290) metal coordination : bond 0.00522 ( 8) metal coordination : angle 4.22771 ( 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 548 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 379 time to evaluate : 1.040 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: A 25 LYS cc_start: 0.7848 (ttpt) cc_final: 0.7375 (ttmm) REVERT: A 127 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8098 (pt0) REVERT: A 145 LYS cc_start: 0.8838 (tttt) cc_final: 0.8383 (tttm) REVERT: A 212 ASP cc_start: 0.6990 (OUTLIER) cc_final: 0.6489 (t0) REVERT: A 223 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7972 (mt) REVERT: B 10 LYS cc_start: 0.8699 (mttp) cc_final: 0.8373 (mtmm) REVERT: B 38 THR cc_start: 0.7777 (OUTLIER) cc_final: 0.6951 (m) REVERT: B 71 LYS cc_start: 0.6208 (tppt) cc_final: 0.5736 (tppt) REVERT: B 125 LYS cc_start: 0.7529 (tttt) cc_final: 0.7172 (tptm) REVERT: B 145 LYS cc_start: 0.7539 (tttt) cc_final: 0.7103 (tttp) REVERT: B 147 GLN cc_start: 0.6630 (tt0) cc_final: 0.5826 (mt0) REVERT: B 200 LYS cc_start: 0.8182 (tttt) cc_final: 0.7684 (tttp) REVERT: C 31 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.6100 (mm110) REVERT: C 36 GLN cc_start: 0.7663 (tt0) cc_final: 0.7308 (tt0) REVERT: C 96 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7899 (pp) REVERT: C 130 MET cc_start: 0.8786 (ttm) cc_final: 0.8451 (ttp) REVERT: C 161 LYS cc_start: 0.8673 (mttt) cc_final: 0.8036 (pttm) REVERT: C 223 LEU cc_start: 0.8528 (mt) cc_final: 0.8316 (tp) REVERT: C 241 LEU cc_start: 0.8900 (tp) cc_final: 0.8114 (pp) REVERT: C 246 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7233 (tp) REVERT: C 315 MET cc_start: 0.8901 (ttm) cc_final: 0.8549 (ttm) REVERT: C 446 ASP cc_start: 0.8317 (m-30) cc_final: 0.8114 (m-30) REVERT: C 504 GLU cc_start: 0.8670 (tt0) cc_final: 0.8437 (tm-30) REVERT: C 510 GLN cc_start: 0.8242 (tp40) cc_final: 0.7869 (tp-100) REVERT: C 513 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7897 (mt0) REVERT: C 538 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7002 (pp) REVERT: C 542 ARG cc_start: 0.8220 (mtt180) cc_final: 0.7159 (ptp-170) REVERT: C 546 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7175 (mp0) REVERT: C 637 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.6794 (ptt-90) REVERT: C 641 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6801 (mm-30) REVERT: C 645 PHE cc_start: 0.7822 (m-80) cc_final: 0.7104 (m-80) REVERT: C 788 SER cc_start: 0.8446 (OUTLIER) cc_final: 0.7885 (p) REVERT: C 805 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8292 (ptp) REVERT: C 1073 LYS cc_start: 0.8755 (pttt) cc_final: 0.8498 (pttp) REVERT: C 1157 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.6860 (pp30) REVERT: C 1174 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7537 (mt-10) REVERT: C 1211 ARG cc_start: 0.7879 (mtp85) cc_final: 0.7661 (mtp85) REVERT: C 1290 MET cc_start: 0.8634 (ttm) cc_final: 0.8240 (ttm) REVERT: C 1296 ASP cc_start: 0.8887 (t0) cc_final: 0.8569 (t0) REVERT: C 1321 GLU cc_start: 0.8101 (tp30) cc_final: 0.7676 (tp30) REVERT: D 29 MET cc_start: 0.7032 (ttm) cc_final: 0.6810 (ttm) REVERT: D 39 LYS cc_start: 0.8876 (mtmt) cc_final: 0.8598 (mtmm) REVERT: D 172 PHE cc_start: 0.6384 (m-80) cc_final: 0.6155 (m-80) REVERT: D 200 GLN cc_start: 0.8411 (mm-40) cc_final: 0.7935 (tm-30) REVERT: D 322 ARG cc_start: 0.8661 (mtp85) cc_final: 0.8150 (ptt90) REVERT: D 372 MET cc_start: 0.7713 (mtm) cc_final: 0.7469 (mtm) REVERT: D 395 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7890 (tptt) REVERT: D 441 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7768 (mm) REVERT: D 484 MET cc_start: 0.9256 (mtp) cc_final: 0.8989 (mtp) REVERT: D 525 MET cc_start: 0.8402 (ptp) cc_final: 0.8188 (ptm) REVERT: D 610 ARG cc_start: 0.8210 (mmt-90) cc_final: 0.7508 (mtm110) REVERT: D 765 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8238 (mt-10) REVERT: D 785 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7373 (t70) REVERT: D 788 LEU cc_start: 0.8228 (mm) cc_final: 0.7931 (mp) REVERT: D 905 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6747 (mpt180) REVERT: D 918 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7201 (pt) REVERT: D 954 ASN cc_start: 0.7346 (OUTLIER) cc_final: 0.6960 (t0) REVERT: D 981 GLU cc_start: 0.7654 (tt0) cc_final: 0.7062 (tt0) REVERT: D 983 LYS cc_start: 0.8680 (mmmm) cc_final: 0.7992 (mppt) REVERT: D 1025 MET cc_start: 0.7075 (tpt) cc_final: 0.6850 (tpt) REVERT: D 1149 ARG cc_start: 0.8551 (mmm160) cc_final: 0.7725 (tpp-160) REVERT: D 1172 LYS cc_start: 0.7370 (mmtm) cc_final: 0.6218 (mmpt) REVERT: D 1260 MET cc_start: 0.8878 (mtp) cc_final: 0.8642 (mtp) REVERT: D 1291 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8140 (tm-30) REVERT: D 1345 ARG cc_start: 0.8910 (mtp85) cc_final: 0.8523 (ttm-80) REVERT: D 1368 ASP cc_start: 0.6931 (OUTLIER) cc_final: 0.5691 (m-30) REVERT: E 8 ASP cc_start: 0.8398 (m-30) cc_final: 0.8186 (m-30) REVERT: E 43 ASN cc_start: 0.8836 (m-40) cc_final: 0.8344 (t0) REVERT: E 62 GLN cc_start: 0.8302 (tp-100) cc_final: 0.8016 (tp-100) REVERT: F 53 ARG cc_start: 0.7043 (mtt-85) cc_final: 0.6746 (mtp180) REVERT: F 90 SER cc_start: 0.8401 (OUTLIER) cc_final: 0.8132 (p) REVERT: F 92 ARG cc_start: 0.7609 (ttm110) cc_final: 0.7101 (ttt-90) REVERT: F 96 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7875 (mt-10) REVERT: F 111 ASN cc_start: 0.8157 (t0) cc_final: 0.7773 (t0) REVERT: F 151 ARG cc_start: 0.6462 (OUTLIER) cc_final: 0.6024 (ttp80) REVERT: F 200 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8259 (tm-30) REVERT: F 240 ASP cc_start: 0.8192 (t0) cc_final: 0.7127 (t0) REVERT: F 269 LYS cc_start: 0.8587 (tppt) cc_final: 0.8315 (tppt) REVERT: J 24 ARG cc_start: 0.7592 (mmt90) cc_final: 0.7157 (tpp80) REVERT: J 37 CYS cc_start: 0.8008 (t) cc_final: 0.7672 (t) REVERT: J 56 TRP cc_start: 0.6419 (p-90) cc_final: 0.5347 (p-90) REVERT: J 67 PHE cc_start: 0.8026 (m-80) cc_final: 0.7677 (m-80) REVERT: J 76 PHE cc_start: 0.8211 (t80) cc_final: 0.7869 (t80) REVERT: J 101 ARG cc_start: 0.8007 (ttm110) cc_final: 0.7588 (mtt90) REVERT: J 103 PHE cc_start: 0.8193 (t80) cc_final: 0.7917 (t80) REVERT: J 114 MET cc_start: 0.5133 (ttt) cc_final: 0.4900 (ttt) outliers start: 169 outliers final: 118 residues processed: 516 average time/residue: 0.2075 time to fit residues: 168.3975 Evaluate side-chains 486 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 345 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 74 VAL Chi-restraints excluded: chain A residue 120 ASP 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 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 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 31 GLN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 179 TYR 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 309 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 483 ASP 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 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 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 1056 VAL Chi-restraints excluded: chain C residue 1077 SER 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 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 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 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 262 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 371 LYS 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 563 LEU 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 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 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 954 ASN 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 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 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 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: 5.9990 chunk 48 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 242 optimal weight: 2.9990 chunk 360 optimal weight: 10.0000 chunk 339 optimal weight: 0.7980 chunk 259 optimal weight: 0.6980 chunk 219 optimal weight: 0.6980 chunk 346 optimal weight: 3.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN C 628 HIS D 665 GLN ** D 875 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.148956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.097399 restraints weight = 44082.073| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 3.13 r_work: 0.3149 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 30912 Z= 0.191 Angle : 0.619 10.910 42153 Z= 0.321 Chirality : 0.043 0.245 4797 Planarity : 0.004 0.048 5196 Dihedral : 17.660 173.383 5104 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.45 % Favored : 93.52 % Rotamer: Outliers : 5.67 % Allowed : 21.17 % Favored : 73.17 % 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: -1.75 (0.14), residues: 3596 helix: 0.11 (0.14), residues: 1330 sheet: -2.27 (0.23), residues: 423 loop : -1.87 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 994 TYR 0.021 0.001 TYR A 177 PHE 0.019 0.001 PHE C 186 TRP 0.047 0.001 TRP C 997 HIS 0.007 0.001 HIS D 777 Details of bonding type rmsd covalent geometry : bond 0.00450 (30904) covalent geometry : angle 0.61518 (42141) hydrogen bonds : bond 0.03604 ( 1170) hydrogen bonds : angle 4.58536 ( 3290) metal coordination : bond 0.01002 ( 8) metal coordination : angle 4.29423 ( 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 527 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 353 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7367 (ttmm) REVERT: A 127 GLN cc_start: 0.8621 (mp10) cc_final: 0.8337 (pt0) REVERT: A 145 LYS cc_start: 0.8882 (tttt) cc_final: 0.8380 (tttm) REVERT: A 212 ASP cc_start: 0.7058 (OUTLIER) cc_final: 0.6566 (t70) REVERT: B 10 LYS cc_start: 0.8710 (mttp) cc_final: 0.8385 (mtmm) REVERT: B 71 LYS cc_start: 0.6225 (tppt) cc_final: 0.5912 (tppt) REVERT: B 125 LYS cc_start: 0.7567 (tttt) cc_final: 0.7197 (tptm) REVERT: B 145 LYS cc_start: 0.7776 (tttt) cc_final: 0.7197 (tttm) REVERT: B 147 GLN cc_start: 0.6695 (tt0) cc_final: 0.6003 (mt0) REVERT: B 200 LYS cc_start: 0.8180 (tttt) cc_final: 0.7663 (tttp) REVERT: C 31 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.6180 (mm110) REVERT: C 36 GLN cc_start: 0.7628 (tt0) cc_final: 0.7334 (tt0) REVERT: C 96 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8107 (pp) REVERT: C 130 MET cc_start: 0.8894 (ttm) cc_final: 0.8496 (ttm) REVERT: C 161 LYS cc_start: 0.8598 (mttt) cc_final: 0.8001 (pttm) REVERT: C 223 LEU cc_start: 0.8543 (mt) cc_final: 0.8334 (tp) REVERT: C 246 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7484 (tp) REVERT: C 315 MET cc_start: 0.8902 (ttm) cc_final: 0.8549 (ttm) REVERT: C 424 ASP cc_start: 0.7860 (m-30) cc_final: 0.7210 (m-30) REVERT: C 446 ASP cc_start: 0.8460 (m-30) cc_final: 0.8224 (m-30) REVERT: C 504 GLU cc_start: 0.8645 (tt0) cc_final: 0.8423 (tm-30) REVERT: C 510 GLN cc_start: 0.8205 (tp40) cc_final: 0.7819 (tp-100) REVERT: C 538 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7027 (pp) REVERT: C 542 ARG cc_start: 0.8256 (mtt180) cc_final: 0.7188 (ptp-170) REVERT: C 546 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7216 (mp0) REVERT: C 637 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.6988 (ptt-90) REVERT: C 641 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.6954 (mm-30) REVERT: C 704 MET cc_start: 0.8053 (mmm) cc_final: 0.7258 (tpp) REVERT: C 805 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8361 (ptm) REVERT: C 1073 LYS cc_start: 0.8832 (pttt) cc_final: 0.8573 (pttp) REVERT: C 1157 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.6977 (pp30) REVERT: C 1174 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7597 (mt-10) REVERT: C 1211 ARG cc_start: 0.7921 (mtp85) cc_final: 0.7707 (mtp85) REVERT: C 1290 MET cc_start: 0.8838 (ttm) cc_final: 0.8519 (ttm) REVERT: C 1321 GLU cc_start: 0.8205 (tp30) cc_final: 0.7953 (tp30) REVERT: D 29 MET cc_start: 0.7187 (ttm) cc_final: 0.6909 (ttm) REVERT: D 39 LYS cc_start: 0.8873 (mtmt) cc_final: 0.8621 (mtmm) REVERT: D 200 GLN cc_start: 0.8435 (mm-40) cc_final: 0.7954 (tm-30) REVERT: D 322 ARG cc_start: 0.8734 (mtp85) cc_final: 0.8407 (ptt90) REVERT: D 363 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7321 (pt) REVERT: D 372 MET cc_start: 0.7837 (mtm) cc_final: 0.7632 (mtm) REVERT: D 395 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7935 (tptt) REVERT: D 484 MET cc_start: 0.9286 (mtp) cc_final: 0.9047 (mtp) REVERT: D 610 ARG cc_start: 0.8228 (mmt-90) cc_final: 0.7548 (mtm110) REVERT: D 765 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8242 (mt-10) REVERT: D 785 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7383 (t70) REVERT: D 918 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7245 (pt) REVERT: D 983 LYS cc_start: 0.8622 (mmmm) cc_final: 0.8308 (mmmm) REVERT: D 1025 MET cc_start: 0.7141 (tpt) cc_final: 0.6930 (tpt) REVERT: D 1146 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7846 (mm-30) REVERT: D 1149 ARG cc_start: 0.8527 (mmm160) cc_final: 0.7891 (tpp-160) REVERT: D 1172 LYS cc_start: 0.7552 (mmtm) cc_final: 0.6879 (mmtp) REVERT: D 1260 MET cc_start: 0.8883 (mtp) cc_final: 0.8648 (mtp) REVERT: D 1291 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8177 (tm-30) REVERT: D 1345 ARG cc_start: 0.8917 (mtp85) cc_final: 0.8593 (ttm-80) REVERT: D 1366 HIS cc_start: 0.7649 (OUTLIER) cc_final: 0.6877 (m-70) REVERT: D 1368 ASP cc_start: 0.6945 (OUTLIER) cc_final: 0.5684 (m-30) REVERT: E 43 ASN cc_start: 0.8855 (m-40) cc_final: 0.8399 (t0) REVERT: F 53 ARG cc_start: 0.7114 (mtt-85) cc_final: 0.6867 (mtp180) REVERT: F 90 SER cc_start: 0.8396 (OUTLIER) cc_final: 0.8142 (p) REVERT: F 92 ARG cc_start: 0.7658 (ttm110) cc_final: 0.7099 (ttt-90) REVERT: F 96 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7901 (mt-10) REVERT: F 111 ASN cc_start: 0.8156 (t0) cc_final: 0.7747 (t0) REVERT: F 140 PHE cc_start: 0.6680 (m-80) cc_final: 0.6397 (m-80) REVERT: F 151 ARG cc_start: 0.6513 (OUTLIER) cc_final: 0.6055 (ttp80) REVERT: F 200 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8241 (tm-30) REVERT: F 240 ASP cc_start: 0.8142 (t0) cc_final: 0.7147 (t0) REVERT: F 256 LYS cc_start: 0.7861 (mttp) cc_final: 0.7471 (mptt) REVERT: F 269 LYS cc_start: 0.8570 (tppt) cc_final: 0.8303 (tppt) REVERT: J 24 ARG cc_start: 0.7634 (mmt90) cc_final: 0.7046 (tpp80) REVERT: J 37 CYS cc_start: 0.7987 (t) cc_final: 0.7646 (t) REVERT: J 51 ARG cc_start: 0.6959 (mtt180) cc_final: 0.6410 (mtt-85) REVERT: J 56 TRP cc_start: 0.6425 (p-90) cc_final: 0.5355 (p-90) REVERT: J 67 PHE cc_start: 0.8040 (m-80) cc_final: 0.7727 (m-80) REVERT: J 76 PHE cc_start: 0.8217 (t80) cc_final: 0.7856 (t80) REVERT: J 103 PHE cc_start: 0.8026 (t80) cc_final: 0.7673 (t80) outliers start: 174 outliers final: 125 residues processed: 489 average time/residue: 0.1918 time to fit residues: 149.9197 Evaluate side-chains 476 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 333 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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 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 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 2 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 96 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 297 VAL Chi-restraints excluded: chain C residue 309 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 483 ASP Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 538 LEU 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 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 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 1005 GLU 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 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 65 VAL Chi-restraints excluded: chain D residue 92 VAL 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 262 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 342 LEU 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 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 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 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 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 58 LEU Chi-restraints excluded: chain F residue 60 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 68 THR 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 129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 341 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 227 optimal weight: 0.9980 chunk 312 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 260 optimal weight: 8.9990 chunk 348 optimal weight: 20.0000 chunk 228 optimal weight: 0.5980 chunk 36 optimal weight: 9.9990 chunk 230 optimal weight: 3.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS D 294 ASN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 954 ASN ** 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 = 0.3950 r_free = 0.3950 target = 0.146593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.094927 restraints weight = 44278.400| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.14 r_work: 0.3107 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 30912 Z= 0.270 Angle : 0.677 10.828 42153 Z= 0.350 Chirality : 0.045 0.259 4797 Planarity : 0.004 0.052 5196 Dihedral : 17.707 177.202 5090 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.79 % Favored : 92.19 % Rotamer: Outliers : 5.93 % Allowed : 21.62 % Favored : 72.45 % 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: -1.83 (0.14), residues: 3596 helix: 0.01 (0.14), residues: 1322 sheet: -2.24 (0.24), residues: 428 loop : -1.89 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1304 TYR 0.045 0.002 TYR F 67 PHE 0.020 0.002 PHE D 437 TRP 0.047 0.002 TRP C 997 HIS 0.012 0.001 HIS J 104 Details of bonding type rmsd covalent geometry : bond 0.00644 (30904) covalent geometry : angle 0.67304 (42141) hydrogen bonds : bond 0.03929 ( 1170) hydrogen bonds : angle 4.70566 ( 3290) metal coordination : bond 0.01506 ( 8) metal coordination : angle 4.63999 ( 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 526 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 344 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7409 (ttmm) REVERT: A 127 GLN cc_start: 0.8660 (mp10) cc_final: 0.8398 (pt0) REVERT: A 145 LYS cc_start: 0.8867 (tttt) cc_final: 0.8383 (tttm) REVERT: A 183 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8990 (mm) REVERT: A 212 ASP cc_start: 0.7138 (OUTLIER) cc_final: 0.6675 (t70) REVERT: B 10 LYS cc_start: 0.8748 (mttp) cc_final: 0.8425 (mtmm) REVERT: B 125 LYS cc_start: 0.7535 (tttt) cc_final: 0.7150 (tptm) REVERT: B 145 LYS cc_start: 0.7819 (tttt) cc_final: 0.7490 (tttp) REVERT: B 147 GLN cc_start: 0.6809 (tt0) cc_final: 0.6101 (mt0) REVERT: B 200 LYS cc_start: 0.8185 (tttt) cc_final: 0.7700 (tttp) REVERT: C 31 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.6538 (mm110) REVERT: C 36 GLN cc_start: 0.7695 (tt0) cc_final: 0.7381 (tt0) REVERT: C 130 MET cc_start: 0.8940 (ttm) cc_final: 0.8633 (ttp) REVERT: C 161 LYS cc_start: 0.8623 (mttt) cc_final: 0.8037 (pttm) REVERT: C 241 LEU cc_start: 0.8731 (tp) cc_final: 0.7576 (pt) REVERT: C 246 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7391 (mp) REVERT: C 315 MET cc_start: 0.8943 (ttm) cc_final: 0.8591 (ttm) REVERT: C 424 ASP cc_start: 0.8042 (m-30) cc_final: 0.7569 (m-30) REVERT: C 446 ASP cc_start: 0.8497 (m-30) cc_final: 0.8260 (m-30) REVERT: C 504 GLU cc_start: 0.8714 (tt0) cc_final: 0.8494 (tm-30) REVERT: C 510 GLN cc_start: 0.8149 (tp40) cc_final: 0.7826 (tp-100) REVERT: C 516 ASP cc_start: 0.7372 (p0) cc_final: 0.7077 (p0) REVERT: C 538 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7022 (pp) REVERT: C 542 ARG cc_start: 0.8271 (mtt180) cc_final: 0.7241 (ptp-170) REVERT: C 546 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7317 (mp0) REVERT: C 637 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7250 (ptt-90) REVERT: C 641 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.6868 (mm-30) REVERT: C 805 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8425 (ptm) REVERT: C 1022 LYS cc_start: 0.5029 (OUTLIER) cc_final: 0.4806 (tmmt) REVERT: C 1073 LYS cc_start: 0.8867 (pttt) cc_final: 0.8602 (pttp) REVERT: C 1157 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7213 (pp30) REVERT: C 1174 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7652 (mt-10) REVERT: C 1321 GLU cc_start: 0.8276 (tp30) cc_final: 0.8009 (tp30) REVERT: D 29 MET cc_start: 0.7430 (ttm) cc_final: 0.7119 (ttm) REVERT: D 39 LYS cc_start: 0.8924 (mtmt) cc_final: 0.8657 (mtmm) REVERT: D 200 GLN cc_start: 0.8456 (mm-40) cc_final: 0.7956 (tm-30) REVERT: D 259 ARG cc_start: 0.7868 (ttt-90) cc_final: 0.7521 (mtp85) REVERT: D 301 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: D 322 ARG cc_start: 0.8747 (mtp85) cc_final: 0.8416 (ptt90) REVERT: D 372 MET cc_start: 0.7927 (mtm) cc_final: 0.7726 (mtm) REVERT: D 395 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8051 (tptt) REVERT: D 484 MET cc_start: 0.9300 (mtp) cc_final: 0.9064 (mtp) REVERT: D 610 ARG cc_start: 0.8275 (mmt-90) cc_final: 0.7835 (ttp80) REVERT: D 765 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8223 (mt-10) REVERT: D 785 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7388 (t70) REVERT: D 905 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.7046 (mpt180) REVERT: D 918 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7283 (pt) REVERT: D 983 LYS cc_start: 0.8486 (mmmm) cc_final: 0.8187 (mmmm) REVERT: D 1149 ARG cc_start: 0.8545 (mmm160) cc_final: 0.7911 (tpp-160) REVERT: D 1260 MET cc_start: 0.8936 (mtp) cc_final: 0.8700 (mtm) REVERT: D 1345 ARG cc_start: 0.8877 (mtp85) cc_final: 0.8595 (ttm-80) REVERT: D 1366 HIS cc_start: 0.7654 (OUTLIER) cc_final: 0.6957 (m-70) REVERT: D 1368 ASP cc_start: 0.6978 (OUTLIER) cc_final: 0.5691 (m-30) REVERT: E 43 ASN cc_start: 0.8895 (m-40) cc_final: 0.8454 (t0) REVERT: F 90 SER cc_start: 0.8416 (OUTLIER) cc_final: 0.8188 (p) REVERT: F 92 ARG cc_start: 0.7598 (ttm110) cc_final: 0.7055 (ttt-90) REVERT: F 96 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7757 (mt-10) REVERT: F 111 ASN cc_start: 0.8198 (t0) cc_final: 0.7792 (t0) REVERT: F 140 PHE cc_start: 0.6652 (m-80) cc_final: 0.6361 (m-80) REVERT: F 200 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8351 (tm-30) REVERT: F 236 ASP cc_start: 0.7716 (t0) cc_final: 0.7428 (t0) REVERT: F 240 ASP cc_start: 0.8075 (t0) cc_final: 0.7056 (t0) REVERT: F 269 LYS cc_start: 0.8583 (tppt) cc_final: 0.8319 (tppt) REVERT: J 37 CYS cc_start: 0.7886 (t) cc_final: 0.7575 (t) REVERT: J 56 TRP cc_start: 0.6436 (p-90) cc_final: 0.5407 (p-90) REVERT: J 67 PHE cc_start: 0.8027 (m-80) cc_final: 0.7728 (m-80) REVERT: J 76 PHE cc_start: 0.8205 (t80) cc_final: 0.7870 (t80) REVERT: J 82 TRP cc_start: 0.6476 (m100) cc_final: 0.5872 (m100) REVERT: J 103 PHE cc_start: 0.8052 (t80) cc_final: 0.7693 (t80) REVERT: J 104 HIS cc_start: 0.6888 (t-170) cc_final: 0.6537 (t-170) REVERT: J 131 LEU cc_start: 0.4747 (OUTLIER) cc_final: 0.4407 (mt) outliers start: 182 outliers final: 142 residues processed: 494 average time/residue: 0.2007 time to fit residues: 158.7497 Evaluate side-chains 487 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 325 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 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 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 57 THR 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 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 160 ASP 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 268 ARG Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 483 ASP 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 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 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 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 913 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 963 GLU 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 1082 ILE 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 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 65 VAL 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 292 VAL Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 342 LEU 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 399 LYS Chi-restraints excluded: chain D residue 401 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 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 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 1135 THR 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 1292 LEU Chi-restraints excluded: chain D residue 1318 SER 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 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 131 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 284 optimal weight: 50.0000 chunk 192 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 101 optimal weight: 0.0770 chunk 275 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 142 optimal weight: 20.0000 chunk 132 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 285 optimal weight: 0.0970 chunk 224 optimal weight: 0.5980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN C 628 HIS D 294 ASN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 954 ASN D1326 GLN F 267 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.151176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.098530 restraints weight = 43905.227| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.95 r_work: 0.3186 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2988 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= 0.122 Angle : 0.581 10.960 42153 Z= 0.303 Chirality : 0.042 0.274 4797 Planarity : 0.004 0.048 5196 Dihedral : 17.379 176.456 5087 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.39 % Favored : 94.58 % Rotamer: Outliers : 5.01 % Allowed : 22.40 % Favored : 72.58 % 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: -1.45 (0.14), residues: 3596 helix: 0.43 (0.15), residues: 1324 sheet: -2.06 (0.24), residues: 417 loop : -1.75 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 101 TYR 0.049 0.001 TYR F 67 PHE 0.016 0.001 PHE A 8 TRP 0.053 0.001 TRP C 997 HIS 0.006 0.001 HIS J 104 Details of bonding type rmsd covalent geometry : bond 0.00277 (30904) covalent geometry : angle 0.57803 (42141) hydrogen bonds : bond 0.03268 ( 1170) hydrogen bonds : angle 4.36324 ( 3290) metal coordination : bond 0.00432 ( 8) metal coordination : angle 3.77269 ( 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 511 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 357 time to evaluate : 1.197 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: A 25 LYS cc_start: 0.7854 (ttpt) cc_final: 0.7362 (ttmm) REVERT: A 127 GLN cc_start: 0.8629 (mp10) cc_final: 0.8351 (pt0) REVERT: A 212 ASP cc_start: 0.6991 (OUTLIER) cc_final: 0.6557 (t70) REVERT: B 10 LYS cc_start: 0.8712 (mttp) cc_final: 0.8397 (mtmm) REVERT: B 38 THR cc_start: 0.7708 (OUTLIER) cc_final: 0.6946 (m) REVERT: B 125 LYS cc_start: 0.7473 (tttt) cc_final: 0.7099 (tptm) REVERT: B 200 LYS cc_start: 0.8198 (tttt) cc_final: 0.7412 (tttm) REVERT: C 31 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.6068 (mm110) REVERT: C 36 GLN cc_start: 0.7583 (tt0) cc_final: 0.7278 (tt0) REVERT: C 96 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7919 (pp) REVERT: C 130 MET cc_start: 0.8690 (ttm) cc_final: 0.8352 (ttp) REVERT: C 161 LYS cc_start: 0.8547 (mttt) cc_final: 0.7973 (pttm) REVERT: C 223 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8343 (tp) REVERT: C 239 MET cc_start: 0.5433 (mtm) cc_final: 0.5228 (mtm) REVERT: C 241 LEU cc_start: 0.8790 (tp) cc_final: 0.7718 (pt) REVERT: C 246 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7368 (mp) REVERT: C 315 MET cc_start: 0.8963 (ttm) cc_final: 0.8609 (ttm) REVERT: C 369 MET cc_start: 0.8719 (ttp) cc_final: 0.8162 (tmm) REVERT: C 439 LYS cc_start: 0.7933 (mttp) cc_final: 0.7466 (mtmt) REVERT: C 446 ASP cc_start: 0.8342 (m-30) cc_final: 0.8132 (m-30) REVERT: C 510 GLN cc_start: 0.8159 (tp40) cc_final: 0.7842 (tp40) REVERT: C 516 ASP cc_start: 0.7213 (p0) cc_final: 0.6912 (p0) REVERT: C 538 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7390 (pt) REVERT: C 542 ARG cc_start: 0.8375 (mtt180) cc_final: 0.7410 (ptp-170) REVERT: C 546 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7302 (mp0) REVERT: C 637 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7268 (ptt-90) REVERT: C 641 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6908 (mm-30) REVERT: C 645 PHE cc_start: 0.7644 (m-80) cc_final: 0.7166 (m-80) REVERT: C 820 GLU cc_start: 0.8362 (tt0) cc_final: 0.7858 (tt0) REVERT: C 1073 LYS cc_start: 0.8797 (pttt) cc_final: 0.8484 (pttp) REVERT: C 1157 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.6849 (pp30) REVERT: C 1174 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7641 (mt-10) REVERT: C 1211 ARG cc_start: 0.7790 (mtp85) cc_final: 0.7522 (mtp85) REVERT: C 1296 ASP cc_start: 0.8847 (t0) cc_final: 0.8597 (t0) REVERT: D 29 MET cc_start: 0.6961 (ttm) cc_final: 0.6740 (ttm) REVERT: D 39 LYS cc_start: 0.8891 (mtmt) cc_final: 0.8650 (mtmm) REVERT: D 200 GLN cc_start: 0.8444 (mm-40) cc_final: 0.7949 (tm-30) REVERT: D 259 ARG cc_start: 0.7865 (ttt-90) cc_final: 0.7578 (mtp85) REVERT: D 304 ASP cc_start: 0.7600 (m-30) cc_final: 0.7162 (m-30) REVERT: D 322 ARG cc_start: 0.8766 (mtp85) cc_final: 0.8441 (ptt90) REVERT: D 363 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7381 (pt) REVERT: D 395 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7887 (tptt) REVERT: D 484 MET cc_start: 0.9296 (mtp) cc_final: 0.9063 (mtp) REVERT: D 610 ARG cc_start: 0.8172 (mmt-90) cc_final: 0.7823 (ttp80) REVERT: D 765 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8318 (mt-10) REVERT: D 785 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7360 (t70) REVERT: D 788 LEU cc_start: 0.8218 (mm) cc_final: 0.7949 (mp) REVERT: D 905 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.6943 (mpt180) REVERT: D 918 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7312 (pt) REVERT: D 954 ASN cc_start: 0.7461 (OUTLIER) cc_final: 0.7048 (t0) REVERT: D 983 LYS cc_start: 0.8160 (mmmm) cc_final: 0.7700 (mppt) REVERT: D 1146 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7886 (mm-30) REVERT: D 1149 ARG cc_start: 0.8531 (mmm160) cc_final: 0.7916 (tpp-160) REVERT: D 1167 LYS cc_start: 0.6682 (OUTLIER) cc_final: 0.6308 (ptmm) REVERT: D 1345 ARG cc_start: 0.8788 (mtp85) cc_final: 0.8510 (ttm110) REVERT: D 1366 HIS cc_start: 0.7672 (OUTLIER) cc_final: 0.6936 (m-70) REVERT: D 1368 ASP cc_start: 0.7046 (OUTLIER) cc_final: 0.5803 (m-30) REVERT: E 43 ASN cc_start: 0.8943 (m-40) cc_final: 0.8449 (t0) REVERT: F 64 GLU cc_start: 0.8782 (tp30) cc_final: 0.8454 (tp30) REVERT: F 92 ARG cc_start: 0.7726 (ttm110) cc_final: 0.7183 (tmm-80) REVERT: F 96 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7671 (mt-10) REVERT: F 111 ASN cc_start: 0.8061 (t0) cc_final: 0.7688 (t0) REVERT: F 200 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8233 (tm-30) REVERT: F 235 LEU cc_start: 0.8448 (mt) cc_final: 0.8077 (mt) REVERT: F 236 ASP cc_start: 0.7564 (t0) cc_final: 0.7201 (t0) REVERT: F 240 ASP cc_start: 0.8120 (t0) cc_final: 0.7064 (t0) REVERT: F 256 LYS cc_start: 0.7863 (mttp) cc_final: 0.7633 (mptt) REVERT: F 269 LYS cc_start: 0.8519 (tppt) cc_final: 0.8312 (tptt) REVERT: J 24 ARG cc_start: 0.7597 (mmt90) cc_final: 0.7312 (mmt90) REVERT: J 37 CYS cc_start: 0.7953 (t) cc_final: 0.7635 (t) REVERT: J 51 ARG cc_start: 0.6743 (mtt180) cc_final: 0.6277 (mtt-85) REVERT: J 56 TRP cc_start: 0.6298 (p-90) cc_final: 0.5280 (p-90) REVERT: J 82 TRP cc_start: 0.6559 (m100) cc_final: 0.6055 (m100) REVERT: J 103 PHE cc_start: 0.8020 (t80) cc_final: 0.7670 (t80) REVERT: J 104 HIS cc_start: 0.6873 (t-170) cc_final: 0.6571 (t-170) REVERT: J 131 LEU cc_start: 0.4695 (OUTLIER) cc_final: 0.4327 (mt) outliers start: 154 outliers final: 107 residues processed: 475 average time/residue: 0.1982 time to fit residues: 149.1292 Evaluate side-chains 464 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 337 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 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 27 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 223 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 309 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 483 ASP 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 565 GLU 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 690 VAL Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 830 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 959 ASP Chi-restraints excluded: chain C residue 963 GLU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1005 GLU 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 1255 THR Chi-restraints excluded: chain C residue 1293 VAL 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 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 292 VAL Chi-restraints excluded: chain D residue 342 LEU 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 527 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 545 HIS 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 641 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 776 THR Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain D residue 803 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 954 ASN 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 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 131 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 294 optimal weight: 1.9990 chunk 58 optimal weight: 0.0970 chunk 118 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 300 optimal weight: 3.9990 chunk 333 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 311 optimal weight: 0.3980 chunk 124 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 247 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN C 628 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN J 7 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.150637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.099205 restraints weight = 43992.561| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.14 r_work: 0.3175 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.3093 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= 0.142 Angle : 0.589 10.943 42153 Z= 0.306 Chirality : 0.042 0.324 4797 Planarity : 0.004 0.045 5196 Dihedral : 17.203 175.536 5068 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.28 % Favored : 93.69 % Rotamer: Outliers : 4.62 % Allowed : 22.76 % Favored : 72.61 % 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: -1.37 (0.14), residues: 3596 helix: 0.53 (0.15), residues: 1325 sheet: -2.04 (0.24), residues: 424 loop : -1.73 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 407 TYR 0.044 0.001 TYR F 67 PHE 0.019 0.001 PHE D 172 TRP 0.052 0.001 TRP C 997 HIS 0.007 0.001 HIS J 104 Details of bonding type rmsd covalent geometry : bond 0.00330 (30904) covalent geometry : angle 0.58589 (42141) hydrogen bonds : bond 0.03293 ( 1170) hydrogen bonds : angle 4.30791 ( 3290) metal coordination : bond 0.00658 ( 8) metal coordination : angle 3.67111 ( 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 486 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 344 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLN cc_start: 0.8618 (mp10) cc_final: 0.8334 (pt0) REVERT: A 212 ASP cc_start: 0.7034 (OUTLIER) cc_final: 0.6614 (t70) REVERT: B 10 LYS cc_start: 0.8699 (mttp) cc_final: 0.8385 (mtmm) REVERT: B 125 LYS cc_start: 0.7491 (tttt) cc_final: 0.7116 (tptm) REVERT: B 200 LYS cc_start: 0.8198 (tttt) cc_final: 0.7429 (tttm) REVERT: C 31 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.6222 (mm110) REVERT: C 36 GLN cc_start: 0.7580 (tt0) cc_final: 0.7273 (tt0) REVERT: C 96 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7925 (pp) REVERT: C 130 MET cc_start: 0.8766 (ttm) cc_final: 0.8443 (ttp) REVERT: C 161 LYS cc_start: 0.8504 (mttt) cc_final: 0.7977 (pttm) REVERT: C 241 LEU cc_start: 0.8776 (tp) cc_final: 0.7708 (pt) REVERT: C 246 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7344 (mp) REVERT: C 315 MET cc_start: 0.8979 (ttm) cc_final: 0.8628 (ttm) REVERT: C 446 ASP cc_start: 0.8369 (m-30) cc_final: 0.8158 (m-30) REVERT: C 510 GLN cc_start: 0.8267 (tp40) cc_final: 0.7901 (tp40) REVERT: C 516 ASP cc_start: 0.7012 (p0) cc_final: 0.6807 (p0) REVERT: C 538 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7353 (pt) REVERT: C 542 ARG cc_start: 0.8370 (mtt180) cc_final: 0.7394 (ptp-170) REVERT: C 546 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7315 (mp0) REVERT: C 637 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7287 (ptt-90) REVERT: C 641 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7082 (mm-30) REVERT: C 645 PHE cc_start: 0.7615 (m-80) cc_final: 0.7178 (m-80) REVERT: C 1073 LYS cc_start: 0.8820 (pttt) cc_final: 0.8506 (pttp) REVERT: C 1157 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.6910 (pp30) REVERT: C 1174 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7633 (mt-10) REVERT: C 1211 ARG cc_start: 0.7893 (mtp85) cc_final: 0.7649 (mtp85) REVERT: C 1221 PHE cc_start: 0.8383 (m-10) cc_final: 0.8031 (m-10) REVERT: D 29 MET cc_start: 0.7129 (ttm) cc_final: 0.6879 (ttm) REVERT: D 39 LYS cc_start: 0.8927 (mtmt) cc_final: 0.8674 (mtmm) REVERT: D 200 GLN cc_start: 0.8435 (mm-40) cc_final: 0.7951 (tm-30) REVERT: D 259 ARG cc_start: 0.7926 (ttt-90) cc_final: 0.7613 (mtp85) REVERT: D 264 ASP cc_start: 0.8660 (m-30) cc_final: 0.8434 (m-30) REVERT: D 304 ASP cc_start: 0.7621 (m-30) cc_final: 0.7168 (m-30) REVERT: D 322 ARG cc_start: 0.8774 (mtp85) cc_final: 0.8446 (ptt90) REVERT: D 395 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7904 (tptt) REVERT: D 484 MET cc_start: 0.9306 (mtp) cc_final: 0.9071 (mtp) REVERT: D 525 MET cc_start: 0.8531 (ptp) cc_final: 0.8187 (ptm) REVERT: D 610 ARG cc_start: 0.8178 (mmt-90) cc_final: 0.7818 (ttp80) REVERT: D 644 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7765 (mtt) REVERT: D 765 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8343 (mt-10) REVERT: D 905 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.7008 (mpt180) REVERT: D 918 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7339 (pt) REVERT: D 983 LYS cc_start: 0.8113 (mmmm) cc_final: 0.7667 (mppt) REVERT: D 1146 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7917 (mm-30) REVERT: D 1149 ARG cc_start: 0.8449 (mmm160) cc_final: 0.7824 (tpp-160) REVERT: D 1167 LYS cc_start: 0.6651 (OUTLIER) cc_final: 0.6203 (ptmm) REVERT: D 1345 ARG cc_start: 0.8780 (mtp85) cc_final: 0.8423 (ttm-80) REVERT: D 1366 HIS cc_start: 0.7756 (OUTLIER) cc_final: 0.6963 (m-70) REVERT: D 1368 ASP cc_start: 0.7028 (OUTLIER) cc_final: 0.5790 (m-30) REVERT: E 43 ASN cc_start: 0.8941 (m-40) cc_final: 0.8458 (t0) REVERT: F 64 GLU cc_start: 0.8778 (tp30) cc_final: 0.8458 (tp30) REVERT: F 92 ARG cc_start: 0.7727 (ttm110) cc_final: 0.7192 (tmm-80) REVERT: F 96 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7660 (mt-10) REVERT: F 111 ASN cc_start: 0.8083 (t0) cc_final: 0.7764 (t0) REVERT: F 140 PHE cc_start: 0.6679 (m-80) cc_final: 0.6439 (m-80) REVERT: F 200 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8253 (tm-30) REVERT: F 236 ASP cc_start: 0.7629 (t0) cc_final: 0.7237 (t0) REVERT: F 240 ASP cc_start: 0.8124 (t0) cc_final: 0.7066 (t0) REVERT: F 269 LYS cc_start: 0.8514 (tppt) cc_final: 0.8313 (tptt) REVERT: J 24 ARG cc_start: 0.7643 (mmt90) cc_final: 0.7311 (mmt90) REVERT: J 37 CYS cc_start: 0.7675 (t) cc_final: 0.7378 (t) REVERT: J 56 TRP cc_start: 0.6292 (p-90) cc_final: 0.5283 (p-90) REVERT: J 76 PHE cc_start: 0.8124 (t80) cc_final: 0.7560 (t80) REVERT: J 82 TRP cc_start: 0.6594 (m100) cc_final: 0.5963 (m100) REVERT: J 103 PHE cc_start: 0.8055 (t80) cc_final: 0.7720 (t80) REVERT: J 104 HIS cc_start: 0.6926 (t-170) cc_final: 0.6571 (t-170) REVERT: J 131 LEU cc_start: 0.4621 (OUTLIER) cc_final: 0.3799 (mt) outliers start: 142 outliers final: 114 residues processed: 454 average time/residue: 0.1928 time to fit residues: 138.4037 Evaluate side-chains 463 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 333 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 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 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 48 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 147 GLN 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 20 GLN 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 188 PHE 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 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 565 GLU 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 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 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 959 ASP Chi-restraints excluded: chain C residue 963 GLU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1005 GLU 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 1255 THR Chi-restraints excluded: chain C residue 1293 VAL 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 102 MET 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 140 TYR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 172 PHE 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 292 VAL Chi-restraints excluded: chain D residue 342 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 434 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 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 587 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 724 MET 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 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 1261 LEU Chi-restraints excluded: chain D residue 1353 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 131 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 158 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 277 optimal weight: 20.0000 chunk 128 optimal weight: 0.4980 chunk 149 optimal weight: 0.8980 chunk 288 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS D 164 GLN ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.151609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.100511 restraints weight = 43830.142| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.20 r_work: 0.3190 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30912 Z= 0.127 Angle : 0.577 10.062 42153 Z= 0.301 Chirality : 0.042 0.343 4797 Planarity : 0.004 0.045 5196 Dihedral : 17.050 174.165 5061 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.36 % Allowed : 23.22 % Favored : 72.42 % 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: -1.23 (0.14), residues: 3596 helix: 0.67 (0.15), residues: 1326 sheet: -1.97 (0.24), residues: 424 loop : -1.66 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 407 TYR 0.042 0.001 TYR F 67 PHE 0.020 0.001 PHE D 172 TRP 0.048 0.001 TRP C 997 HIS 0.006 0.001 HIS J 104 Details of bonding type rmsd covalent geometry : bond 0.00293 (30904) covalent geometry : angle 0.57453 (42141) hydrogen bonds : bond 0.03162 ( 1170) hydrogen bonds : angle 4.21621 ( 3290) metal coordination : bond 0.00532 ( 8) metal coordination : angle 3.38064 ( 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 486 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 352 time to evaluate : 1.048 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: A 127 GLN cc_start: 0.8601 (mp10) cc_final: 0.8315 (pt0) REVERT: A 212 ASP cc_start: 0.7015 (OUTLIER) cc_final: 0.6609 (t70) REVERT: B 10 LYS cc_start: 0.8667 (mttp) cc_final: 0.8356 (mtmm) REVERT: B 125 LYS cc_start: 0.7489 (tttt) cc_final: 0.7137 (tptm) REVERT: B 132 HIS cc_start: 0.8553 (m-70) cc_final: 0.8300 (m-70) REVERT: B 200 LYS cc_start: 0.8185 (tttt) cc_final: 0.7420 (tttm) REVERT: C 31 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.6082 (mm110) REVERT: C 36 GLN cc_start: 0.7549 (tt0) cc_final: 0.7242 (tt0) REVERT: C 96 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7877 (pp) REVERT: C 130 MET cc_start: 0.8584 (ttm) cc_final: 0.8279 (ttp) REVERT: C 161 LYS cc_start: 0.8463 (mttt) cc_final: 0.7948 (pttm) REVERT: C 241 LEU cc_start: 0.8758 (tp) cc_final: 0.7692 (pt) REVERT: C 246 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7464 (mp) REVERT: C 315 MET cc_start: 0.9007 (ttm) cc_final: 0.8483 (ttm) REVERT: C 446 ASP cc_start: 0.8374 (m-30) cc_final: 0.8149 (m-30) REVERT: C 510 GLN cc_start: 0.8254 (tp40) cc_final: 0.7865 (tp40) REVERT: C 516 ASP cc_start: 0.7448 (p0) cc_final: 0.7064 (p0) REVERT: C 538 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7389 (pt) REVERT: C 542 ARG cc_start: 0.8455 (mtt180) cc_final: 0.7612 (ptp-170) REVERT: C 546 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7307 (mp0) REVERT: C 549 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8362 (t0) REVERT: C 573 ASN cc_start: 0.8227 (m-40) cc_final: 0.7996 (t0) REVERT: C 609 ILE cc_start: 0.8209 (pt) cc_final: 0.7998 (mp) REVERT: C 637 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7267 (ptt-90) REVERT: C 641 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7171 (mm-30) REVERT: C 820 GLU cc_start: 0.8332 (tt0) cc_final: 0.7864 (tt0) REVERT: C 1034 ARG cc_start: 0.8870 (ttm110) cc_final: 0.8641 (mmm-85) REVERT: C 1073 LYS cc_start: 0.8734 (pttt) cc_final: 0.8398 (pttp) REVERT: C 1157 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.6877 (pp30) REVERT: C 1174 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7584 (mt-10) REVERT: C 1211 ARG cc_start: 0.7882 (mtp85) cc_final: 0.7644 (mtp85) REVERT: C 1221 PHE cc_start: 0.8291 (m-10) cc_final: 0.7887 (m-10) REVERT: C 1296 ASP cc_start: 0.8842 (t0) cc_final: 0.8575 (t0) REVERT: C 1340 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7169 (pt0) REVERT: D 29 MET cc_start: 0.7035 (ttm) cc_final: 0.6804 (ttm) REVERT: D 39 LYS cc_start: 0.8928 (mtmt) cc_final: 0.8677 (mtmm) REVERT: D 200 GLN cc_start: 0.8435 (mm-40) cc_final: 0.7950 (tm-30) REVERT: D 259 ARG cc_start: 0.7947 (ttt-90) cc_final: 0.7645 (mtp85) REVERT: D 322 ARG cc_start: 0.8773 (mtp85) cc_final: 0.8452 (ptt90) REVERT: D 395 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7865 (tptt) REVERT: D 484 MET cc_start: 0.9309 (mtp) cc_final: 0.9059 (mtp) REVERT: D 525 MET cc_start: 0.8543 (ptp) cc_final: 0.8195 (ptm) REVERT: D 610 ARG cc_start: 0.8183 (mmt-90) cc_final: 0.7826 (ttp80) REVERT: D 644 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7772 (mtt) REVERT: D 765 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8354 (mt-10) REVERT: D 788 LEU cc_start: 0.8181 (mm) cc_final: 0.7957 (mp) REVERT: D 905 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.7023 (mpt180) REVERT: D 918 ILE cc_start: 0.7675 (OUTLIER) cc_final: 0.7289 (pt) REVERT: D 983 LYS cc_start: 0.8121 (mmmm) cc_final: 0.7669 (mppt) REVERT: D 1146 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7914 (mm-30) REVERT: D 1149 ARG cc_start: 0.8440 (mmm160) cc_final: 0.7919 (tpp-160) REVERT: D 1152 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8698 (mm-30) REVERT: D 1167 LYS cc_start: 0.6890 (OUTLIER) cc_final: 0.6626 (pptt) REVERT: D 1174 ARG cc_start: 0.3631 (mmp80) cc_final: 0.3427 (mmp80) REVERT: D 1345 ARG cc_start: 0.8771 (mtp85) cc_final: 0.8517 (ttm110) REVERT: D 1366 HIS cc_start: 0.7741 (OUTLIER) cc_final: 0.6961 (m-70) REVERT: D 1368 ASP cc_start: 0.7025 (OUTLIER) cc_final: 0.5845 (m-30) REVERT: E 43 ASN cc_start: 0.8956 (m-40) cc_final: 0.8512 (t0) REVERT: F 64 GLU cc_start: 0.8714 (tp30) cc_final: 0.8381 (tp30) REVERT: F 90 SER cc_start: 0.8340 (OUTLIER) cc_final: 0.8081 (p) REVERT: F 92 ARG cc_start: 0.7729 (ttm110) cc_final: 0.7195 (tmm-80) REVERT: F 96 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7548 (mt-10) REVERT: F 140 PHE cc_start: 0.6652 (m-80) cc_final: 0.6400 (m-80) REVERT: F 200 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8266 (tm-30) REVERT: F 236 ASP cc_start: 0.7474 (t0) cc_final: 0.7053 (t0) REVERT: F 240 ASP cc_start: 0.8104 (t0) cc_final: 0.7038 (t0) REVERT: J 24 ARG cc_start: 0.7618 (mmt90) cc_final: 0.7273 (mmt90) REVERT: J 37 CYS cc_start: 0.7674 (t) cc_final: 0.7360 (t) REVERT: J 51 ARG cc_start: 0.6796 (mpp80) cc_final: 0.6414 (mpp80) REVERT: J 56 TRP cc_start: 0.6211 (p-90) cc_final: 0.5203 (p-90) REVERT: J 76 PHE cc_start: 0.8099 (t80) cc_final: 0.7472 (t80) REVERT: J 82 TRP cc_start: 0.6593 (m100) cc_final: 0.5966 (m100) REVERT: J 103 PHE cc_start: 0.8093 (t80) cc_final: 0.7764 (t80) outliers start: 134 outliers final: 105 residues processed: 452 average time/residue: 0.1959 time to fit residues: 140.2061 Evaluate side-chains 465 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 342 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 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 212 ASP Chi-restraints excluded: chain A residue 217 ILE 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 48 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 147 GLN 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 20 GLN 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 188 PHE 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 397 LEU Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 565 GLU 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 690 VAL Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 898 GLU Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 963 GLU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1005 GLU 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 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 102 MET Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 140 TYR 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 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 486 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 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 587 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 644 MET 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 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 982 LEU Chi-restraints excluded: chain D residue 997 VAL 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 1261 LEU Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1353 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 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 92 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 176 optimal weight: 0.1980 chunk 242 optimal weight: 3.9990 chunk 302 optimal weight: 8.9990 chunk 144 optimal weight: 4.9990 chunk 313 optimal weight: 0.6980 chunk 15 optimal weight: 8.9990 chunk 139 optimal weight: 0.9990 chunk 309 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 340 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.151610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.101044 restraints weight = 43818.094| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 3.23 r_work: 0.3188 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30912 Z= 0.132 Angle : 0.584 10.404 42153 Z= 0.304 Chirality : 0.042 0.347 4797 Planarity : 0.004 0.049 5196 Dihedral : 16.994 174.036 5054 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.23 % Allowed : 23.48 % Favored : 72.29 % 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: -1.17 (0.14), residues: 3596 helix: 0.71 (0.15), residues: 1327 sheet: -1.88 (0.25), residues: 422 loop : -1.65 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 101 TYR 0.040 0.001 TYR F 67 PHE 0.019 0.001 PHE D 172 TRP 0.079 0.002 TRP C 997 HIS 0.005 0.001 HIS D 450 Details of bonding type rmsd covalent geometry : bond 0.00306 (30904) covalent geometry : angle 0.58091 (42141) hydrogen bonds : bond 0.03172 ( 1170) hydrogen bonds : angle 4.19721 ( 3290) metal coordination : bond 0.00580 ( 8) metal coordination : angle 3.34859 ( 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 475 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 345 time to evaluate : 1.162 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 127 GLN cc_start: 0.8618 (mp10) cc_final: 0.8321 (pt0) REVERT: A 196 THR cc_start: 0.8602 (m) cc_final: 0.8400 (t) REVERT: A 212 ASP cc_start: 0.6988 (OUTLIER) cc_final: 0.6602 (t70) REVERT: B 10 LYS cc_start: 0.8645 (mttp) cc_final: 0.8336 (mtmm) REVERT: B 125 LYS cc_start: 0.7490 (tttt) cc_final: 0.7139 (tptm) REVERT: B 132 HIS cc_start: 0.8540 (m-70) cc_final: 0.8284 (m-70) REVERT: B 200 LYS cc_start: 0.8088 (tttt) cc_final: 0.7332 (tttm) REVERT: C 31 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.6080 (mm110) REVERT: C 36 GLN cc_start: 0.7525 (tt0) cc_final: 0.7224 (tt0) REVERT: C 96 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7803 (pp) REVERT: C 130 MET cc_start: 0.8642 (ttm) cc_final: 0.8305 (ttp) REVERT: C 161 LYS cc_start: 0.8450 (mttt) cc_final: 0.7936 (pttm) REVERT: C 246 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7697 (mp) REVERT: C 315 MET cc_start: 0.8823 (ttm) cc_final: 0.8443 (ttm) REVERT: C 376 PRO cc_start: 0.8208 (Cg_endo) cc_final: 0.7912 (Cg_exo) REVERT: C 439 LYS cc_start: 0.7802 (mttp) cc_final: 0.7505 (mttt) REVERT: C 446 ASP cc_start: 0.8369 (m-30) cc_final: 0.8151 (m-30) REVERT: C 510 GLN cc_start: 0.8260 (tp40) cc_final: 0.7862 (tp40) REVERT: C 516 ASP cc_start: 0.7449 (p0) cc_final: 0.7105 (p0) REVERT: C 538 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7279 (pt) REVERT: C 542 ARG cc_start: 0.8419 (mtt180) cc_final: 0.7595 (ptp-170) REVERT: C 546 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7348 (mp0) REVERT: C 609 ILE cc_start: 0.8176 (pt) cc_final: 0.7974 (mp) REVERT: C 637 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7371 (ptt-90) REVERT: C 641 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7163 (mm-30) REVERT: C 711 ASP cc_start: 0.7943 (m-30) cc_final: 0.7613 (m-30) REVERT: C 1034 ARG cc_start: 0.8861 (ttm110) cc_final: 0.8639 (mmm-85) REVERT: C 1073 LYS cc_start: 0.8714 (pttt) cc_final: 0.8377 (pttp) REVERT: C 1157 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.6863 (pp30) REVERT: C 1211 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7639 (mtp85) REVERT: C 1221 PHE cc_start: 0.8138 (m-10) cc_final: 0.7647 (m-10) REVERT: C 1270 PHE cc_start: 0.8080 (t80) cc_final: 0.7590 (t80) REVERT: C 1296 ASP cc_start: 0.8850 (t0) cc_final: 0.8574 (t0) REVERT: C 1340 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7167 (pt0) REVERT: D 29 MET cc_start: 0.7005 (ttm) cc_final: 0.6770 (ttm) REVERT: D 39 LYS cc_start: 0.8905 (mtmt) cc_final: 0.8661 (mtmm) REVERT: D 200 GLN cc_start: 0.8424 (mm-40) cc_final: 0.7936 (tm-30) REVERT: D 259 ARG cc_start: 0.7951 (ttt-90) cc_final: 0.7668 (mtp85) REVERT: D 264 ASP cc_start: 0.8731 (m-30) cc_final: 0.8337 (m-30) REVERT: D 301 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7450 (tm-30) REVERT: D 322 ARG cc_start: 0.8767 (mtp85) cc_final: 0.8447 (ptt90) REVERT: D 371 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.8097 (mptt) REVERT: D 395 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7862 (tptt) REVERT: D 484 MET cc_start: 0.9304 (mtp) cc_final: 0.9046 (mtp) REVERT: D 525 MET cc_start: 0.8546 (ptp) cc_final: 0.8194 (ptm) REVERT: D 610 ARG cc_start: 0.8186 (mmt-90) cc_final: 0.7821 (ttp80) REVERT: D 644 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7768 (mtt) REVERT: D 765 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8346 (mt-10) REVERT: D 788 LEU cc_start: 0.8155 (mm) cc_final: 0.7912 (mp) REVERT: D 905 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.7045 (mpt180) REVERT: D 918 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7286 (pt) REVERT: D 983 LYS cc_start: 0.8094 (mmmm) cc_final: 0.7644 (mppt) REVERT: D 1146 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7816 (mm-30) REVERT: D 1149 ARG cc_start: 0.8401 (mmm160) cc_final: 0.7853 (tpp-160) REVERT: D 1152 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8700 (mm-30) REVERT: D 1167 LYS cc_start: 0.6900 (OUTLIER) cc_final: 0.6614 (pptt) REVERT: D 1345 ARG cc_start: 0.8760 (mtp85) cc_final: 0.8508 (ttm110) REVERT: D 1366 HIS cc_start: 0.7725 (OUTLIER) cc_final: 0.7028 (m-70) REVERT: D 1368 ASP cc_start: 0.6902 (OUTLIER) cc_final: 0.5695 (m-30) REVERT: E 43 ASN cc_start: 0.9022 (m-40) cc_final: 0.8494 (t0) REVERT: F 64 GLU cc_start: 0.8719 (tp30) cc_final: 0.8377 (tp30) REVERT: F 92 ARG cc_start: 0.7680 (ttm110) cc_final: 0.7371 (tmm-80) REVERT: F 140 PHE cc_start: 0.6652 (m-80) cc_final: 0.6392 (m-80) REVERT: F 200 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8261 (tm-30) REVERT: F 240 ASP cc_start: 0.8081 (t0) cc_final: 0.7010 (t0) REVERT: J 37 CYS cc_start: 0.7524 (t) cc_final: 0.7163 (t) REVERT: J 51 ARG cc_start: 0.6579 (mpp80) cc_final: 0.6156 (mpp80) REVERT: J 56 TRP cc_start: 0.6152 (p-90) cc_final: 0.5139 (p-90) REVERT: J 76 PHE cc_start: 0.8103 (t80) cc_final: 0.7474 (t80) REVERT: J 82 TRP cc_start: 0.6545 (m100) cc_final: 0.5924 (m100) REVERT: J 95 ARG cc_start: 0.8054 (tpt-90) cc_final: 0.7837 (tpp80) REVERT: J 103 PHE cc_start: 0.8080 (t80) cc_final: 0.7808 (t80) outliers start: 130 outliers final: 105 residues processed: 445 average time/residue: 0.1941 time to fit residues: 136.3540 Evaluate side-chains 457 residues out of total 3089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 334 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 124 VAL Chi-restraints excluded: chain A residue 171 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 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 48 LEU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 147 GLN 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 20 GLN 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 188 PHE 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 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 538 LEU 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 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 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 959 ASP Chi-restraints excluded: chain C residue 963 GLU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1005 GLU 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 102 MET 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 301 GLU Chi-restraints excluded: chain D residue 342 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 486 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 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 644 MET 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 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 1167 LYS 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 1353 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 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 92 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 141 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 346 optimal weight: 30.0000 chunk 104 optimal weight: 0.0670 chunk 74 optimal weight: 10.0000 chunk 316 optimal weight: 2.9990 chunk 333 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 238 optimal weight: 0.7980 chunk 208 optimal weight: 6.9990 chunk 47 optimal weight: 0.0040 overall best weight: 0.9132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.151824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.100438 restraints weight = 43963.965| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.17 r_work: 0.3188 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30912 Z= 0.129 Angle : 0.579 10.248 42153 Z= 0.301 Chirality : 0.042 0.361 4797 Planarity : 0.004 0.044 5196 Dihedral : 16.930 173.918 5051 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.14 % Allowed : 23.64 % Favored : 72.22 % 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: -1.12 (0.14), residues: 3596 helix: 0.75 (0.15), residues: 1327 sheet: -1.86 (0.25), residues: 428 loop : -1.61 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 996 TYR 0.043 0.001 TYR F 67 PHE 0.019 0.001 PHE D 172 TRP 0.080 0.002 TRP C 997 HIS 0.005 0.001 HIS D 450 Details of bonding type rmsd covalent geometry : bond 0.00301 (30904) covalent geometry : angle 0.57598 (42141) hydrogen bonds : bond 0.03104 ( 1170) hydrogen bonds : angle 4.16284 ( 3290) metal coordination : bond 0.00565 ( 8) metal coordination : angle 3.27763 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8349.06 seconds wall clock time: 143 minutes 19.93 seconds (8599.93 seconds total)