Starting phenix.real_space_refine on Mon Sep 14 01:24:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8acp_15352/09_2026/8acp_15352.cif Found real_map, /net/cci-nas-00/data/ceres_data/8acp_15352/09_2026/8acp_15352.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8acp_15352/09_2026/8acp_15352.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8acp_15352/09_2026/8acp_15352.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8acp_15352/09_2026/8acp_15352.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8acp_15352/09_2026/8acp_15352.cif" model { file = "/net/cci-nas-00/data/ceres_data/8acp_15352/09_2026/8acp_15352.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8acp_15352/09_2026/8acp_15352.cif" } resolution = 4.5 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= 0.002 sd= 0.015 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 104 5.49 5 Mg 1 5.21 5 S 105 5.16 5 C 16376 2.51 5 N 4739 2.21 5 O 5410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26737 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1767 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 219} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1759 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 10402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1319, 10402 Classifications: {'peptide': 1319} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1263} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 10379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10379 Classifications: {'peptide': 1337} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 55, 'TRANS': 1281} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 221 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "N" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 142 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "R" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1733 Classifications: {'RNAv2': 81} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 3, 'rna3p_pur': 35, 'rna3p_pyr': 35} Link IDs: {'rna2p': 11, 'rna3p': 69} Chain breaks: 1 Chain: "T" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 331 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} 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 14377 SG CYS D 70 105.642 124.115 112.402 1.00339.00 S ATOM 14391 SG CYS D 72 104.319 125.938 115.400 1.00350.02 S ATOM 14499 SG CYS D 85 107.637 123.850 115.735 1.00336.25 S ATOM 14523 SG CYS D 88 104.246 122.257 115.327 1.00321.99 S ATOM 20211 SG CYS D 814 106.674 62.154 93.235 1.00174.08 S ATOM 20776 SG CYS D 888 103.217 63.923 93.045 1.00155.42 S ATOM 20827 SG CYS D 895 106.615 65.348 91.587 1.00156.46 S ATOM 20848 SG CYS D 898 104.731 62.421 89.996 1.00150.46 S Time building chain proxies: 5.09, per 1000 atoms: 0.19 Number of scatterers: 26737 At special positions: 0 Unit cell: (142.23, 165.504, 166.366, 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 105 16.00 P 104 15.00 Mg 1 11.99 O 5410 8.00 N 4739 7.00 C 16376 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: 2.23 Conformation dependent library (CDL) restraints added in 886.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 85 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " Number of angles added : 12 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5798 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 46 sheets defined 38.7% alpha, 15.4% beta 38 base pairs and 61 stacking pairs defined. Time for finding SS restraints: 3.56 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.863A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 88 removed outlier: 3.855A pdb=" N ILE A 81 " --> pdb=" O ASP A 77 " (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 232 removed outlier: 3.724A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.651A pdb=" N SER B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.684A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 230 removed outlier: 3.939A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.714A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.627A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP C 33 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (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 163 through 167 removed outlier: 3.506A pdb=" N SER C 166 " --> pdb=" O LYS C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 213 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 293 removed outlier: 4.143A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 288 through 293' 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 removed outlier: 3.655A pdb=" N ARG C 371 " --> pdb=" O TYR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 391 removed outlier: 3.878A pdb=" N SER C 391 " --> pdb=" O ASN C 387 " (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 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.706A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.643A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 544 through 549 Processing helix chain 'C' and resid 608 through 612 Processing helix chain 'C' and resid 662 through 667 removed outlier: 3.970A pdb=" N LEU C 667 " --> pdb=" O VAL C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.630A pdb=" N HIS C 673 " --> pdb=" O PHE C 670 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP C 674 " --> pdb=" O LEU C 671 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 670 through 674' Processing helix chain 'C' and resid 675 through 688 Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 826 Processing helix chain 'C' and resid 858 through 864 removed outlier: 3.984A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 980 removed outlier: 3.617A pdb=" N VAL C 978 " --> pdb=" O ARG C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 991 removed outlier: 3.828A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 999 removed outlier: 3.602A pdb=" N TRP C 997 " --> pdb=" O PRO C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1102 through 1107 removed outlier: 3.585A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1133 removed outlier: 3.736A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE C1124 " --> pdb=" O ALA C1120 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.936A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN C1146 " --> pdb=" O ARG C1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 4.058A pdb=" N THR C1163 " --> pdb=" O ASP C1160 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE C1164 " --> pdb=" O LEU C1161 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1160 through 1164' Processing helix chain 'C' and resid 1166 through 1176 Processing helix chain 'C' and resid 1177 through 1179 No H-bonds generated for 'chain 'C' and resid 1177 through 1179' Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1262 through 1266 removed outlier: 3.678A pdb=" N PHE C1265 " --> pdb=" O LYS C1262 " (cutoff:3.500A) Processing helix chain 'C' and resid 1272 through 1281 removed outlier: 3.825A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1293 Processing helix chain 'C' and resid 1298 through 1310 removed outlier: 3.545A pdb=" N VAL C1309 " --> pdb=" O TYR C1305 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP C1310 " --> pdb=" O LYS C1306 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1334 removed outlier: 3.795A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY C1334 " --> pdb=" O ILE C1330 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 95 through 101 removed outlier: 3.600A pdb=" N ARG D 99 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU D 100 " --> pdb=" O LYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 119 removed outlier: 3.901A pdb=" N LEU D 117 " --> pdb=" O HIS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 removed outlier: 4.251A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 180 through 192 removed outlier: 3.615A pdb=" N ALA D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 211 through 231 removed outlier: 3.913A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN D 229 " --> pdb=" O GLU D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 284 Processing helix chain 'D' and resid 288 through 309 removed outlier: 3.628A pdb=" N ASN D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 370 through 389 Proline residue: D 379 - end of helix Processing helix chain 'D' and resid 393 through 404 removed outlier: 3.510A pdb=" N ARG D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 417 removed outlier: 4.142A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (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 452 through 458 removed outlier: 4.053A pdb=" N ALA D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 485 through 489 Processing helix chain 'D' and resid 503 through 514 Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.531A pdb=" N GLU D 534 " --> pdb=" O PRO D 530 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 583 removed outlier: 3.506A pdb=" N ALA D 577 " --> pdb=" O THR D 573 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.792A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 610 removed outlier: 3.611A pdb=" N SER D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 640 through 644 Processing helix chain 'D' and resid 648 through 670 removed outlier: 4.224A pdb=" N GLU D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.625A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 4.073A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY D 782 " --> pdb=" O GLY D 778 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER D 793 " --> pdb=" O LYS D 789 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLY D 794 " --> pdb=" O THR D 790 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.753A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 874 removed outlier: 3.987A pdb=" N GLU D 873 " --> pdb=" O CYS D 869 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLU D 874 " --> pdb=" O ASP D 870 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 900 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.626A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1244 removed outlier: 3.814A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY D1225 " --> pdb=" O LEU D1221 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL D1226 " --> pdb=" O ARG D1222 " (cutoff:3.500A) removed outlier: 9.206A pdb=" N HIS D1227 " --> pdb=" O LEU D1223 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA D1228 " --> pdb=" O ARG D1224 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 3.881A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL D1257 " --> pdb=" O ILE D1253 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1294 removed outlier: 3.671A pdb=" N LEU D1292 " --> pdb=" O ALA D1288 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 4.224A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1338 Processing helix chain 'D' and resid 1347 through 1354 Processing helix chain 'D' and resid 1360 through 1373 removed outlier: 4.106A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 17 through 28 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 4.762A pdb=" N HIS A 23 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR A 207 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LYS A 25 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N MET A 205 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N THR A 27 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE A 203 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLU A 29 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LEU A 201 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 104 removed outlier: 3.603A pdb=" N LEU A 102 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET A 142 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.617A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 153 removed outlier: 4.393A pdb=" N GLY A 151 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR A 177 " --> pdb=" O GLY A 151 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 153 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 175 " --> pdb=" O VAL A 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 23 through 27 removed outlier: 3.796A pdb=" N GLU B 206 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 105 removed outlier: 7.432A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 108 through 110 removed outlier: 3.881A pdb=" N GLY B 108 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.409A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.241A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 9.429A pdb=" N ALA C 94 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N MET C 124 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEU C 96 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N VAL C 122 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N VAL C 98 " --> pdb=" O GLN C 120 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLN C 120 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU C 100 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS C 118 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU C 102 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASP C 116 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE C 104 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB3, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.605A pdb=" N SER C 531 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 160 removed outlier: 4.127A pdb=" N LEU C 171 " --> pdb=" O ASP C 160 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 284 through 286 removed outlier: 4.615A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.964A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 296 through 297 removed outlier: 4.128A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 7.060A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC1, first strand: chain 'C' and resid 633 through 637 Processing sheet with id=AC2, first strand: chain 'C' and resid 716 through 718 removed outlier: 7.015A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP C 781 " --> pdb=" O ALA C 718 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 749 through 752 removed outlier: 6.841A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.502A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC6, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 5.007A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL C1097 " --> pdb=" O LEU C 817 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 1066 through 1067 Processing sheet with id=AC8, first strand: chain 'C' and resid 830 through 840 removed outlier: 3.521A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 887 through 888 Processing sheet with id=AD1, first strand: chain 'C' and resid 1087 through 1088 Processing sheet with id=AD2, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 6.078A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD4, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AD5, first strand: chain 'C' and resid 1335 through 1341 removed outlier: 3.785A pdb=" N GLU C1338 " --> pdb=" O LYS D 21 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS D 21 " --> pdb=" O GLU C1338 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU C1340 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ALA D 19 " --> pdb=" O GLU C1340 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 103 through 106 removed outlier: 3.555A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 144 through 145 Processing sheet with id=AD8, first strand: chain 'D' and resid 254 through 255 removed outlier: 3.530A pdb=" N ARG D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.603A pdb=" N ARG D 551 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 825 through 826 removed outlier: 4.069A pdb=" N VAL D 825 " --> pdb=" O GLU D 833 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU D 833 " --> pdb=" O VAL D 825 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'D' and resid 949 through 952 removed outlier: 6.985A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU D1015 " --> pdb=" O VAL D 952 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN D1019 " --> pdb=" O VAL D1002 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 957 through 961 Processing sheet with id=AE4, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE5, first strand: chain 'D' and resid 1025 through 1028 removed outlier: 5.605A pdb=" N MET D1025 " --> pdb=" O ARG D1123 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG D1123 " --> pdb=" O MET D1025 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL D1027 " --> pdb=" O LEU D1121 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1034 through 1036 removed outlier: 3.515A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1046 through 1048 removed outlier: 3.546A pdb=" N ALA D1105 " --> pdb=" O VAL D1061 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1156 through 1157 removed outlier: 3.536A pdb=" N ASP D1208 " --> pdb=" O ALA D1157 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1162 through 1163 removed outlier: 3.755A pdb=" N TYR D1186 " --> pdb=" O ILE D1177 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1278 through 1279 removed outlier: 6.351A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) 968 hydrogen bonds defined for protein. 2742 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 95 hydrogen bonds 178 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 61 stacking parallelities Total time for adding SS restraints: 7.02 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6776 1.33 - 1.45: 5075 1.45 - 1.57: 15124 1.57 - 1.69: 203 1.69 - 1.81: 182 Bond restraints: 27360 Sorted by residual: bond pdb=" C1' DC T 15 " pdb=" N1 DC T 15 " ideal model delta sigma weight residual 1.468 1.501 -0.033 1.40e-02 5.10e+03 5.64e+00 bond pdb=" C1' DC T 23 " pdb=" N1 DC T 23 " ideal model delta sigma weight residual 1.468 1.500 -0.032 1.40e-02 5.10e+03 5.22e+00 bond pdb=" C3' DT N 260 " pdb=" C2' DT N 260 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 5.01e+00 bond pdb=" C2' DC T 23 " pdb=" C1' DC T 23 " ideal model delta sigma weight residual 1.518 1.537 -0.019 1.00e-02 1.00e+04 3.71e+00 bond pdb=" C3' DC T 23 " pdb=" C2' DC T 23 " ideal model delta sigma weight residual 1.516 1.531 -0.015 8.00e-03 1.56e+04 3.64e+00 ... (remaining 27355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 36534 1.94 - 3.87: 780 3.87 - 5.81: 101 5.81 - 7.74: 28 7.74 - 9.68: 2 Bond angle restraints: 37445 Sorted by residual: angle pdb=" C3' A R 54 " pdb=" O3' A R 54 " pdb=" P U R 55 " ideal model delta sigma weight residual 119.70 125.59 -5.89 1.20e+00 6.94e-01 2.41e+01 angle pdb=" N3 DT N 260 " pdb=" C4 DT N 260 " pdb=" O4 DT N 260 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT N 257 " pdb=" C4 DT N 257 " pdb=" O4 DT N 257 " ideal model delta sigma weight residual 119.90 122.31 -2.41 6.00e-01 2.78e+00 1.61e+01 angle pdb=" N3 DT T 9 " pdb=" C4 DT T 9 " pdb=" O4 DT T 9 " ideal model delta sigma weight residual 119.90 122.26 -2.36 6.00e-01 2.78e+00 1.54e+01 angle pdb=" N3 DT T 5 " pdb=" C4 DT T 5 " pdb=" O4 DT T 5 " ideal model delta sigma weight residual 119.90 122.20 -2.30 6.00e-01 2.78e+00 1.47e+01 ... (remaining 37440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.76: 16021 33.76 - 67.52: 511 67.52 - 101.28: 40 101.28 - 135.04: 0 135.04 - 168.80: 1 Dihedral angle restraints: 16573 sinusoidal: 7558 harmonic: 9015 Sorted by residual: dihedral pdb=" C4' A R 22 " pdb=" C3' A R 22 " pdb=" C2' A R 22 " pdb=" C1' A R 22 " ideal model delta sinusoidal sigma weight residual 36.35 -37.37 73.71 1 3.10e+00 1.04e-01 7.19e+02 dihedral pdb=" C4' G R 35 " pdb=" C3' G R 35 " pdb=" C2' G R 35 " pdb=" C1' G R 35 " ideal model delta sinusoidal sigma weight residual 36.34 -36.01 72.35 1 3.10e+00 1.04e-01 6.96e+02 dihedral pdb=" C4' G R 53 " pdb=" C3' G R 53 " pdb=" C2' G R 53 " pdb=" C1' G R 53 " ideal model delta sinusoidal sigma weight residual 36.34 -35.77 72.11 1 3.10e+00 1.04e-01 6.92e+02 ... (remaining 16570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3726 0.067 - 0.134: 485 0.134 - 0.201: 19 0.201 - 0.268: 92 0.268 - 0.334: 12 Chirality restraints: 4334 Sorted by residual: chirality pdb=" P U R 55 " pdb=" OP1 U R 55 " pdb=" OP2 U R 55 " pdb=" O5' U R 55 " both_signs ideal model delta sigma weight residual True 2.17 -2.51 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" C3' A R 22 " pdb=" C4' A R 22 " pdb=" O3' A R 22 " pdb=" C2' A R 22 " both_signs ideal model delta sigma weight residual False -2.50 -2.80 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" C2' A R 54 " pdb=" C3' A R 54 " pdb=" O2' A R 54 " pdb=" C1' A R 54 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 4331 not shown) Planarity restraints: 4516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C1276 " -0.033 2.00e-02 2.50e+03 2.78e-02 1.93e+01 pdb=" CG TRP C1276 " 0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP C1276 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP C1276 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C1276 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C1276 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C1276 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1276 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1276 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C1276 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 115 " 0.011 2.00e-02 2.50e+03 1.32e-02 4.37e+00 pdb=" CG TRP D 115 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP D 115 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP D 115 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 115 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP D 115 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 115 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 115 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 115 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP D 115 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET D1095 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO D1096 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO D1096 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D1096 " -0.028 5.00e-02 4.00e+02 ... (remaining 4513 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 607 2.64 - 3.20: 26359 3.20 - 3.77: 45686 3.77 - 4.33: 59491 4.33 - 4.90: 89701 Nonbonded interactions: 221844 Sorted by model distance: nonbonded pdb=" N GLY D 463 " pdb="MG MG D1501 " model vdw 2.072 2.250 nonbonded pdb=" OG SER C 421 " pdb=" OD1 ASP C 423 " model vdw 2.107 3.040 nonbonded pdb=" O GLU D 652 " pdb=" OG SER D 655 " model vdw 2.143 3.040 nonbonded pdb=" N2 G R 46 " pdb=" O6 G R 61 " model vdw 2.156 3.120 nonbonded pdb=" OD2 ASP D 785 " pdb=" OG1 THR D 931 " model vdw 2.168 3.040 ... (remaining 221839 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 6 through 158 or resid 160 through 234)) selection = chain 'B' } 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 group one per residue 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: 4.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 30.470 Find NCS groups from input model: 0.200 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 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 : 0.003 0.033 27368 Z= 0.148 Angle : 0.671 9.680 37457 Z= 0.349 Chirality : 0.056 0.334 4334 Planarity : 0.004 0.050 4516 Dihedral : 15.600 168.800 10775 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.08 % Allowed : 0.30 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.15), residues: 3123 helix: 0.24 (0.16), residues: 1032 sheet: -0.49 (0.25), residues: 412 loop : -1.68 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 944 TYR 0.014 0.001 TYR C 105 PHE 0.011 0.001 PHE C 828 TRP 0.074 0.003 TRP C1276 HIS 0.002 0.001 HIS C1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.15 (27360) covalent geometry : angle 0.66660 / 0.35 (37445) hydrogen bonds : bond 0.20316 / 13.76 ( 1055) hydrogen bonds : angle 7.68096 / 5.25 ( 2920) metal coordination : bond 0.00623 / 0.36 ( 8) metal coordination : angle 4.31392 / 2.45 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 167 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 205 MET cc_start: 0.9500 (tpt) cc_final: 0.9189 (tpt) REVERT: C 403 MET cc_start: 0.9384 (tpp) cc_final: 0.9182 (mmp) REVERT: C 462 ASN cc_start: 0.9345 (m110) cc_final: 0.9038 (m110) REVERT: C 519 ASN cc_start: 0.8828 (t0) cc_final: 0.8324 (t0) REVERT: C 606 LEU cc_start: 0.9305 (mp) cc_final: 0.8544 (tp) REVERT: C 741 MET cc_start: 0.9146 (ppp) cc_final: 0.8892 (ppp) REVERT: C 768 MET cc_start: 0.8300 (tmm) cc_final: 0.7869 (tmm) REVERT: C 785 ASP cc_start: 0.7187 (m-30) cc_final: 0.6943 (m-30) REVERT: C 951 MET cc_start: 0.9220 (ptp) cc_final: 0.8915 (mpp) REVERT: C 1170 MET cc_start: 0.9385 (mmp) cc_final: 0.9053 (mmp) REVERT: C 1273 MET cc_start: 0.9077 (mmm) cc_final: 0.8265 (mmm) REVERT: C 1276 TRP cc_start: 0.8524 (m-90) cc_final: 0.7994 (m-90) REVERT: D 102 MET cc_start: 0.8943 (ppp) cc_final: 0.8549 (ppp) REVERT: D 180 MET cc_start: 0.5941 (mmp) cc_final: 0.5247 (mmt) REVERT: D 348 ASP cc_start: 0.9190 (p0) cc_final: 0.8762 (p0) REVERT: D 449 LEU cc_start: 0.9665 (tp) cc_final: 0.9434 (tp) REVERT: D 484 MET cc_start: 0.8477 (mpp) cc_final: 0.7995 (mpp) REVERT: D 485 MET cc_start: 0.9540 (mmp) cc_final: 0.8952 (mmm) REVERT: D 601 ILE cc_start: 0.9550 (tp) cc_final: 0.9274 (tp) REVERT: D 625 MET cc_start: 0.9131 (tmm) cc_final: 0.8897 (tmm) REVERT: D 743 MET cc_start: 0.8749 (tpt) cc_final: 0.8236 (tpp) REVERT: D 1260 MET cc_start: 0.8899 (tpt) cc_final: 0.8493 (tpt) outliers start: 2 outliers final: 1 residues processed: 168 average time/residue: 0.1471 time to fit residues: 42.3989 Evaluate side-chains 140 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 40.0000 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 20.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 HIS ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 517 GLN ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1350 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.045822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.031634 restraints weight = 257843.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.032705 restraints weight = 155358.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.033425 restraints weight = 110846.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.033902 restraints weight = 88257.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.034229 restraints weight = 75904.145| |-----------------------------------------------------------------------------| r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27368 Z= 0.221 Angle : 0.801 17.730 37457 Z= 0.386 Chirality : 0.071 2.226 4334 Planarity : 0.005 0.056 4516 Dihedral : 12.339 165.578 4668 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.08 % Allowed : 6.35 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.15), residues: 3123 helix: 0.23 (0.15), residues: 1118 sheet: -0.79 (0.24), residues: 445 loop : -1.83 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1048 TYR 0.016 0.001 TYR D 631 PHE 0.015 0.002 PHE D 116 TRP 0.030 0.002 TRP C1276 HIS 0.006 0.001 HIS D 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.22 (27360) covalent geometry : angle 0.79582 / 0.39 (37445) hydrogen bonds : bond 0.05996 / 3.89 ( 1055) hydrogen bonds : angle 6.20565 / 4.28 ( 2920) metal coordination : bond 0.01135 / 0.76 ( 8) metal coordination : angle 5.20816 / 3.16 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 159 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 205 MET cc_start: 0.9424 (tpt) cc_final: 0.9172 (tpt) REVERT: C 315 MET cc_start: 0.9017 (mmp) cc_final: 0.8778 (mmm) REVERT: C 370 MET cc_start: 0.8248 (ppp) cc_final: 0.7945 (ppp) REVERT: C 462 ASN cc_start: 0.9441 (m110) cc_final: 0.9160 (m110) REVERT: C 515 MET cc_start: 0.7917 (tmm) cc_final: 0.7616 (tmm) REVERT: C 519 ASN cc_start: 0.9039 (t0) cc_final: 0.8561 (t0) REVERT: C 606 LEU cc_start: 0.9490 (mp) cc_final: 0.8734 (tp) REVERT: C 1170 MET cc_start: 0.9446 (mmp) cc_final: 0.9113 (mmm) REVERT: C 1243 MET cc_start: 0.9439 (tpt) cc_final: 0.9183 (tpt) REVERT: C 1273 MET cc_start: 0.9220 (mmm) cc_final: 0.8965 (mmm) REVERT: C 1287 LEU cc_start: 0.9674 (tp) cc_final: 0.9456 (tp) REVERT: D 102 MET cc_start: 0.9095 (ppp) cc_final: 0.8490 (ppp) REVERT: D 180 MET cc_start: 0.6300 (mmp) cc_final: 0.5385 (mmt) REVERT: D 348 ASP cc_start: 0.9286 (p0) cc_final: 0.8818 (p0) REVERT: D 449 LEU cc_start: 0.9672 (tp) cc_final: 0.9436 (tp) REVERT: D 484 MET cc_start: 0.8648 (mpp) cc_final: 0.8255 (mpp) REVERT: D 485 MET cc_start: 0.9563 (mmp) cc_final: 0.9063 (mmm) REVERT: D 601 ILE cc_start: 0.9678 (tp) cc_final: 0.9475 (tp) REVERT: D 625 MET cc_start: 0.9294 (tmm) cc_final: 0.9005 (tmm) REVERT: D 743 MET cc_start: 0.9109 (tpt) cc_final: 0.8773 (tpp) REVERT: D 932 MET cc_start: 0.8948 (mtm) cc_final: 0.8689 (mtt) outliers start: 2 outliers final: 1 residues processed: 160 average time/residue: 0.1449 time to fit residues: 39.6397 Evaluate side-chains 137 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 144 optimal weight: 9.9990 chunk 210 optimal weight: 4.9990 chunk 243 optimal weight: 5.9990 chunk 276 optimal weight: 50.0000 chunk 283 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 273 optimal weight: 9.9990 chunk 221 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 chunk 306 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS C 69 GLN ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1238 GLN D1244 GLN ** D1289 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 = 0.3298 r_free = 0.3298 target = 0.045673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.031496 restraints weight = 258518.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.032548 restraints weight = 155437.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.033254 restraints weight = 110778.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.033735 restraints weight = 88404.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.034035 restraints weight = 75968.973| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 27368 Z= 0.216 Angle : 0.727 12.924 37457 Z= 0.360 Chirality : 0.069 2.893 4334 Planarity : 0.005 0.057 4516 Dihedral : 12.637 170.172 4668 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 0.04 % Allowed : 5.48 % Favored : 94.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.14), residues: 3123 helix: 0.20 (0.15), residues: 1114 sheet: -0.89 (0.25), residues: 407 loop : -1.84 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 77 TYR 0.021 0.002 TYR C 555 PHE 0.012 0.001 PHE C 156 TRP 0.014 0.002 TRP C1276 HIS 0.005 0.001 HIS C1116 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.22 (27360) covalent geometry : angle 0.72085 / 0.36 (37445) hydrogen bonds : bond 0.05150 / 3.35 ( 1055) hydrogen bonds : angle 5.97793 / 4.13 ( 2920) metal coordination : bond 0.01002 / 0.67 ( 8) metal coordination : angle 5.13929 / 3.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 205 MET cc_start: 0.9306 (tpt) cc_final: 0.9059 (tpt) REVERT: C 462 ASN cc_start: 0.9462 (m110) cc_final: 0.9166 (m110) REVERT: C 515 MET cc_start: 0.8001 (tmm) cc_final: 0.7412 (tmm) REVERT: C 519 ASN cc_start: 0.9038 (t0) cc_final: 0.8617 (t0) REVERT: C 606 LEU cc_start: 0.9517 (mp) cc_final: 0.8761 (tp) REVERT: C 826 ASP cc_start: 0.7855 (m-30) cc_final: 0.7655 (m-30) REVERT: C 1170 MET cc_start: 0.9443 (mmp) cc_final: 0.9114 (mmp) REVERT: C 1287 LEU cc_start: 0.9688 (tp) cc_final: 0.9455 (tp) REVERT: D 102 MET cc_start: 0.9173 (ppp) cc_final: 0.8539 (ppp) REVERT: D 348 ASP cc_start: 0.9301 (p0) cc_final: 0.8847 (p0) REVERT: D 484 MET cc_start: 0.8687 (mpp) cc_final: 0.8267 (mpp) REVERT: D 485 MET cc_start: 0.9581 (mmp) cc_final: 0.9058 (mmm) REVERT: D 601 ILE cc_start: 0.9653 (tp) cc_final: 0.9423 (tp) REVERT: D 604 MET cc_start: 0.9224 (mmp) cc_final: 0.9016 (mmm) REVERT: D 625 MET cc_start: 0.9283 (tmm) cc_final: 0.8960 (tmm) REVERT: D 743 MET cc_start: 0.9079 (tpt) cc_final: 0.8557 (tpt) REVERT: D 932 MET cc_start: 0.8958 (mtm) cc_final: 0.8637 (mtt) REVERT: D 1189 MET cc_start: 0.8432 (tpp) cc_final: 0.8212 (tpp) REVERT: D 1307 LEU cc_start: 0.8871 (tp) cc_final: 0.8647 (tp) outliers start: 1 outliers final: 1 residues processed: 155 average time/residue: 0.1602 time to fit residues: 43.3826 Evaluate side-chains 134 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 123 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 chunk 236 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 191 optimal weight: 30.0000 chunk 173 optimal weight: 0.8980 chunk 270 optimal weight: 7.9990 chunk 264 optimal weight: 8.9990 chunk 196 optimal weight: 8.9990 chunk 216 optimal weight: 7.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 GLN D 504 GLN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1289 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 = 0.3295 r_free = 0.3295 target = 0.045517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.031239 restraints weight = 248153.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.032325 restraints weight = 148742.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.033055 restraints weight = 105585.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.033556 restraints weight = 83691.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.033895 restraints weight = 71481.810| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27368 Z= 0.186 Angle : 0.691 13.858 37457 Z= 0.341 Chirality : 0.067 3.003 4334 Planarity : 0.004 0.055 4516 Dihedral : 12.723 177.018 4668 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.14), residues: 3123 helix: 0.27 (0.15), residues: 1112 sheet: -0.77 (0.25), residues: 399 loop : -1.84 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 77 TYR 0.019 0.001 TYR C1229 PHE 0.020 0.001 PHE C 464 TRP 0.013 0.001 TRP C1276 HIS 0.004 0.001 HIS C1116 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.19 (27360) covalent geometry : angle 0.68295 / 0.34 (37445) hydrogen bonds : bond 0.04712 / 3.04 ( 1055) hydrogen bonds : angle 5.74107 / 3.97 ( 2920) metal coordination : bond 0.00950 / 0.63 ( 8) metal coordination : angle 5.73391 / 3.51 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 MET cc_start: 0.8647 (mmm) cc_final: 0.8063 (tpp) REVERT: C 291 TYR cc_start: 0.8674 (t80) cc_final: 0.8428 (t80) REVERT: C 315 MET cc_start: 0.9023 (mmp) cc_final: 0.8759 (mmm) REVERT: C 462 ASN cc_start: 0.9473 (m110) cc_final: 0.9183 (m110) REVERT: C 515 MET cc_start: 0.8085 (tmm) cc_final: 0.7716 (tmm) REVERT: C 519 ASN cc_start: 0.9077 (t0) cc_final: 0.8617 (t0) REVERT: C 606 LEU cc_start: 0.9518 (mp) cc_final: 0.8759 (tp) REVERT: C 1170 MET cc_start: 0.9411 (mmp) cc_final: 0.9076 (mmp) REVERT: C 1273 MET cc_start: 0.9169 (mpp) cc_final: 0.8733 (mpp) REVERT: C 1287 LEU cc_start: 0.9661 (tp) cc_final: 0.9386 (tp) REVERT: D 102 MET cc_start: 0.9222 (ppp) cc_final: 0.8565 (ppp) REVERT: D 180 MET cc_start: 0.6188 (mmp) cc_final: 0.4991 (mmt) REVERT: D 348 ASP cc_start: 0.9320 (p0) cc_final: 0.8895 (p0) REVERT: D 449 LEU cc_start: 0.9672 (tp) cc_final: 0.9471 (tp) REVERT: D 484 MET cc_start: 0.8651 (mpp) cc_final: 0.8285 (mpp) REVERT: D 485 MET cc_start: 0.9597 (mmp) cc_final: 0.9081 (mmm) REVERT: D 604 MET cc_start: 0.9188 (mmp) cc_final: 0.8941 (mmp) REVERT: D 625 MET cc_start: 0.9333 (tmm) cc_final: 0.8883 (tmm) REVERT: D 743 MET cc_start: 0.9104 (tpt) cc_final: 0.8749 (tpt) REVERT: D 932 MET cc_start: 0.8967 (mtm) cc_final: 0.8644 (mtt) REVERT: D 1189 MET cc_start: 0.8467 (tpp) cc_final: 0.8218 (tpp) REVERT: D 1260 MET cc_start: 0.8905 (tpt) cc_final: 0.8701 (tpt) REVERT: D 1307 LEU cc_start: 0.8867 (tp) cc_final: 0.8503 (tp) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1490 time to fit residues: 41.1605 Evaluate side-chains 134 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 90 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 312 optimal weight: 20.0000 chunk 142 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 chunk 77 optimal weight: 30.0000 chunk 105 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS C 69 GLN ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1238 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.045126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.030870 restraints weight = 249751.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.031951 restraints weight = 149473.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.032665 restraints weight = 106163.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.033175 restraints weight = 84236.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.033511 restraints weight = 71738.081| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27368 Z= 0.217 Angle : 0.706 15.231 37457 Z= 0.350 Chirality : 0.062 2.638 4334 Planarity : 0.004 0.057 4516 Dihedral : 12.780 177.363 4668 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.04 % Allowed : 3.68 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.14), residues: 3123 helix: 0.20 (0.16), residues: 1114 sheet: -0.82 (0.25), residues: 400 loop : -1.86 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 919 TYR 0.021 0.002 TYR C1229 PHE 0.021 0.002 PHE C 464 TRP 0.013 0.002 TRP D 868 HIS 0.006 0.001 HIS C1116 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.22 (27360) covalent geometry : angle 0.69876 / 0.35 (37445) hydrogen bonds : bond 0.04796 / 3.09 ( 1055) hydrogen bonds : angle 5.75998 / 3.99 ( 2920) metal coordination : bond 0.01017 / 0.68 ( 8) metal coordination : angle 5.52015 / 3.43 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 291 TYR cc_start: 0.8722 (t80) cc_final: 0.8486 (t80) REVERT: C 315 MET cc_start: 0.9078 (mmp) cc_final: 0.8826 (mmm) REVERT: C 462 ASN cc_start: 0.9479 (m110) cc_final: 0.9196 (m110) REVERT: C 515 MET cc_start: 0.8021 (tmm) cc_final: 0.6737 (tmm) REVERT: C 519 ASN cc_start: 0.9058 (t0) cc_final: 0.8596 (t0) REVERT: C 606 LEU cc_start: 0.9532 (mp) cc_final: 0.8801 (tp) REVERT: C 741 MET cc_start: 0.9137 (ppp) cc_final: 0.8912 (ppp) REVERT: C 1170 MET cc_start: 0.9446 (mmp) cc_final: 0.9105 (mmm) REVERT: C 1273 MET cc_start: 0.9183 (mpp) cc_final: 0.8720 (mpp) REVERT: C 1287 LEU cc_start: 0.9677 (tp) cc_final: 0.9414 (tp) REVERT: D 102 MET cc_start: 0.9241 (ppp) cc_final: 0.8585 (ppp) REVERT: D 348 ASP cc_start: 0.9310 (p0) cc_final: 0.8906 (p0) REVERT: D 449 LEU cc_start: 0.9683 (tp) cc_final: 0.9465 (tp) REVERT: D 484 MET cc_start: 0.8703 (mpp) cc_final: 0.8355 (mpp) REVERT: D 485 MET cc_start: 0.9627 (mmp) cc_final: 0.9130 (mmm) REVERT: D 604 MET cc_start: 0.9183 (mmp) cc_final: 0.8974 (mmp) REVERT: D 625 MET cc_start: 0.9338 (tmm) cc_final: 0.8920 (tmm) REVERT: D 743 MET cc_start: 0.9190 (tpt) cc_final: 0.8818 (tpt) REVERT: D 932 MET cc_start: 0.8951 (mtm) cc_final: 0.8624 (mtt) REVERT: D 1189 MET cc_start: 0.8513 (tpp) cc_final: 0.8278 (tpp) outliers start: 1 outliers final: 1 residues processed: 157 average time/residue: 0.1585 time to fit residues: 42.9184 Evaluate side-chains 134 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 103 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 317 optimal weight: 40.0000 chunk 240 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 278 optimal weight: 0.5980 chunk 279 optimal weight: 9.9990 chunk 190 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 115 optimal weight: 20.0000 chunk 249 optimal weight: 9.9990 overall best weight: 3.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 ASN ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1289 ASN ** 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 = 0.3299 r_free = 0.3299 target = 0.045698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.031604 restraints weight = 254879.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.032688 restraints weight = 153300.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.033414 restraints weight = 109162.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.033907 restraints weight = 86826.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.034246 restraints weight = 74419.236| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27368 Z= 0.154 Angle : 0.684 15.757 37457 Z= 0.333 Chirality : 0.056 1.981 4334 Planarity : 0.004 0.059 4516 Dihedral : 12.757 178.621 4668 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.15), residues: 3123 helix: 0.26 (0.16), residues: 1113 sheet: -0.72 (0.26), residues: 388 loop : -1.82 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 77 TYR 0.017 0.001 TYR C1229 PHE 0.021 0.001 PHE C 464 TRP 0.012 0.001 TRP D 868 HIS 0.004 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (27360) covalent geometry : angle 0.67789 / 0.33 (37445) hydrogen bonds : bond 0.04478 / 2.86 ( 1055) hydrogen bonds : angle 5.59330 / 3.87 ( 2920) metal coordination : bond 0.00767 / 0.53 ( 8) metal coordination : angle 5.22943 / 3.22 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 142 GLU cc_start: 0.8696 (pt0) cc_final: 0.8432 (pt0) REVERT: C 291 TYR cc_start: 0.8731 (t80) cc_final: 0.8470 (t80) REVERT: C 315 MET cc_start: 0.9096 (mmp) cc_final: 0.8854 (mmm) REVERT: C 462 ASN cc_start: 0.9497 (m110) cc_final: 0.9219 (m110) REVERT: C 519 ASN cc_start: 0.8984 (t0) cc_final: 0.8493 (t0) REVERT: C 606 LEU cc_start: 0.9553 (mp) cc_final: 0.8832 (tp) REVERT: C 826 ASP cc_start: 0.7898 (m-30) cc_final: 0.7665 (m-30) REVERT: C 1170 MET cc_start: 0.9437 (mmp) cc_final: 0.9084 (mmm) REVERT: C 1273 MET cc_start: 0.9085 (mpp) cc_final: 0.8573 (mpp) REVERT: C 1287 LEU cc_start: 0.9679 (tp) cc_final: 0.9405 (tp) REVERT: D 102 MET cc_start: 0.9228 (ppp) cc_final: 0.8540 (ppp) REVERT: D 348 ASP cc_start: 0.9303 (p0) cc_final: 0.8888 (p0) REVERT: D 466 MET cc_start: 0.8971 (mtp) cc_final: 0.8767 (mtm) REVERT: D 484 MET cc_start: 0.8691 (mpp) cc_final: 0.8321 (mpp) REVERT: D 485 MET cc_start: 0.9599 (mmp) cc_final: 0.9041 (mmm) REVERT: D 604 MET cc_start: 0.9226 (mmp) cc_final: 0.8880 (mmm) REVERT: D 625 MET cc_start: 0.9353 (tmm) cc_final: 0.8914 (tmm) REVERT: D 644 MET cc_start: 0.8902 (mpp) cc_final: 0.8693 (mpp) REVERT: D 743 MET cc_start: 0.9149 (tpt) cc_final: 0.8763 (tpt) REVERT: D 932 MET cc_start: 0.8913 (mtm) cc_final: 0.8579 (mtt) REVERT: D 1189 MET cc_start: 0.8555 (tpp) cc_final: 0.8308 (tpp) REVERT: D 1307 LEU cc_start: 0.8885 (tp) cc_final: 0.8501 (tp) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1562 time to fit residues: 42.1898 Evaluate side-chains 134 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 61 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 316 optimal weight: 20.0000 chunk 69 optimal weight: 0.4980 chunk 306 optimal weight: 0.6980 chunk 172 optimal weight: 10.0000 chunk 250 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 overall best weight: 5.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS C 69 GLN ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1289 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 = 0.3279 r_free = 0.3279 target = 0.045049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.031012 restraints weight = 259381.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.032066 restraints weight = 156664.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.032768 restraints weight = 112135.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.033237 restraints weight = 89592.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.033555 restraints weight = 77057.107| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 27368 Z= 0.232 Angle : 0.733 15.240 37457 Z= 0.361 Chirality : 0.051 1.164 4334 Planarity : 0.005 0.060 4516 Dihedral : 12.723 178.596 4668 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.14), residues: 3123 helix: 0.15 (0.16), residues: 1114 sheet: -0.82 (0.25), residues: 390 loop : -1.87 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D1290 TYR 0.044 0.002 TYR C 346 PHE 0.021 0.002 PHE C 464 TRP 0.011 0.002 TRP D 868 HIS 0.006 0.001 HIS C1116 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.23 (27360) covalent geometry : angle 0.72623 / 0.36 (37445) hydrogen bonds : bond 0.04785 / 3.07 ( 1055) hydrogen bonds : angle 5.74625 / 3.99 ( 2920) metal coordination : bond 0.01039 / 0.70 ( 8) metal coordination : angle 5.40521 / 3.34 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 291 TYR cc_start: 0.8822 (t80) cc_final: 0.8512 (t80) REVERT: C 462 ASN cc_start: 0.9493 (m110) cc_final: 0.9219 (m110) REVERT: C 515 MET cc_start: 0.7914 (tmm) cc_final: 0.7564 (tmm) REVERT: C 519 ASN cc_start: 0.9017 (t0) cc_final: 0.8527 (t0) REVERT: C 606 LEU cc_start: 0.9543 (mp) cc_final: 0.8875 (tp) REVERT: C 741 MET cc_start: 0.9120 (ppp) cc_final: 0.8869 (ppp) REVERT: C 826 ASP cc_start: 0.7849 (m-30) cc_final: 0.7646 (m-30) REVERT: C 1170 MET cc_start: 0.9451 (mmp) cc_final: 0.9099 (mmm) REVERT: C 1273 MET cc_start: 0.9104 (mpp) cc_final: 0.8593 (mpp) REVERT: C 1287 LEU cc_start: 0.9677 (tp) cc_final: 0.9421 (tp) REVERT: D 102 MET cc_start: 0.9243 (ppp) cc_final: 0.8571 (ppp) REVERT: D 180 MET cc_start: 0.6355 (mmp) cc_final: 0.5124 (mmt) REVERT: D 348 ASP cc_start: 0.9339 (p0) cc_final: 0.8934 (p0) REVERT: D 484 MET cc_start: 0.8699 (mpp) cc_final: 0.8370 (mpp) REVERT: D 485 MET cc_start: 0.9615 (mmp) cc_final: 0.9131 (mmm) REVERT: D 604 MET cc_start: 0.9197 (mmp) cc_final: 0.8922 (mmm) REVERT: D 625 MET cc_start: 0.9336 (tmm) cc_final: 0.8903 (tmm) REVERT: D 644 MET cc_start: 0.8964 (mpp) cc_final: 0.8740 (mpp) REVERT: D 743 MET cc_start: 0.9195 (tpt) cc_final: 0.8829 (tpt) REVERT: D 932 MET cc_start: 0.8913 (mtm) cc_final: 0.8513 (mtt) REVERT: D 1189 MET cc_start: 0.8574 (tpp) cc_final: 0.8343 (tpp) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1526 time to fit residues: 39.3495 Evaluate side-chains 131 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 310 optimal weight: 20.0000 chunk 288 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 302 optimal weight: 6.9990 chunk 75 optimal weight: 0.2980 chunk 264 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 68 optimal weight: 20.0000 chunk 25 optimal weight: 0.8980 chunk 225 optimal weight: 8.9990 chunk 316 optimal weight: 20.0000 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 799 ASN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** 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 = 0.3293 r_free = 0.3293 target = 0.045528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.031436 restraints weight = 258272.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.032505 restraints weight = 155353.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.033226 restraints weight = 110831.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.033720 restraints weight = 88220.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.034035 restraints weight = 75737.807| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 27368 Z= 0.177 Angle : 0.691 11.091 37457 Z= 0.338 Chirality : 0.048 0.538 4334 Planarity : 0.004 0.061 4516 Dihedral : 12.692 179.229 4668 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 0.04 % Allowed : 1.65 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.14), residues: 3123 helix: 0.21 (0.15), residues: 1113 sheet: -0.79 (0.26), residues: 379 loop : -1.85 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 919 TYR 0.017 0.001 TYR C1229 PHE 0.022 0.002 PHE C 464 TRP 0.013 0.001 TRP C1276 HIS 0.004 0.001 HIS C1116 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.18 (27360) covalent geometry : angle 0.68504 / 0.34 (37445) hydrogen bonds : bond 0.04513 / 2.89 ( 1055) hydrogen bonds : angle 5.59147 / 3.88 ( 2920) metal coordination : bond 0.00867 / 0.60 ( 8) metal coordination : angle 5.19027 / 3.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 ASN cc_start: 0.9414 (t0) cc_final: 0.9094 (t0) REVERT: C 130 MET cc_start: 0.8746 (mmm) cc_final: 0.8064 (tpp) REVERT: C 291 TYR cc_start: 0.8831 (t80) cc_final: 0.8525 (t80) REVERT: C 315 MET cc_start: 0.9117 (mmp) cc_final: 0.8854 (mmm) REVERT: C 462 ASN cc_start: 0.9502 (m110) cc_final: 0.9228 (m110) REVERT: C 515 MET cc_start: 0.7957 (tmm) cc_final: 0.7554 (tmm) REVERT: C 519 ASN cc_start: 0.8965 (t0) cc_final: 0.8478 (t0) REVERT: C 606 LEU cc_start: 0.9525 (mp) cc_final: 0.8818 (tp) REVERT: C 741 MET cc_start: 0.9069 (ppp) cc_final: 0.8849 (ppp) REVERT: C 826 ASP cc_start: 0.7822 (m-30) cc_final: 0.7613 (m-30) REVERT: C 1099 ASN cc_start: 0.8496 (t0) cc_final: 0.8295 (t0) REVERT: C 1170 MET cc_start: 0.9444 (mmp) cc_final: 0.9088 (mmm) REVERT: C 1273 MET cc_start: 0.9086 (mpp) cc_final: 0.8559 (mpp) REVERT: C 1287 LEU cc_start: 0.9682 (tp) cc_final: 0.9425 (tp) REVERT: D 102 MET cc_start: 0.9206 (ppp) cc_final: 0.8518 (ppp) REVERT: D 180 MET cc_start: 0.6460 (mmp) cc_final: 0.5323 (mmt) REVERT: D 348 ASP cc_start: 0.9303 (p0) cc_final: 0.8914 (p0) REVERT: D 466 MET cc_start: 0.8985 (mtp) cc_final: 0.8747 (mtm) REVERT: D 484 MET cc_start: 0.8698 (mpp) cc_final: 0.8359 (mpp) REVERT: D 485 MET cc_start: 0.9591 (mmp) cc_final: 0.9075 (mmm) REVERT: D 604 MET cc_start: 0.9225 (mmp) cc_final: 0.8885 (mmp) REVERT: D 625 MET cc_start: 0.9358 (tmm) cc_final: 0.8917 (tmm) REVERT: D 743 MET cc_start: 0.9205 (tpt) cc_final: 0.8793 (tpt) REVERT: D 932 MET cc_start: 0.8889 (mtm) cc_final: 0.8458 (mtt) REVERT: D 1189 MET cc_start: 0.8628 (tpp) cc_final: 0.8411 (tpp) REVERT: D 1307 LEU cc_start: 0.8886 (tp) cc_final: 0.8532 (tp) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.1603 time to fit residues: 43.5907 Evaluate side-chains 131 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 229 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 273 optimal weight: 0.3980 chunk 269 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 233 optimal weight: 0.9980 chunk 84 optimal weight: 0.0980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS C 799 ASN C 932 GLN ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 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 = 0.3319 r_free = 0.3319 target = 0.046305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.032094 restraints weight = 252245.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.033209 restraints weight = 150543.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.033956 restraints weight = 106893.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.034453 restraints weight = 84915.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.034798 restraints weight = 72642.829| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27368 Z= 0.119 Angle : 0.685 9.804 37457 Z= 0.331 Chirality : 0.048 0.395 4334 Planarity : 0.004 0.062 4516 Dihedral : 12.588 179.317 4668 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 0.04 % Allowed : 0.98 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.15), residues: 3123 helix: 0.27 (0.16), residues: 1107 sheet: -0.77 (0.25), residues: 396 loop : -1.75 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 77 TYR 0.015 0.001 TYR C 555 PHE 0.021 0.001 PHE C 464 TRP 0.017 0.001 TRP C1276 HIS 0.004 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (27360) covalent geometry : angle 0.68009 / 0.33 (37445) hydrogen bonds : bond 0.04208 / 2.69 ( 1055) hydrogen bonds : angle 5.41943 / 3.74 ( 2920) metal coordination : bond 0.00529 / 0.38 ( 8) metal coordination : angle 4.54169 / 2.80 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 ASN cc_start: 0.9364 (t0) cc_final: 0.9110 (t0) REVERT: C 130 MET cc_start: 0.8689 (mmm) cc_final: 0.8070 (tpp) REVERT: C 239 MET cc_start: 0.6895 (ptp) cc_final: 0.6578 (pmm) REVERT: C 291 TYR cc_start: 0.8798 (t80) cc_final: 0.8571 (t80) REVERT: C 315 MET cc_start: 0.9112 (mmp) cc_final: 0.8842 (mmm) REVERT: C 462 ASN cc_start: 0.9520 (m110) cc_final: 0.9250 (m110) REVERT: C 515 MET cc_start: 0.7975 (tmm) cc_final: 0.7591 (tmm) REVERT: C 519 ASN cc_start: 0.8871 (t0) cc_final: 0.8356 (t0) REVERT: C 606 LEU cc_start: 0.9517 (mp) cc_final: 0.8802 (tp) REVERT: C 826 ASP cc_start: 0.7801 (m-30) cc_final: 0.7601 (m-30) REVERT: C 951 MET cc_start: 0.9304 (ptp) cc_final: 0.9059 (mpp) REVERT: C 1085 MET cc_start: 0.7963 (mtt) cc_final: 0.7643 (mtt) REVERT: C 1119 MET cc_start: 0.9056 (mmm) cc_final: 0.8794 (mmp) REVERT: C 1170 MET cc_start: 0.9418 (mmp) cc_final: 0.9070 (mmm) REVERT: C 1273 MET cc_start: 0.9002 (mpp) cc_final: 0.8558 (pmm) REVERT: C 1276 TRP cc_start: 0.8540 (m-10) cc_final: 0.8117 (m-90) REVERT: C 1287 LEU cc_start: 0.9648 (tp) cc_final: 0.9374 (tp) REVERT: D 102 MET cc_start: 0.9176 (ppp) cc_final: 0.8481 (ppp) REVERT: D 348 ASP cc_start: 0.9290 (p0) cc_final: 0.8875 (p0) REVERT: D 428 THR cc_start: 0.8608 (p) cc_final: 0.8156 (p) REVERT: D 484 MET cc_start: 0.8704 (mpp) cc_final: 0.8266 (mpp) REVERT: D 485 MET cc_start: 0.9568 (mmp) cc_final: 0.8950 (mmm) REVERT: D 604 MET cc_start: 0.9195 (mmp) cc_final: 0.8824 (mmp) REVERT: D 625 MET cc_start: 0.9348 (tmm) cc_final: 0.8922 (tmm) REVERT: D 644 MET cc_start: 0.8909 (mpp) cc_final: 0.8656 (mpp) REVERT: D 743 MET cc_start: 0.9194 (tpt) cc_final: 0.8750 (tpt) REVERT: D 932 MET cc_start: 0.8817 (mtm) cc_final: 0.8397 (mtt) REVERT: D 1189 MET cc_start: 0.8560 (tpp) cc_final: 0.8318 (tpp) outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.1569 time to fit residues: 44.9747 Evaluate side-chains 143 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 191 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 287 optimal weight: 20.0000 chunk 195 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 216 optimal weight: 5.9990 chunk 230 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 799 ASN ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1238 GLN ** D1249 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 = 0.3286 r_free = 0.3286 target = 0.045281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.031213 restraints weight = 258713.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.032277 restraints weight = 156037.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.032975 restraints weight = 111711.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.033453 restraints weight = 89333.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.033778 restraints weight = 76768.749| |-----------------------------------------------------------------------------| r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27368 Z= 0.207 Angle : 0.707 10.069 37457 Z= 0.349 Chirality : 0.047 0.351 4334 Planarity : 0.005 0.063 4516 Dihedral : 12.631 179.695 4668 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.04 % Allowed : 0.60 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.15), residues: 3123 helix: 0.20 (0.15), residues: 1116 sheet: -0.84 (0.25), residues: 394 loop : -1.81 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 77 TYR 0.020 0.002 TYR C1229 PHE 0.020 0.002 PHE C 464 TRP 0.013 0.002 TRP C1276 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.21 (27360) covalent geometry : angle 0.70081 / 0.35 (37445) hydrogen bonds : bond 0.04571 / 2.95 ( 1055) hydrogen bonds : angle 5.59622 / 3.88 ( 2920) metal coordination : bond 0.00930 / 0.64 ( 8) metal coordination : angle 5.11586 / 3.20 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 MET cc_start: 0.8886 (mmm) cc_final: 0.8264 (tpp) REVERT: C 239 MET cc_start: 0.6843 (ptp) cc_final: 0.6559 (pmm) REVERT: C 291 TYR cc_start: 0.8809 (t80) cc_final: 0.8591 (t80) REVERT: C 315 MET cc_start: 0.9123 (mmp) cc_final: 0.8865 (mmm) REVERT: C 462 ASN cc_start: 0.9509 (m110) cc_final: 0.9236 (m110) REVERT: C 515 MET cc_start: 0.8070 (tmm) cc_final: 0.7631 (tmm) REVERT: C 519 ASN cc_start: 0.8970 (t0) cc_final: 0.8445 (t0) REVERT: C 606 LEU cc_start: 0.9533 (mp) cc_final: 0.8859 (tp) REVERT: C 741 MET cc_start: 0.9091 (ppp) cc_final: 0.8781 (ppp) REVERT: C 1085 MET cc_start: 0.8124 (mtt) cc_final: 0.7891 (mtt) REVERT: C 1170 MET cc_start: 0.9443 (mmp) cc_final: 0.9099 (mmp) REVERT: C 1273 MET cc_start: 0.9050 (mpp) cc_final: 0.8541 (mpp) REVERT: C 1287 LEU cc_start: 0.9677 (tp) cc_final: 0.9432 (tp) REVERT: D 180 MET cc_start: 0.6394 (mmp) cc_final: 0.5232 (mmt) REVERT: D 348 ASP cc_start: 0.9319 (p0) cc_final: 0.8942 (p0) REVERT: D 484 MET cc_start: 0.8711 (mpp) cc_final: 0.8334 (mpp) REVERT: D 485 MET cc_start: 0.9593 (mmp) cc_final: 0.9109 (mmm) REVERT: D 604 MET cc_start: 0.9208 (mmp) cc_final: 0.8879 (mmp) REVERT: D 625 MET cc_start: 0.9350 (tmm) cc_final: 0.8870 (tmm) REVERT: D 644 MET cc_start: 0.8920 (mpp) cc_final: 0.8693 (mpp) REVERT: D 743 MET cc_start: 0.9210 (tpt) cc_final: 0.8831 (tpt) REVERT: D 932 MET cc_start: 0.8801 (mtm) cc_final: 0.8349 (mtt) REVERT: D 1189 MET cc_start: 0.8639 (tpp) cc_final: 0.8412 (tpp) REVERT: D 1260 MET cc_start: 0.8946 (tpt) cc_final: 0.8725 (tpt) REVERT: D 1307 LEU cc_start: 0.8909 (tp) cc_final: 0.8589 (tp) outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.1596 time to fit residues: 44.0608 Evaluate side-chains 134 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 185 optimal weight: 4.9990 chunk 273 optimal weight: 10.0000 chunk 231 optimal weight: 0.9990 chunk 236 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 253 optimal weight: 0.9990 chunk 283 optimal weight: 0.7980 chunk 189 optimal weight: 0.9990 chunk 256 optimal weight: 4.9990 chunk 55 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 799 ASN ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** 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 = 0.3313 r_free = 0.3313 target = 0.046159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.031957 restraints weight = 250128.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.033062 restraints weight = 150076.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.033809 restraints weight = 106762.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.034305 restraints weight = 84797.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.034650 restraints weight = 72660.126| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 27368 Z= 0.122 Angle : 0.679 9.909 37457 Z= 0.329 Chirality : 0.048 0.322 4334 Planarity : 0.004 0.071 4516 Dihedral : 12.568 178.962 4668 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.04 % Allowed : 0.34 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.15), residues: 3123 helix: 0.21 (0.15), residues: 1110 sheet: -0.81 (0.25), residues: 396 loop : -1.73 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 77 TYR 0.014 0.001 TYR C 555 PHE 0.021 0.001 PHE C 464 TRP 0.021 0.001 TRP C1276 HIS 0.004 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (27360) covalent geometry : angle 0.67364 / 0.33 (37445) hydrogen bonds : bond 0.04224 / 2.71 ( 1055) hydrogen bonds : angle 5.40480 / 3.74 ( 2920) metal coordination : bond 0.00556 / 0.41 ( 8) metal coordination : angle 4.69220 / 2.90 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4605.03 seconds wall clock time: 80 minutes 48.82 seconds (4848.82 seconds total)