Starting phenix.real_space_refine on Tue Mar 19 00:13:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyb_33516/03_2024/7xyb_33516.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyb_33516/03_2024/7xyb_33516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyb_33516/03_2024/7xyb_33516.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyb_33516/03_2024/7xyb_33516.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyb_33516/03_2024/7xyb_33516.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyb_33516/03_2024/7xyb_33516.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 65 5.49 5 Mg 1 5.21 5 S 66 5.16 5 C 13839 2.51 5 N 4180 2.21 5 O 4374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 15": "OD1" <-> "OD2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A GLU 122": "OE1" <-> "OE2" Residue "A TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B ASP 77": "OD1" <-> "OD2" Residue "B TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 211": "OD1" <-> "OD2" Residue "C ASP 33": "OD1" <-> "OD2" Residue "C GLU 37": "OE1" <-> "OE2" Residue "C PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 601": "OD1" <-> "OD2" Residue "C GLU 646": "OE1" <-> "OE2" Residue "C PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 680": "OD1" <-> "OD2" Residue "C PHE 809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1181": "OD1" <-> "OD2" Residue "C PHE 1202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1237": "OE1" <-> "OE2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 284": "OD1" <-> "OD2" Residue "D ASP 304": "OD1" <-> "OD2" Residue "D TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 505": "OD1" <-> "OD2" Residue "D TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 677": "OE1" <-> "OE2" Residue "D TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 913": "OE1" <-> "OE2" Residue "D GLU 1254": "OE1" <-> "OE2" Residue "D TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1327": "OE1" <-> "OE2" Residue "D GLU 1334": "OE1" <-> "OE2" Residue "E GLU 53": "OE1" <-> "OE2" Residue "E ASP 60": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22525 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1583 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1506 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain breaks: 3 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASP:plan': 4, 'ARG:plan': 5, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 92 Chain: "C" Number of atoms: 7672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1190, 7672 Classifications: {'peptide': 1190} Incomplete info: {'truncation_to_alanine': 445} Link IDs: {'PTRANS': 49, 'TRANS': 1140} Chain breaks: 3 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1682 Unresolved non-hydrogen angles: 2143 Unresolved non-hydrogen dihedrals: 1339 Unresolved non-hydrogen chiralities: 161 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 7, 'TYR:plan': 14, 'ASN:plan1': 21, 'TRP:plan': 2, 'ASP:plan': 47, 'PHE:plan': 18, 'GLU:plan': 63, 'ARG:plan': 38} Unresolved non-hydrogen planarities: 970 Chain: "D" Number of atoms: 9118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1338, 9118 Classifications: {'peptide': 1338} Incomplete info: {'truncation_to_alanine': 293} Link IDs: {'PTRANS': 60, 'TRANS': 1277} Chain breaks: 2 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1315 Unresolved non-hydrogen angles: 1673 Unresolved non-hydrogen dihedrals: 1055 Unresolved non-hydrogen chiralities: 108 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 8, 'TYR:plan': 7, 'ASN:plan1': 15, 'TRP:plan': 3, 'ASP:plan': 45, 'PHE:plan': 15, 'GLU:plan': 58, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 767 Chain: "E" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 460 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 64} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 45 Chain: "G" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 833 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 557 Unresolved non-hydrogen angles: 707 Unresolved non-hydrogen dihedrals: 475 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 3, 'TYR:plan': 1, 'TRP:plan': 5, 'ASP:plan': 5, 'PHE:plan': 7, 'GLU:plan': 14, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 335 Chain: "R" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 310 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 10} Chain: "N" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 500 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain breaks: 1 Chain: "T" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 542 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.72, per 1000 atoms: 0.56 Number of scatterers: 22525 At special positions: 0 Unit cell: (142.29, 127.41, 147.87, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 66 16.00 P 65 15.00 Mg 1 11.99 O 4374 8.00 N 4180 7.00 C 13839 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 888 " - pdb=" SG CYS D 895 " distance=2.24 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 10.36 Conformation dependent library (CDL) restraints added in 4.3 seconds 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5886 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 47 sheets defined 41.0% alpha, 14.5% beta 25 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 8.64 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 4.426A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.517A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 211 through 229 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.924A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.701A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 153 through 157 Processing helix chain 'B' and resid 211 through 228 removed outlier: 3.782A pdb=" N LEU B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.941A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 60 Processing helix chain 'C' and resid 85 through 93 Processing helix chain 'C' and resid 166 through 170 removed outlier: 3.860A pdb=" N HIS C 169 " --> pdb=" O GLY C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'C' and resid 222 through 229 Processing helix chain 'C' and resid 350 through 357 Processing helix chain 'C' and resid 363 through 376 Processing helix chain 'C' and resid 382 through 396 removed outlier: 3.960A pdb=" N SER C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 415 Processing helix chain 'C' and resid 428 through 442 Processing helix chain 'C' and resid 460 through 484 removed outlier: 3.584A pdb=" N MET C 464 " --> pdb=" O CYS C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 498 removed outlier: 3.537A pdb=" N ILE C 498 " --> pdb=" O PRO C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 514 Processing helix chain 'C' and resid 524 through 533 removed outlier: 3.549A pdb=" N GLU C 528 " --> pdb=" O ASN C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 548 removed outlier: 3.945A pdb=" N ALA C 548 " --> pdb=" O ARG C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 560 Processing helix chain 'C' and resid 614 through 617 removed outlier: 3.565A pdb=" N ALA C 617 " --> pdb=" O ILE C 614 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 614 through 617' Processing helix chain 'C' and resid 661 through 665 removed outlier: 3.644A pdb=" N VAL C 665 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 672 Processing helix chain 'C' and resid 675 through 679 Processing helix chain 'C' and resid 680 through 692 Processing helix chain 'C' and resid 708 through 717 removed outlier: 4.504A pdb=" N ASN C 712 " --> pdb=" O GLY C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 831 Processing helix chain 'C' and resid 863 through 870 removed outlier: 3.525A pdb=" N LEU C 867 " --> pdb=" O GLY C 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 947 through 984 Processing helix chain 'C' and resid 1021 through 1055 removed outlier: 3.646A pdb=" N GLN C1055 " --> pdb=" O ARG C1051 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1123 removed outlier: 4.370A pdb=" N SER C1122 " --> pdb=" O LEU C1118 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG C1123 " --> pdb=" O GLY C1119 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1118 through 1123' Processing helix chain 'C' and resid 1126 through 1151 Processing helix chain 'C' and resid 1154 through 1167 removed outlier: 3.529A pdb=" N LEU C1158 " --> pdb=" O LYS C1154 " (cutoff:3.500A) Processing helix chain 'C' and resid 1179 through 1192 removed outlier: 3.883A pdb=" N LEU C1185 " --> pdb=" O ASP C1181 " (cutoff:3.500A) Processing helix chain 'C' and resid 1206 through 1217 Processing helix chain 'C' and resid 1253 through 1257 removed outlier: 3.502A pdb=" N ASP C1256 " --> pdb=" O LEU C1253 " (cutoff:3.500A) Processing helix chain 'C' and resid 1286 through 1296 Processing helix chain 'C' and resid 1299 through 1308 Processing helix chain 'C' and resid 1312 through 1325 removed outlier: 3.952A pdb=" N THR C1317 " --> pdb=" O VAL C1313 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LYS C1318 " --> pdb=" O ASN C1314 " (cutoff:3.500A) Processing helix chain 'C' and resid 1335 through 1348 removed outlier: 3.581A pdb=" N ASN C1339 " --> pdb=" O PRO C1335 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.895A pdb=" N ILE D 135 " --> pdb=" O THR D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 181 through 190 Processing helix chain 'D' and resid 193 through 208 Proline residue: D 206 - end of helix Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 238 removed outlier: 3.710A pdb=" N VAL D 238 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 284 removed outlier: 3.525A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 333 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 418 removed outlier: 3.900A pdb=" N TRP D 409 " --> pdb=" O LEU D 405 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP D 410 " --> pdb=" O PRO D 406 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D 411 " --> pdb=" O GLU D 407 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 484 Processing helix chain 'D' and resid 503 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.730A pdb=" N GLN D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 593 Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 635 Processing helix chain 'D' and resid 648 through 670 removed outlier: 4.295A pdb=" N ARG D 652 " --> pdb=" O ASP D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 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: 3.865A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 914 through 925 Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1051 through 1055 removed outlier: 3.653A pdb=" N THR D1054 " --> pdb=" O ASP D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.837A pdb=" N ILE D1220 " --> pdb=" O ASN D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1226 through 1244 removed outlier: 3.560A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.308A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1292 removed outlier: 3.506A pdb=" N LEU D1292 " --> pdb=" O GLU D1288 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1324 removed outlier: 3.991A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.517A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1375 Processing helix chain 'E' and resid 7 through 14 Processing helix chain 'E' and resid 17 through 32 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 68 Processing helix chain 'G' and resid 5 through 18 Processing helix chain 'G' and resid 27 through 38 removed outlier: 3.549A pdb=" N PHE G 37 " --> pdb=" O LEU G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 69 Processing helix chain 'G' and resid 72 through 83 Processing helix chain 'G' and resid 86 through 101 Processing helix chain 'G' and resid 105 through 120 Processing helix chain 'G' and resid 126 through 135 Processing helix chain 'G' and resid 137 through 171 removed outlier: 4.287A pdb=" N GLU G 165 " --> pdb=" O LEU G 161 " (cutoff:3.500A) Proline residue: G 166 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 18 Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 105 removed outlier: 6.429A pdb=" N ALA A 146 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N VAL A 56 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY A 148 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N CYS A 54 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 170 " --> pdb=" O ALA A 59 " (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 110 removed outlier: 3.567A pdb=" N ALA A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 152 Processing sheet with id=AA6, first strand: chain 'B' and resid 15 through 16 removed outlier: 3.665A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 61 removed outlier: 6.808A pdb=" N LYS B 144 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA B 59 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS B 142 " --> pdb=" O ALA B 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.568A pdb=" N ALA B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 151 through 152 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 5.978A pdb=" N LYS C 13 " --> pdb=" O ALA C1198 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 70 through 79 removed outlier: 5.312A pdb=" N LEU C 72 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE C 107 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N TYR C 74 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG C 105 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLY C 76 " --> pdb=" O LYS C 103 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS C 103 " --> pdb=" O GLY C 76 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS C 119 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 70 through 79 removed outlier: 5.312A pdb=" N LEU C 72 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE C 107 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N TYR C 74 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG C 105 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLY C 76 " --> pdb=" O LYS C 103 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS C 103 " --> pdb=" O GLY C 76 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 140 through 142 Processing sheet with id=AB6, first strand: chain 'C' and resid 456 through 458 Processing sheet with id=AB7, first strand: chain 'C' and resid 158 through 161 removed outlier: 3.557A pdb=" N LEU C 188 " --> pdb=" O ILE C 180 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 585 through 586 Processing sheet with id=AB9, first strand: chain 'C' and resid 585 through 586 Processing sheet with id=AC1, first strand: chain 'C' and resid 721 through 722 Processing sheet with id=AC2, first strand: chain 'C' and resid 755 through 757 removed outlier: 6.941A pdb=" N ARG C 736 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL C 732 " --> pdb=" O ARG C 736 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL C 738 " --> pdb=" O ASP C 730 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 762 through 763 Processing sheet with id=AC4, first strand: chain 'C' and resid 794 through 795 Processing sheet with id=AC5, first strand: chain 'C' and resid 1083 through 1084 removed outlier: 4.699A pdb=" N THR C1241 " --> pdb=" O PHE C 809 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS C 822 " --> pdb=" O VAL C1114 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE C 821 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE C1096 " --> pdb=" O ILE C 821 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU C 823 " --> pdb=" O ILE C1096 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1083 through 1084 Processing sheet with id=AC7, first strand: chain 'C' and resid 835 through 844 removed outlier: 4.074A pdb=" N ASP C 935 " --> pdb=" O TYR C1070 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA C1072 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL C 933 " --> pdb=" O ALA C1072 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N LYS C1074 " --> pdb=" O GLY C 931 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N GLY C 931 " --> pdb=" O LYS C1074 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 854 through 855 removed outlier: 3.919A pdb=" N GLU C 854 " --> pdb=" O VAL C 892 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 887 through 889 removed outlier: 6.235A pdb=" N LEU C 923 " --> pdb=" O LEU C 888 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1259 through 1261 removed outlier: 3.553A pdb=" N HIS C1259 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1259 through 1261 removed outlier: 3.553A pdb=" N HIS C1259 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1350 through 1351 Processing sheet with id=AD4, first strand: chain 'D' and resid 20 through 21 Processing sheet with id=AD5, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.020A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU D 242 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 44 through 45 removed outlier: 3.794A pdb=" N LYS D 50 " --> pdb=" O ASN D 45 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 145 through 147 Processing sheet with id=AD8, first strand: chain 'D' and resid 253 through 255 Processing sheet with id=AD9, first strand: chain 'D' and resid 316 through 317 removed outlier: 4.056A pdb=" N THR D 317 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ARG D 322 " --> pdb=" O THR D 317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 526 through 527 removed outlier: 6.842A pdb=" N PHE D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N ASN D 553 " --> pdb=" O PHE D 527 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLY D 558 " --> pdb=" O GLN D 562 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N GLN D 562 " --> pdb=" O GLY D 558 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 706 through 708 Processing sheet with id=AE3, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE4, first strand: chain 'D' and resid 991 through 996 removed outlier: 3.876A pdb=" N GLU D 993 " --> pdb=" O VAL D 984 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1025 through 1026 Processing sheet with id=AE6, first strand: chain 'D' and resid 1033 through 1034 removed outlier: 3.578A pdb=" N GLY D1033 " --> pdb=" O VAL D1115 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1036 through 1038 Processing sheet with id=AE8, first strand: chain 'D' and resid 1046 through 1047 removed outlier: 3.712A pdb=" N ILE D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL D1107 " --> pdb=" O ILE D1059 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1155 through 1156 Processing sheet with id=AF1, first strand: chain 'D' and resid 1172 through 1174 Processing sheet with id=AF2, first strand: chain 'D' and resid 1277 through 1279 removed outlier: 7.027A pdb=" N LYS D1301 " --> pdb=" O SER D1267 " (cutoff:3.500A) 1103 hydrogen bonds defined for protein. 3078 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 124 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 12.97 Time building geometry restraints manager: 11.02 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: 5054 1.33 - 1.45: 4674 1.45 - 1.57: 12960 1.57 - 1.69: 126 1.69 - 1.82: 115 Bond restraints: 22929 Sorted by residual: bond pdb=" N GLU D 52 " pdb=" CA GLU D 52 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.17e-02 7.31e+03 8.44e+00 bond pdb=" N LEU G 45 " pdb=" CA LEU G 45 " ideal model delta sigma weight residual 1.453 1.488 -0.034 1.30e-02 5.92e+03 7.00e+00 bond pdb=" N ILE G 42 " pdb=" CA ILE G 42 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 6.90e+00 bond pdb=" O3' DG N 119 " pdb=" P DG N 120 " ideal model delta sigma weight residual 1.607 1.646 -0.039 1.50e-02 4.44e+03 6.68e+00 bond pdb=" N GLY C 851 " pdb=" CA GLY C 851 " ideal model delta sigma weight residual 1.443 1.477 -0.035 1.37e-02 5.33e+03 6.48e+00 ... (remaining 22924 not shown) Histogram of bond angle deviations from ideal: 98.02 - 105.21: 622 105.21 - 112.40: 12355 112.40 - 119.59: 7091 119.59 - 126.78: 11118 126.78 - 133.97: 338 Bond angle restraints: 31524 Sorted by residual: angle pdb=" C THR D 43 " pdb=" CA THR D 43 " pdb=" CB THR D 43 " ideal model delta sigma weight residual 116.53 101.83 14.70 1.47e+00 4.63e-01 1.00e+02 angle pdb=" N LYS C1277 " pdb=" CA LYS C1277 " pdb=" C LYS C1277 " ideal model delta sigma weight residual 111.28 103.79 7.49 1.09e+00 8.42e-01 4.72e+01 angle pdb=" O3' U R 61 " pdb=" C3' U R 61 " pdb=" C2' U R 61 " ideal model delta sigma weight residual 109.50 119.16 -9.66 1.50e+00 4.44e-01 4.14e+01 angle pdb=" N GLU G 35 " pdb=" CA GLU G 35 " pdb=" C GLU G 35 " ideal model delta sigma weight residual 113.41 105.70 7.71 1.22e+00 6.72e-01 3.99e+01 angle pdb=" N ARG G 34 " pdb=" CA ARG G 34 " pdb=" C ARG G 34 " ideal model delta sigma weight residual 113.20 106.07 7.13 1.21e+00 6.83e-01 3.48e+01 ... (remaining 31519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 12169 17.89 - 35.78: 1070 35.78 - 53.67: 357 53.67 - 71.56: 118 71.56 - 89.45: 13 Dihedral angle restraints: 13727 sinusoidal: 4624 harmonic: 9103 Sorted by residual: dihedral pdb=" CB CYS D 888 " pdb=" SG CYS D 888 " pdb=" SG CYS D 895 " pdb=" CB CYS D 895 " ideal model delta sinusoidal sigma weight residual -86.00 -171.12 85.12 1 1.00e+01 1.00e-02 8.78e+01 dihedral pdb=" CA ALA G 27 " pdb=" C ALA G 27 " pdb=" N MET G 28 " pdb=" CA MET G 28 " ideal model delta harmonic sigma weight residual 180.00 155.36 24.64 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" C THR D 43 " pdb=" N THR D 43 " pdb=" CA THR D 43 " pdb=" CB THR D 43 " ideal model delta harmonic sigma weight residual -122.00 -111.17 -10.83 0 2.50e+00 1.60e-01 1.87e+01 ... (remaining 13724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3268 0.061 - 0.122: 522 0.122 - 0.183: 42 0.183 - 0.245: 6 0.245 - 0.306: 4 Chirality restraints: 3842 Sorted by residual: chirality pdb=" CA THR D 43 " pdb=" N THR D 43 " pdb=" C THR D 43 " pdb=" CB THR D 43 " both_signs ideal model delta sigma weight residual False 2.53 2.83 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA LYS C1277 " pdb=" N LYS C1277 " pdb=" C LYS C1277 " pdb=" CB LYS C1277 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA ILE D 44 " pdb=" N ILE D 44 " pdb=" C ILE D 44 " pdb=" CB ILE D 44 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 3839 not shown) Planarity restraints: 3969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 42 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.11e+00 pdb=" C GLU D 42 " 0.049 2.00e-02 2.50e+03 pdb=" O GLU D 42 " -0.019 2.00e-02 2.50e+03 pdb=" N THR D 43 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 846 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.97e+00 pdb=" C ARG C 846 " -0.049 2.00e-02 2.50e+03 pdb=" O ARG C 846 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP C 847 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 48 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.84e+00 pdb=" C THR D 48 " 0.048 2.00e-02 2.50e+03 pdb=" O THR D 48 " -0.018 2.00e-02 2.50e+03 pdb=" N PHE D 49 " -0.017 2.00e-02 2.50e+03 ... (remaining 3966 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 248 2.55 - 3.13: 18935 3.13 - 3.72: 38051 3.72 - 4.31: 47327 4.31 - 4.90: 76985 Nonbonded interactions: 181546 Sorted by model distance: nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1601 " model vdw 1.956 2.170 nonbonded pdb=" O3' A R 70 " pdb="MG MG D1601 " model vdw 1.986 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1601 " model vdw 1.994 2.170 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1601 " model vdw 2.083 2.170 nonbonded pdb=" N GLN C 839 " pdb=" OE1 GLN C 839 " model vdw 2.192 2.520 ... (remaining 181541 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 15 or (resid 16 and (name N or name \ CA or name C or name O or name CB )) or resid 17 through 57 or (resid 58 throug \ h 62 and (name N or name CA or name C or name O or name CB )) or resid 63 or (re \ sid 64 through 66 and (name N or name CA or name C or name O or name CB )) or re \ sid 67 through 74 or (resid 75 and (name N or name CA or name C or name O or nam \ e CB )) or resid 76 through 79 or (resid 80 and (name N or name CA or name C or \ name O or name CB )) or resid 81 through 89 or (resid 90 and (name N or name CA \ or name C or name O or name CB or name CG1 or name CG2)) or resid 91 through 92 \ or (resid 93 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 4 or (resid 95 and (name N or name CA or name C or name O or name CB or name CG \ )) or resid 96 through 104 or (resid 105 and (name N or name CA or name C or nam \ e O or name CB )) or resid 109 through 113 or (resid 114 and (name N or name CA \ or name C or name O or name CB )) or resid 115 through 118 or (resid 119 and (na \ me N or name CA or name C or name O or name CB )) or resid 120 through 134 or re \ sid 139 through 141 or (resid 142 and (name N or name CA or name C or name O or \ name CB )) or resid 143 through 157 or (resid 169 and (name N or name CA or name \ C or name O or name CB )) or resid 170 through 182 or (resid 183 and (name N or \ name CA or name C or name O or name CB )) or resid 184 through 217 or (resid 21 \ 8 through 220 and (name N or name CA or name C or name O or name CB )) or resid \ 221 through 230)) selection = (chain 'B' and (resid 8 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2)) or resid 15 through 25 or (resid \ 26 and (name N or name CA or name C or name O or name CB or name CG1 or name CG \ 2)) or resid 27 through 31 or (resid 32 and (name N or name CA or name C or name \ O or name CB )) or resid 33 through 71 or (resid 72 and (name N or name CA or n \ ame C or name O or name CB )) or resid 73 through 116 or (resid 117 and (name N \ or name CA or name C or name O or name CB )) or resid 118 through 126 or (resid \ 127 and (name N or name CA or name C or name O or name CB or name CG )) or resid \ 128 through 139 or (resid 140 and (name N or name CA or name C or name O or nam \ e CB or name CG )) or resid 141 through 151 or (resid 152 and (name N or name CA \ or name C or name O or name CB )) or resid 153 through 193 or (resid 194 throug \ h 196 and (name N or name CA or name C or name O or name CB )) or resid 197 thro \ ugh 212 or (resid 213 through 215 and (name N or name CA or name C or name O or \ name CB )) or resid 216 through 230)) } 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.200 Check model and map are aligned: 0.370 Set scattering table: 0.240 Process input model: 74.670 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.090 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 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 : 0.005 0.045 22929 Z= 0.306 Angle : 0.747 14.698 31524 Z= 0.444 Chirality : 0.045 0.306 3842 Planarity : 0.004 0.052 3969 Dihedral : 16.728 89.453 7838 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.85 % Favored : 94.96 % Rotamer: Outliers : 0.62 % Allowed : 23.17 % Favored : 76.22 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.15), residues: 3157 helix: 1.23 (0.16), residues: 1182 sheet: -1.23 (0.25), residues: 401 loop : -1.31 (0.16), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 812 HIS 0.014 0.002 HIS A 37 PHE 0.031 0.001 PHE A 35 TYR 0.017 0.001 TYR D1241 ARG 0.028 0.001 ARG D1149 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 2.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable