Starting phenix.real_space_refine on Fri Aug 9 09:41:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkc_34849/08_2024/8hkc_34849.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkc_34849/08_2024/8hkc_34849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkc_34849/08_2024/8hkc_34849.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkc_34849/08_2024/8hkc_34849.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkc_34849/08_2024/8hkc_34849.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkc_34849/08_2024/8hkc_34849.cif" } resolution = 2.49 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 83 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 15906 2.51 5 N 4583 2.21 5 O 5098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "B TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 393": "OD1" <-> "OD2" Residue "C ASP 601": "OD1" <-> "OD2" Residue "C ASP 739": "OD1" <-> "OD2" Residue "C ASP 826": "OD1" <-> "OD2" Residue "C GLU 950": "OE1" <-> "OE2" Residue "C PHE 972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1167": "OE1" <-> "OE2" Residue "C ASP 1241": "OD1" <-> "OD2" Residue "F TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 556": "OE1" <-> "OE2" Residue "F TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1343": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25779 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1756 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 9, 'TRANS': 220} Chain: "C" Number of atoms: 9345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1188, 9345 Classifications: {'peptide': 1188} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1134} Chain breaks: 2 Chain: "F" Number of atoms: 9068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1160, 9068 Classifications: {'peptide': 1160} Link IDs: {'PCIS': 2, 'PTRANS': 45, 'TRANS': 1112} Chain breaks: 2 Chain: "G" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 858 Classifications: {'DNA': 42} Link IDs: {'rna3p': 41} Chain breaks: 1 Chain: "H" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 844 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain breaks: 1 Chain: "E" Number of atoms: 2119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2119 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 257} Chain breaks: 1 Chain: "F" 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 13345 SG CYS F 70 44.600 87.044 60.144 1.00 61.00 S ATOM 13359 SG CYS F 72 44.396 90.091 58.044 1.00 68.30 S ATOM 13467 SG CYS F 85 42.520 87.023 56.878 1.00 68.63 S ATOM 13491 SG CYS F 88 46.243 87.082 56.597 1.00 63.21 S ATOM 19179 SG CYS F 814 83.109 29.764 66.322 1.00 54.46 S ATOM 19744 SG CYS F 888 83.604 33.534 66.239 1.00 46.75 S ATOM 19795 SG CYS F 895 82.554 31.746 69.513 1.00 39.20 S ATOM 19816 SG CYS F 898 85.997 31.387 68.282 1.00 38.51 S Time building chain proxies: 14.11, per 1000 atoms: 0.55 Number of scatterers: 25779 At special positions: 0 Unit cell: (157.435, 147.223, 162.541, 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 106 16.00 P 83 15.00 Mg 1 11.99 O 5098 8.00 N 4583 7.00 C 15906 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 - 3.50 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: 11.63 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F1501 " pdb="ZN ZN F1501 " - pdb=" SG CYS F 72 " pdb="ZN ZN F1501 " - pdb=" SG CYS F 85 " pdb="ZN ZN F1501 " - pdb=" SG CYS F 88 " pdb="ZN ZN F1501 " - pdb=" SG CYS F 70 " pdb=" ZN F1502 " pdb="ZN ZN F1502 " - pdb=" SG CYS F 898 " pdb="ZN ZN F1502 " - pdb=" SG CYS F 895 " pdb="ZN ZN F1502 " - pdb=" SG CYS F 814 " pdb="ZN ZN F1502 " - pdb=" SG CYS F 888 " Number of angles added : 12 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5676 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 41 sheets defined 45.0% alpha, 16.7% beta 24 base pairs and 61 stacking pairs defined. Time for finding SS restraints: 8.87 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.697A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 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 161 removed outlier: 3.650A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 228 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.854A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.682A 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 154 through 159 Processing helix chain 'B' and resid 212 through 233 removed outlier: 4.415A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N PHE B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 9 removed outlier: 3.829A pdb=" N LYS C 9 " --> pdb=" O TYR C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.726A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.588A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 4.060A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 378 through 390 removed outlier: 3.994A pdb=" N GLU C 382 " --> pdb=" O ARG C 378 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 437 Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.761A pdb=" N ARG C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 495 through 509 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.951A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 Processing helix chain 'C' and resid 608 through 612 removed outlier: 3.814A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 608 through 612' Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 664 through 668 removed outlier: 3.723A pdb=" N ILE C 668 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 713 removed outlier: 4.051A pdb=" N GLY C 713 " --> pdb=" O ALA C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 741 Processing helix chain 'C' and resid 811 through 815 removed outlier: 3.749A pdb=" N ASP C 814 " --> pdb=" O ASN C 811 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 860 through 864 removed outlier: 3.994A pdb=" N LYS C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 942 through 973 removed outlier: 4.007A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 1027 through 1038 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.609A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.602A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.632A pdb=" N THR C1163 " --> pdb=" O ASP C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 3.722A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.787A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 34 Processing helix chain 'F' and resid 58 through 63 Processing helix chain 'F' and resid 94 through 100 removed outlier: 3.544A pdb=" N VAL F 97 " --> pdb=" O GLN F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 119 removed outlier: 3.597A pdb=" N SER F 119 " --> pdb=" O TRP F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 129 Processing helix chain 'F' and resid 131 through 140 Processing helix chain 'F' and resid 161 through 173 removed outlier: 3.538A pdb=" N GLU F 170 " --> pdb=" O LEU F 166 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU F 171 " --> pdb=" O ASP F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 192 removed outlier: 3.809A pdb=" N ILE F 185 " --> pdb=" O GLY F 181 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET F 192 " --> pdb=" O LEU F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 208 removed outlier: 3.685A pdb=" N GLU F 197 " --> pdb=" O ASP F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 231 Processing helix chain 'F' and resid 233 through 236 Processing helix chain 'F' and resid 246 through 250 Processing helix chain 'F' and resid 263 through 285 removed outlier: 4.066A pdb=" N ASP F 267 " --> pdb=" O SER F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 308 removed outlier: 3.541A pdb=" N VAL F 292 " --> pdb=" O PRO F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.625A pdb=" N MET F 330 " --> pdb=" O SER F 326 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE F 331 " --> pdb=" O LEU F 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 326 through 331' Processing helix chain 'F' and resid 336 through 342 Processing helix chain 'F' and resid 370 through 377 Processing helix chain 'F' and resid 377 through 388 Processing helix chain 'F' and resid 393 through 404 Processing helix chain 'F' and resid 405 through 416 removed outlier: 3.794A pdb=" N TRP F 409 " --> pdb=" O GLU F 405 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP F 410 " --> pdb=" O ALA F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 432 No H-bonds generated for 'chain 'F' and resid 430 through 432' Processing helix chain 'F' and resid 450 through 452 No H-bonds generated for 'chain 'F' and resid 450 through 452' Processing helix chain 'F' and resid 453 through 458 Processing helix chain 'F' and resid 473 through 484 Processing helix chain 'F' and resid 485 through 489 Processing helix chain 'F' and resid 504 through 514 Processing helix chain 'F' and resid 529 through 539 Processing helix chain 'F' and resid 574 through 580 Processing helix chain 'F' and resid 581 through 583 No H-bonds generated for 'chain 'F' and resid 581 through 583' Processing helix chain 'F' and resid 588 through 592 Processing helix chain 'F' and resid 597 through 612 Processing helix chain 'F' and resid 614 through 636 removed outlier: 3.613A pdb=" N GLY F 636 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 644 removed outlier: 3.766A pdb=" N MET F 644 " --> pdb=" O ILE F 641 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 670 removed outlier: 3.557A pdb=" N SER F 670 " --> pdb=" O GLU F 666 " (cutoff:3.500A) Processing helix chain 'F' and resid 674 through 702 Processing helix chain 'F' and resid 720 through 729 Processing helix chain 'F' and resid 733 through 742 removed outlier: 3.668A pdb=" N GLN F 739 " --> pdb=" O ALA F 735 " (cutoff:3.500A) Processing helix chain 'F' and resid 768 through 805 removed outlier: 4.178A pdb=" N HIS F 777 " --> pdb=" O PHE F 773 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY F 778 " --> pdb=" O ILE F 774 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA F 779 " --> pdb=" O SER F 775 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR F 790 " --> pdb=" O THR F 786 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ALA F 791 " --> pdb=" O ALA F 787 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASN F 792 " --> pdb=" O LEU F 788 " (cutoff:3.500A) Processing helix chain 'F' and resid 835 through 840 Processing helix chain 'F' and resid 865 through 875 removed outlier: 3.576A pdb=" N ASN F 875 " --> pdb=" O LEU F 871 " (cutoff:3.500A) Processing helix chain 'F' and resid 896 through 900 Processing helix chain 'F' and resid 914 through 925 removed outlier: 3.665A pdb=" N ILE F 918 " --> pdb=" O ALA F 914 " (cutoff:3.500A) Processing helix chain 'F' and resid 926 through 930 removed outlier: 3.763A pdb=" N LEU F 930 " --> pdb=" O GLY F 927 " (cutoff:3.500A) Processing helix chain 'F' and resid 1137 through 1146 Processing helix chain 'F' and resid 1216 through 1225 removed outlier: 3.560A pdb=" N ILE F1220 " --> pdb=" O ALA F1216 " (cutoff:3.500A) Processing helix chain 'F' and resid 1225 through 1244 removed outlier: 3.895A pdb=" N VAL F1229 " --> pdb=" O GLY F1225 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL F1240 " --> pdb=" O GLU F1236 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN F1244 " --> pdb=" O VAL F1240 " (cutoff:3.500A) Processing helix chain 'F' and resid 1249 through 1261 removed outlier: 4.406A pdb=" N ILE F1253 " --> pdb=" O ASN F1249 " (cutoff:3.500A) Processing helix chain 'F' and resid 1282 through 1293 Processing helix chain 'F' and resid 1294 through 1297 removed outlier: 4.111A pdb=" N LYS F1297 " --> pdb=" O ALA F1294 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1294 through 1297' Processing helix chain 'F' and resid 1308 through 1315 Processing helix chain 'F' and resid 1318 through 1326 removed outlier: 3.523A pdb=" N ALA F1322 " --> pdb=" O SER F1318 " (cutoff:3.500A) Processing helix chain 'F' and resid 1327 through 1339 Processing helix chain 'F' and resid 1346 through 1354 removed outlier: 3.584A pdb=" N ASN F1350 " --> pdb=" O GLY F1346 " (cutoff:3.500A) Processing helix chain 'F' and resid 1359 through 1361 No H-bonds generated for 'chain 'F' and resid 1359 through 1361' Processing helix chain 'F' and resid 1362 through 1376 Processing helix chain 'E' and resid 15 through 26 removed outlier: 3.503A pdb=" N ARG E 21 " --> pdb=" O ASP E 17 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA E 22 " --> pdb=" O SER E 18 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP E 26 " --> pdb=" O ALA E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 45 removed outlier: 3.937A pdb=" N ALA E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU E 37 " --> pdb=" O GLU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 Processing helix chain 'E' and resid 57 through 66 removed outlier: 3.719A pdb=" N VAL E 61 " --> pdb=" O HIS E 57 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL E 62 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS E 63 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE E 64 " --> pdb=" O PHE E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 72 removed outlier: 5.061A pdb=" N GLY E 70 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR E 71 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY E 72 " --> pdb=" O ALA E 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 67 through 72' Processing helix chain 'E' and resid 74 through 92 Processing helix chain 'E' and resid 94 through 98 removed outlier: 3.501A pdb=" N VAL E 97 " --> pdb=" O ASN E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 121 removed outlier: 4.804A pdb=" N HIS E 107 " --> pdb=" O SER E 103 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TRP E 108 " --> pdb=" O PHE E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 143 removed outlier: 3.504A pdb=" N LYS E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE E 137 " --> pdb=" O ARG E 133 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN E 138 " --> pdb=" O LYS E 134 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG E 140 " --> pdb=" O PHE E 136 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LYS E 141 " --> pdb=" O PHE E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 162 removed outlier: 3.620A pdb=" N VAL E 154 " --> pdb=" O ASN E 150 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU E 155 " --> pdb=" O GLN E 151 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET E 156 " --> pdb=" O ASP E 152 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU E 160 " --> pdb=" O MET E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 177 removed outlier: 3.698A pdb=" N ALA E 176 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 232 removed outlier: 3.697A pdb=" N GLY E 211 " --> pdb=" O ASN E 207 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY E 231 " --> pdb=" O ASP E 227 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 245 Processing helix chain 'E' and resid 252 through 261 removed outlier: 3.625A pdb=" N LEU E 256 " --> pdb=" O THR E 252 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG E 259 " --> pdb=" O GLU E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 284 removed outlier: 3.941A pdb=" N LYS E 272 " --> pdb=" O ARG E 268 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN E 273 " --> pdb=" O GLN E 269 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 20 removed outlier: 6.613A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N HIS A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N THR A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL A 192 " --> pdb=" O THR A 196 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 198 " --> pdb=" O ALA A 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.604A pdb=" N MET A 142 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE A 140 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN A 147 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A 55 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.629A pdb=" N ARG A 91 " --> pdb=" O GLU A 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.887A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 13 through 18 removed outlier: 6.800A pdb=" N THR B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE B 16 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LYS B 25 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLN B 18 " --> pdb=" O HIS B 23 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N HIS B 23 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 3.619A 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: 3.660A pdb=" N GLU B 58 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (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 108 through 111 Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.494A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.813A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU C 106 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL C 114 " --> pdb=" O GLU C 106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.636A pdb=" N SER C 147 " --> pdb=" O ARG C 529 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 160 removed outlier: 3.819A pdb=" N LEU C 171 " --> pdb=" O ASP C 160 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 227 through 229 Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 7.195A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 6.810A 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 716 through 717 removed outlier: 6.537A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.186A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC4, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC5, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.201A pdb=" N ILE C 816 " --> pdb=" O LYS C1078 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ASN C1080 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.809A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 849 through 850 removed outlier: 3.534A pdb=" N GLU C 849 " --> pdb=" O VAL C 887 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.814A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD1, first strand: chain 'C' and resid 1251 through 1252 removed outlier: 4.652A pdb=" N TYR C1251 " --> pdb=" O ASP E 203 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1268 through 1270 removed outlier: 3.788A pdb=" N GLN C1268 " --> pdb=" O VAL F 347 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1335 through 1340 removed outlier: 3.511A pdb=" N ALA F 19 " --> pdb=" O GLU C1340 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 103 through 112 removed outlier: 10.222A pdb=" N LEU F 107 " --> pdb=" O PRO F 243 " (cutoff:3.500A) removed outlier: 10.750A pdb=" N SER F 109 " --> pdb=" O VAL F 241 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL F 241 " --> pdb=" O SER F 109 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 159 through 160 removed outlier: 6.840A pdb=" N ASP F 177 " --> pdb=" O ILE F 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 252 through 254 Processing sheet with id=AD7, first strand: chain 'F' and resid 526 through 527 Processing sheet with id=AD8, first strand: chain 'F' and resid 703 through 707 Processing sheet with id=AD9, first strand: chain 'F' and resid 809 through 811 Processing sheet with id=AE1, first strand: chain 'F' and resid 820 through 822 Processing sheet with id=AE2, first strand: chain 'F' and resid 825 through 827 removed outlier: 6.962A pdb=" N VAL F 825 " --> pdb=" O LYS F 832 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 1155 through 1156 Processing sheet with id=AE4, first strand: chain 'F' and resid 1177 through 1178 Processing sheet with id=AE5, first strand: chain 'F' and resid 1279 through 1281 removed outlier: 6.693A pdb=" N THR F1301 " --> pdb=" O VAL F1267 " (cutoff:3.500A) 1088 hydrogen bonds defined for protein. 3075 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 58 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 61 stacking parallelities Total time for adding SS restraints: 11.93 Time building geometry restraints manager: 11.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8431 1.34 - 1.46: 3821 1.46 - 1.58: 13750 1.58 - 1.70: 162 1.70 - 1.82: 185 Bond restraints: 26349 Sorted by residual: bond pdb=" C CYS F 366 " pdb=" N GLY F 367 " ideal model delta sigma weight residual 1.332 1.339 -0.007 5.00e-03 4.00e+04 1.81e+00 bond pdb=" C3' DA H 36 " pdb=" O3' DA H 36 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.56e+00 bond pdb=" C3' DT G 7 " pdb=" O3' DT G 7 " ideal model delta sigma weight residual 1.422 1.453 -0.031 3.00e-02 1.11e+03 1.05e+00 bond pdb=" N ILE F1190 " pdb=" CA ILE F1190 " ideal model delta sigma weight residual 1.454 1.462 -0.008 7.70e-03 1.69e+04 1.00e+00 bond pdb=" C3' DG H 42 " pdb=" O3' DG H 42 " ideal model delta sigma weight residual 1.422 1.451 -0.029 3.00e-02 1.11e+03 9.34e-01 ... (remaining 26344 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.02: 948 106.02 - 113.01: 14316 113.01 - 120.00: 9077 120.00 - 127.00: 11193 127.00 - 133.99: 398 Bond angle restraints: 35932 Sorted by residual: angle pdb=" C GLN F 504 " pdb=" CA GLN F 504 " pdb=" CB GLN F 504 " ideal model delta sigma weight residual 110.42 115.82 -5.40 1.99e+00 2.53e-01 7.37e+00 angle pdb=" C VAL C1186 " pdb=" N PHE C1187 " pdb=" CA PHE C1187 " ideal model delta sigma weight residual 121.54 126.06 -4.52 1.91e+00 2.74e-01 5.61e+00 angle pdb=" CB MET F 698 " pdb=" CG MET F 698 " pdb=" SD MET F 698 " ideal model delta sigma weight residual 112.70 119.63 -6.93 3.00e+00 1.11e-01 5.34e+00 angle pdb=" CA ARG C1034 " pdb=" CB ARG C1034 " pdb=" CG ARG C1034 " ideal model delta sigma weight residual 114.10 118.66 -4.56 2.00e+00 2.50e-01 5.20e+00 angle pdb=" CA TYR F 679 " pdb=" CB TYR F 679 " pdb=" CG TYR F 679 " ideal model delta sigma weight residual 113.90 117.95 -4.05 1.80e+00 3.09e-01 5.07e+00 ... (remaining 35927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.20: 15316 35.20 - 70.40: 566 70.40 - 105.60: 37 105.60 - 140.80: 7 140.80 - 176.00: 2 Dihedral angle restraints: 15928 sinusoidal: 7111 harmonic: 8817 Sorted by residual: dihedral pdb=" C4' DA H 48 " pdb=" C3' DA H 48 " pdb=" O3' DA H 48 " pdb=" P DA H 49 " ideal model delta sinusoidal sigma weight residual -140.00 36.00 -176.00 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC G 28 " pdb=" C3' DC G 28 " pdb=" O3' DC G 28 " pdb=" P DA G 29 " ideal model delta sinusoidal sigma weight residual 220.00 76.31 143.69 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" C4' DA H 36 " pdb=" C3' DA H 36 " pdb=" O3' DA H 36 " pdb=" P DA H 37 " ideal model delta sinusoidal sigma weight residual 220.00 80.83 139.17 1 3.50e+01 8.16e-04 1.38e+01 ... (remaining 15925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 3129 0.041 - 0.082: 661 0.082 - 0.123: 271 0.123 - 0.163: 9 0.163 - 0.204: 1 Chirality restraints: 4071 Sorted by residual: chirality pdb=" CB THR C1184 " pdb=" CA THR C1184 " pdb=" OG1 THR C1184 " pdb=" CG2 THR C1184 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA VAL E 198 " pdb=" N VAL E 198 " pdb=" C VAL E 198 " pdb=" CB VAL E 198 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.89e-01 chirality pdb=" CA ILE A 16 " pdb=" N ILE A 16 " pdb=" C ILE A 16 " pdb=" CB ILE A 16 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 4068 not shown) Planarity restraints: 4413 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 742 " 0.031 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO C 743 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 743 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 743 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 488 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO C 489 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 489 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 489 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 551 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO C 552 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 552 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 552 " 0.021 5.00e-02 4.00e+02 ... (remaining 4410 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 390 2.68 - 3.23: 23180 3.23 - 3.79: 38682 3.79 - 4.34: 52938 4.34 - 4.90: 86709 Nonbonded interactions: 201899 Sorted by model distance: nonbonded pdb=" OD1 ASP F 460 " pdb="MG MG F1503 " model vdw 2.123 2.170 nonbonded pdb=" OD1 ASP F 462 " pdb="MG MG F1503 " model vdw 2.138 2.170 nonbonded pdb=" OE1 GLU C1222 " pdb=" OH TYR F 512 " model vdw 2.225 3.040 nonbonded pdb=" OG1 THR C 843 " pdb=" O GLY C 846 " model vdw 2.247 3.040 nonbonded pdb=" O GLY F 613 " pdb=" OG1 THR F 617 " model vdw 2.256 3.040 ... (remaining 201894 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' selection = (chain 'B' and (resid 6 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB )) or resid 31 through 233)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 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: 0.910 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 80.220 Find NCS groups from input model: 0.530 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:11.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 : 0.002 0.044 26349 Z= 0.122 Angle : 0.454 10.100 35932 Z= 0.245 Chirality : 0.039 0.204 4071 Planarity : 0.003 0.048 4413 Dihedral : 17.034 176.002 10252 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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: 0.81 (0.15), residues: 3045 helix: 1.68 (0.16), residues: 1169 sheet: 0.60 (0.27), residues: 379 loop : -0.36 (0.16), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 33 HIS 0.003 0.000 HIS F 651 PHE 0.009 0.001 PHE F1319 TYR 0.016 0.001 TYR F 679 ARG 0.004 0.000 ARG F 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 2.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLN cc_start: 0.7011 (tp-100) cc_final: 0.6717 (tp-100) REVERT: C 968 GLU cc_start: 0.5574 (pt0) cc_final: 0.5358 (pp20) REVERT: C 1140 LYS cc_start: 0.6940 (mtmt) cc_final: 0.6726 (mtmm) REVERT: F 466 MET cc_start: 0.8181 (mtp) cc_final: 0.7963 (ttm) REVERT: F 1373 ARG cc_start: 0.7122 (ttm170) cc_final: 0.6083 (ttp80) REVERT: E 68 TYR cc_start: 0.8114 (m-80) cc_final: 0.7831 (m-80) REVERT: E 238 ASP cc_start: 0.5990 (t0) cc_final: 0.5497 (t70) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 1.6473 time to fit residues: 528.5770 Evaluate side-chains 203 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 3.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 264 optimal weight: 3.9990 chunk 237 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 160 optimal weight: 0.8980 chunk 126 optimal weight: 10.0000 chunk 245 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 149 optimal weight: 7.9990 chunk 182 optimal weight: 5.9990 chunk 284 optimal weight: 10.0000 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 186 ASN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS C1136 GLN F 229 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 26349 Z= 0.311 Angle : 0.624 9.000 35932 Z= 0.341 Chirality : 0.046 0.181 4071 Planarity : 0.005 0.052 4413 Dihedral : 16.490 174.464 4248 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.38 % Allowed : 6.76 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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: 0.60 (0.15), residues: 3045 helix: 1.56 (0.15), residues: 1197 sheet: 0.34 (0.26), residues: 387 loop : -0.54 (0.15), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 217 HIS 0.010 0.001 HIS F 430 PHE 0.019 0.002 PHE C 812 TYR 0.019 0.002 TYR F 631 ARG 0.007 0.001 ARG F 337 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 216 time to evaluate : 2.872 Fit side-chains revert: symmetry clash REVERT: A 18 GLN cc_start: 0.7027 (tp-100) cc_final: 0.6735 (tp-100) REVERT: B 13 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8091 (tt) REVERT: B 93 GLN cc_start: 0.7202 (OUTLIER) cc_final: 0.6479 (pm20) REVERT: B 95 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7328 (ptmt) REVERT: C 496 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7330 (ttpt) REVERT: C 541 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6616 (mm-30) REVERT: C 542 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6939 (mtm-85) REVERT: C 968 GLU cc_start: 0.5742 (pt0) cc_final: 0.5456 (pp20) REVERT: C 1034 ARG cc_start: 0.7292 (tpp-160) cc_final: 0.7029 (mmm160) REVERT: F 204 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7079 (tp30) REVERT: F 1373 ARG cc_start: 0.7037 (ttm170) cc_final: 0.5944 (ttp80) REVERT: E 68 TYR cc_start: 0.8184 (m-80) cc_final: 0.7909 (m-80) REVERT: E 238 ASP cc_start: 0.5804 (t0) cc_final: 0.5349 (t70) outliers start: 36 outliers final: 11 residues processed: 233 average time/residue: 1.2229 time to fit residues: 326.7193 Evaluate side-chains 219 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 202 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain F residue 825 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 199 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 157 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 236 optimal weight: 10.0000 chunk 193 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 284 optimal weight: 10.0000 chunk 307 optimal weight: 20.0000 chunk 253 optimal weight: 0.9990 chunk 282 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 228 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: