Starting phenix.real_space_refine on Fri Aug 9 09:51:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r9b_4769/08_2024/6r9b_4769.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r9b_4769/08_2024/6r9b_4769.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r9b_4769/08_2024/6r9b_4769.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r9b_4769/08_2024/6r9b_4769.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r9b_4769/08_2024/6r9b_4769.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r9b_4769/08_2024/6r9b_4769.cif" } resolution = 3.8 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= 0.005 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: 4 Type Number sf(0) Gaussians S 113 5.16 5 C 16142 2.51 5 N 4503 2.21 5 O 5122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B ARG 33": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "C ARG 10": "NH1" <-> "NH2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C ARG 97": "NH1" <-> "NH2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C ARG 151": "NH1" <-> "NH2" Residue "C ARG 175": "NH1" <-> "NH2" Residue "C ARG 197": "NH1" <-> "NH2" Residue "C ASP 199": "OD1" <-> "OD2" Residue "C ARG 201": "NH1" <-> "NH2" Residue "C ARG 233": "NH1" <-> "NH2" Residue "C ARG 247": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C ARG 275": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ARG 368": "NH1" <-> "NH2" Residue "C ARG 394": "NH1" <-> "NH2" Residue "C ARG 452": "NH1" <-> "NH2" Residue "C ARG 478": "NH1" <-> "NH2" Residue "C ARG 528": "NH1" <-> "NH2" Residue "C ARG 529": "NH1" <-> "NH2" Residue "C ARG 542": "NH1" <-> "NH2" Residue "C ARG 678": "NH1" <-> "NH2" Residue "C ARG 694": "NH1" <-> "NH2" Residue "C ARG 706": "NH1" <-> "NH2" Residue "C ARG 821": "NH1" <-> "NH2" Residue "C ARG 841": "NH1" <-> "NH2" Residue "C ARG 903": "NH1" <-> "NH2" Residue "C ARG 919": "NH1" <-> "NH2" Residue "C ARG 936": "NH1" <-> "NH2" Residue "C ARG 974": "NH1" <-> "NH2" Residue "C ARG 976": "NH1" <-> "NH2" Residue "C ARG 994": "NH1" <-> "NH2" Residue "C ARG 996": "NH1" <-> "NH2" Residue "C ARG 1059": "NH1" <-> "NH2" Residue "C ARG 1106": "NH1" <-> "NH2" Residue "C ARG 1211": "NH1" <-> "NH2" Residue "C ARG 1223": "NH1" <-> "NH2" Residue "D ARG 31": "NH1" <-> "NH2" Residue "D ARG 47": "NH1" <-> "NH2" Residue "D PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 156": "NH1" <-> "NH2" Residue "D ARG 202": "NH1" <-> "NH2" Residue "D ARG 214": "NH1" <-> "NH2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D ARG 259": "NH1" <-> "NH2" Residue "D ARG 281": "NH1" <-> "NH2" Residue "D ARG 293": "NH1" <-> "NH2" Residue "D ARG 311": "NH1" <-> "NH2" Residue "D ARG 352": "NH1" <-> "NH2" Residue "D ARG 362": "NH1" <-> "NH2" Residue "D ARG 417": "NH1" <-> "NH2" Residue "D ARG 515": "NH1" <-> "NH2" Residue "D ARG 535": "NH1" <-> "NH2" Residue "D ARG 678": "NH1" <-> "NH2" Residue "D ARG 709": "NH1" <-> "NH2" Residue "D ARG 731": "NH1" <-> "NH2" Residue "D ARG 738": "NH1" <-> "NH2" Residue "D ARG 780": "NH1" <-> "NH2" Residue "D ARG 838": "NH1" <-> "NH2" Residue "D ARG 883": "NH1" <-> "NH2" Residue "D ARG 1036": "NH1" <-> "NH2" Residue "D ARG 1075": "NH1" <-> "NH2" Residue "D ARG 1123": "NH1" <-> "NH2" Residue "D ARG 1140": "NH1" <-> "NH2" Residue "D ARG 1148": "NH1" <-> "NH2" Residue "D ARG 1149": "NH1" <-> "NH2" Residue "D ARG 1174": "NH1" <-> "NH2" Residue "D ARG 1203": "NH1" <-> "NH2" Residue "D ARG 1206": "NH1" <-> "NH2" Residue "D ARG 1222": "NH1" <-> "NH2" Residue "D ARG 1242": "NH1" <-> "NH2" Residue "D ARG 1258": "NH1" <-> "NH2" Residue "D ARG 1262": "NH1" <-> "NH2" Residue "D ARG 1284": "NH1" <-> "NH2" Residue "D ARG 1341": "NH1" <-> "NH2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "F TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 84": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25880 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1790 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 223} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1648 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 3, 'HIS:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 10260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10260 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved non-hydrogen bonds: 330 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 288 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 7, 'HIS:plan': 1, 'PHE:plan': 7, 'GLU:plan': 1, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 186 Chain: "D" Number of atoms: 9901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1323, 9901 Classifications: {'peptide': 1323} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 54, 'TRANS': 1268} Chain breaks: 6 Unresolved non-hydrogen bonds: 432 Unresolved non-hydrogen angles: 537 Unresolved non-hydrogen dihedrals: 371 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 5, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 7, 'GLU:plan': 5, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 266 Chain: "E" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 567 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 847 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 2, 'TRANS': 102} Time building chain proxies: 14.44, per 1000 atoms: 0.56 Number of scatterers: 25880 At special positions: 0 Unit cell: (135.04, 168.8, 173.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 113 16.00 O 5122 8.00 N 4503 7.00 C 16142 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 814 " - pdb=" SG CYS D 895 " distance=2.87 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: 10.33 Conformation dependent library (CDL) restraints added in 4.8 seconds 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6312 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 29 sheets defined 37.6% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.00 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.621A pdb=" N ARG A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.588A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.664A pdb=" N ASP A 114 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 115 " --> pdb=" O ALA A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 115' Processing helix chain 'A' and resid 154 through 160 Processing helix chain 'A' and resid 212 through 227 Processing helix chain 'B' and resid 35 through 48 removed outlier: 3.528A pdb=" N ARG B 45 " --> pdb=" O ASN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 88 Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.812A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 28 through 39 removed outlier: 4.187A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 57 Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.751A pdb=" N GLN C 86 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE C 87 " --> pdb=" O GLU C 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 83 through 87' Processing helix chain 'C' and resid 198 through 201 removed outlier: 3.875A pdb=" N ARG C 201 " --> pdb=" O ILE C 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 198 through 201' Processing helix chain 'C' and resid 206 through 211 Processing helix chain 'C' and resid 212 through 214 No H-bonds generated for 'chain 'C' and resid 212 through 214' Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.644A pdb=" N PHE C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 280 removed outlier: 4.175A pdb=" N LEU C 277 " --> pdb=" O HIS C 273 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 removed outlier: 4.466A pdb=" N ALA C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 289 through 294' Processing helix chain 'C' and resid 320 through 329 removed outlier: 3.735A pdb=" N LYS C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 379 through 390 removed outlier: 3.973A pdb=" N SER C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE C 390 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.698A pdb=" N ARG C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY C 482 " --> pdb=" O ARG C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 removed outlier: 3.608A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA C 501 " --> pdb=" O PRO C 497 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS C 503 " --> pdb=" O SER C 499 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU C 504 " --> pdb=" O ALA C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 526 removed outlier: 4.106A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE C 524 " --> pdb=" O PRO C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.583A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 685 removed outlier: 3.663A pdb=" N MET C 681 " --> pdb=" O ASN C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 711 Processing helix chain 'C' and resid 789 through 793 removed outlier: 3.673A pdb=" N GLY C 792 " --> pdb=" O THR C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 826 removed outlier: 4.128A pdb=" N VAL C 823 " --> pdb=" O SER C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 865 Processing helix chain 'C' and resid 896 through 898 No H-bonds generated for 'chain 'C' and resid 896 through 898' Processing helix chain 'C' and resid 899 through 906 Processing helix chain 'C' and resid 945 through 979 removed outlier: 3.671A pdb=" N GLU C 949 " --> pdb=" O ALA C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 994 through 1000 Processing helix chain 'C' and resid 1005 through 1039 Processing helix chain 'C' and resid 1102 through 1107 Processing helix chain 'C' and resid 1108 through 1134 removed outlier: 3.770A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1169 through 1176 Processing helix chain 'C' and resid 1192 through 1202 removed outlier: 4.514A pdb=" N LEU C1198 " --> pdb=" O GLU C1194 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1242 removed outlier: 3.652A pdb=" N ASP C1241 " --> pdb=" O LEU C1238 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.734A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1291 Processing helix chain 'C' and resid 1297 through 1311 Processing helix chain 'C' and resid 1322 through 1331 Processing helix chain 'D' and resid 26 through 33 removed outlier: 4.192A pdb=" N ILE D 30 " --> pdb=" O SER D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 122 through 128 removed outlier: 3.605A pdb=" N LEU D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU D 128 " --> pdb=" O ILE D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 137 Processing helix chain 'D' and resid 161 through 173 removed outlier: 3.647A pdb=" N GLY D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 190 removed outlier: 4.299A pdb=" N GLN D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 208 Processing helix chain 'D' and resid 210 through 215 Processing helix chain 'D' and resid 217 through 229 Processing helix chain 'D' and resid 233 through 238 removed outlier: 3.534A pdb=" N ILE D 238 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 285 Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.530A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA D 305 " --> pdb=" O GLU D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 402 Processing helix chain 'D' and resid 405 through 418 removed outlier: 3.500A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 505 through 513 Processing helix chain 'D' and resid 530 through 539 removed outlier: 4.335A pdb=" N ARG D 538 " --> pdb=" O GLU D 534 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 583 removed outlier: 3.547A pdb=" N ALA D 577 " --> pdb=" O THR D 573 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 removed outlier: 3.803A pdb=" N GLY D 613 " --> pdb=" O TYR D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 5.015A pdb=" N ALA D 633 " --> pdb=" O PHE D 629 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 removed outlier: 3.580A pdb=" N ILE D 653 " --> pdb=" O LYS D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 700 Processing helix chain 'D' and resid 720 through 729 removed outlier: 3.610A pdb=" N MET D 724 " --> pdb=" O ASN D 720 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY D 729 " --> pdb=" O MET D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.658A pdb=" N ALA D 741 " --> pdb=" O ILE D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 787 Processing helix chain 'D' and resid 788 through 803 removed outlier: 3.751A pdb=" N LEU D 796 " --> pdb=" O ASN D 792 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR D 797 " --> pdb=" O SER D 793 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG D 799 " --> pdb=" O TYR D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 840 removed outlier: 3.521A pdb=" N LEU D 840 " --> pdb=" O ARG D 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.618A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 892 removed outlier: 3.527A pdb=" N ASP D 891 " --> pdb=" O CYS D 888 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE D 892 " --> pdb=" O ASP D 889 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 888 through 892' Processing helix chain 'D' and resid 914 through 922 removed outlier: 3.683A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN D 921 " --> pdb=" O VAL D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 931 through 936 removed outlier: 3.530A pdb=" N PHE D 935 " --> pdb=" O THR D 931 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS D 936 " --> pdb=" O MET D 932 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 931 through 936' Processing helix chain 'D' and resid 1063 through 1068 Processing helix chain 'D' and resid 1134 through 1138 removed outlier: 3.770A pdb=" N LEU D1138 " --> pdb=" O ILE D1134 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1134 through 1138' Processing helix chain 'D' and resid 1141 through 1146 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1245 removed outlier: 3.902A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1260 removed outlier: 3.611A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1286 removed outlier: 3.862A pdb=" N LYS D1286 " --> pdb=" O TYR D1282 " (cutoff:3.500A) Processing helix chain 'D' and resid 1286 through 1294 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.566A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU D1334 " --> pdb=" O ARG D1330 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1353 Processing helix chain 'D' and resid 1362 through 1371 Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 33 removed outlier: 4.083A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 60 through 75 removed outlier: 3.720A pdb=" N GLN E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 26 Processing helix chain 'F' and resid 29 through 43 removed outlier: 4.055A pdb=" N ASP F 35 " --> pdb=" O ASP F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 58 Processing helix chain 'F' and resid 76 through 96 removed outlier: 3.767A pdb=" N ILE F 80 " --> pdb=" O ASP F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 108 removed outlier: 4.073A pdb=" N ASN F 102 " --> pdb=" O GLU F 98 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL F 108 " --> pdb=" O TYR F 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 26 removed outlier: 4.037A pdb=" N VAL G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 43 removed outlier: 3.855A pdb=" N ILE G 37 " --> pdb=" O LEU G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 58 removed outlier: 3.763A pdb=" N PHE G 53 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER G 58 " --> pdb=" O SER G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 71 removed outlier: 3.927A pdb=" N LEU G 70 " --> pdb=" O ASP G 67 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET G 71 " --> pdb=" O SER G 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 67 through 71' Processing helix chain 'G' and resid 76 through 108 removed outlier: 3.751A pdb=" N ILE G 80 " --> pdb=" O ASP G 76 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLU G 98 " --> pdb=" O TRP G 94 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ASP G 99 " --> pdb=" O GLU G 95 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL G 108 " --> pdb=" O TYR G 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 3.526A pdb=" N VAL A 14 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 202 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN A 186 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 184 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 100 removed outlier: 4.062A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.940A pdb=" N ARG A 91 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 122 " --> pdb=" O ARG A 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 25 through 28 removed outlier: 3.723A pdb=" N VAL B 26 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 61 removed outlier: 3.602A pdb=" N VAL B 98 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 66 through 70 Processing sheet with id=AA7, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.050A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 154 through 156 removed outlier: 3.723A pdb=" N GLY C 154 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 177 " --> pdb=" O GLY C 154 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU C 187 " --> pdb=" O PHE C 195 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE C 195 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU C 204 " --> pdb=" O VAL C 196 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 228 through 231 Processing sheet with id=AB1, first strand: chain 'C' and resid 256 through 257 removed outlier: 3.551A pdb=" N LYS C 260 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.844A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 604 through 605 removed outlier: 3.839A pdb=" N HIS C 604 " --> pdb=" O TYR C 591 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 616 through 617 removed outlier: 3.795A pdb=" N ILE C 616 " --> pdb=" O ARG C 637 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 724 through 728 removed outlier: 6.787A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AB7, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AB8, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 3.904A pdb=" N ALA C1067 " --> pdb=" O LEU C1233 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER C1077 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C1097 " --> pdb=" O LEU C 817 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET C 800 " --> pdb=" O MET C1230 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET C1230 " --> pdb=" O MET C 800 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE C 804 " --> pdb=" O THR C1226 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 831 through 835 removed outlier: 7.750A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE C 929 " --> pdb=" O TYR C1053 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 838 through 839 Processing sheet with id=AC2, first strand: chain 'C' and resid 882 through 884 Processing sheet with id=AC3, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 4.068A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG D 352 " --> pdb=" O HIS C1244 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG C1246 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 103 through 106 removed outlier: 3.529A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE D 105 " --> pdb=" O LEU D 242 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 368 through 369 removed outlier: 6.518A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 548 through 552 removed outlier: 3.983A pdb=" N VAL D 548 " --> pdb=" O THR D 572 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 843 through 844 removed outlier: 4.381A pdb=" N VAL D 843 " --> pdb=" O ARG D 883 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 950 through 951 removed outlier: 7.074A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 956 through 957 removed outlier: 3.703A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL D1011 " --> pdb=" O GLY D 956 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 965 through 967 removed outlier: 4.238A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D1003 " --> pdb=" O LEU D 973 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 1264 through 1265 867 hydrogen bonds defined for protein. 2517 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.45 Time building geometry restraints manager: 11.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7923 1.34 - 1.46: 3827 1.46 - 1.58: 14294 1.58 - 1.70: 0 1.70 - 1.82: 198 Bond restraints: 26242 Sorted by residual: bond pdb=" C GLU A 29 " pdb=" N PRO A 30 " ideal model delta sigma weight residual 1.335 1.377 -0.042 8.70e-03 1.32e+04 2.30e+01 bond pdb=" C LYS D 749 " pdb=" N PRO D 750 " ideal model delta sigma weight residual 1.336 1.389 -0.053 1.20e-02 6.94e+03 1.95e+01 bond pdb=" C ARG D 250 " pdb=" N PRO D 251 " ideal model delta sigma weight residual 1.332 1.355 -0.023 1.12e-02 7.97e+03 4.37e+00 bond pdb=" CA CYS D 895 " pdb=" CB CYS D 895 " ideal model delta sigma weight residual 1.530 1.497 0.033 1.69e-02 3.50e+03 3.88e+00 bond pdb=" CA CYS D 895 " pdb=" C CYS D 895 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.34e-02 5.57e+03 3.78e+00 ... (remaining 26237 not shown) Histogram of bond angle deviations from ideal: 96.64 - 104.61: 437 104.61 - 112.57: 13347 112.57 - 120.54: 11794 120.54 - 128.50: 9847 128.50 - 136.47: 116 Bond angle restraints: 35541 Sorted by residual: angle pdb=" C GLY C1318 " pdb=" N MET C1319 " pdb=" CA MET C1319 " ideal model delta sigma weight residual 120.67 136.47 -15.80 1.34e+00 5.57e-01 1.39e+02 angle pdb=" N SER D 143 " pdb=" CA SER D 143 " pdb=" C SER D 143 " ideal model delta sigma weight residual 111.17 121.16 -9.99 1.41e+00 5.03e-01 5.02e+01 angle pdb=" N ILE D 500 " pdb=" CA ILE D 500 " pdb=" C ILE D 500 " ideal model delta sigma weight residual 106.72 117.23 -10.51 1.59e+00 3.96e-01 4.37e+01 angle pdb=" C GLY C1102 " pdb=" N VAL C1103 " pdb=" CA VAL C1103 " ideal model delta sigma weight residual 120.24 124.26 -4.02 6.30e-01 2.52e+00 4.07e+01 angle pdb=" N TYR D 144 " pdb=" CA TYR D 144 " pdb=" C TYR D 144 " ideal model delta sigma weight residual 110.80 124.35 -13.55 2.13e+00 2.20e-01 4.04e+01 ... (remaining 35536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.17: 15360 15.17 - 30.34: 576 30.34 - 45.52: 150 45.52 - 60.69: 25 60.69 - 75.86: 21 Dihedral angle restraints: 16132 sinusoidal: 6347 harmonic: 9785 Sorted by residual: dihedral pdb=" C VAL D 886 " pdb=" N VAL D 886 " pdb=" CA VAL D 886 " pdb=" CB VAL D 886 " ideal model delta harmonic sigma weight residual -122.00 -142.71 20.71 0 2.50e+00 1.60e-01 6.86e+01 dihedral pdb=" N VAL D 886 " pdb=" C VAL D 886 " pdb=" CA VAL D 886 " pdb=" CB VAL D 886 " ideal model delta harmonic sigma weight residual 123.40 143.29 -19.89 0 2.50e+00 1.60e-01 6.33e+01 dihedral pdb=" CB CYS D 814 " pdb=" SG CYS D 814 " pdb=" SG CYS D 895 " pdb=" CB CYS D 895 " ideal model delta sinusoidal sigma weight residual 93.00 26.32 66.68 1 1.00e+01 1.00e-02 5.80e+01 ... (remaining 16129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.169: 4078 0.169 - 0.337: 27 0.337 - 0.506: 4 0.506 - 0.674: 1 0.674 - 0.843: 1 Chirality restraints: 4111 Sorted by residual: chirality pdb=" CA VAL D 886 " pdb=" N VAL D 886 " pdb=" C VAL D 886 " pdb=" CB VAL D 886 " both_signs ideal model delta sigma weight residual False 2.44 1.60 0.84 2.00e-01 2.50e+01 1.77e+01 chirality pdb=" CA TYR D 144 " pdb=" N TYR D 144 " pdb=" C TYR D 144 " pdb=" CB TYR D 144 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.42e+00 chirality pdb=" CA VAL D 501 " pdb=" N VAL D 501 " pdb=" C VAL D 501 " pdb=" CB VAL D 501 " both_signs ideal model delta sigma weight residual False 2.44 2.88 -0.44 2.00e-01 2.50e+01 4.73e+00 ... (remaining 4108 not shown) Planarity restraints: 4712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 925 " 0.057 5.00e-02 4.00e+02 8.51e-02 1.16e+01 pdb=" N PRO D 926 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO D 926 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 926 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 923 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.55e+00 pdb=" C ILE D 923 " 0.044 2.00e-02 2.50e+03 pdb=" O ILE D 923 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY D 924 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D 426 " 0.042 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO D 427 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 427 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 427 " 0.036 5.00e-02 4.00e+02 ... (remaining 4709 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 7196 2.82 - 3.34: 22113 3.34 - 3.86: 39480 3.86 - 4.38: 43068 4.38 - 4.90: 75038 Nonbonded interactions: 186895 Sorted by model distance: nonbonded pdb=" OG SER C 815 " pdb=" O VAL C1075 " model vdw 2.296 3.040 nonbonded pdb=" O ARG D 425 " pdb=" OG1 THR D 428 " model vdw 2.303 3.040 nonbonded pdb=" OG SER D1032 " pdb=" O ILE D1115 " model vdw 2.310 3.040 nonbonded pdb=" OH TYR F 7 " pdb=" OD2 ASP F 92 " model vdw 2.310 3.040 nonbonded pdb=" OD1 ASP A 15 " pdb=" OG1 THR A 27 " model vdw 2.324 3.040 ... (remaining 186890 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 60 or (resid 61 through 62 and (nam \ e N or name CA or name C or name O or name CB )) or resid 63 through 70 or (resi \ d 71 and (name N or name CA or name C or name O or name CB )) or resid 72 throug \ h 77 or (resid 78 and (name N or name CA or name C or name O or name CB )) or re \ sid 79 through 116 or (resid 117 and (name N or name CA or name C or name O or n \ ame CB )) or resid 118 through 122 or (resid 123 and (name N or name CA or name \ C or name O or name CB )) or resid 124 or (resid 125 and (name N or name CA or n \ ame C or name O or name CB )) or resid 126 through 131 or (resid 132 and (name N \ or name CA or name C or name O or name CB )) or resid 133 through 141 or (resid \ 142 through 143 and (name N or name CA or name C or name O or name CB )) or res \ id 144 through 159 or resid 172 through 176 or (resid 177 and (name N or name CA \ or name C or name O or name CB )) or resid 178 through 234 or (resid 235 and (n \ ame N or name CA or name C or name O or name CB )) or resid 236 through 237)) selection = (chain 'B' and (resid 6 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 114 or (resid 115 and (name N or name \ CA or name C or name O or name CB )) or resid 116 through 236 or (resid 237 and \ (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = chain 'F' selection = (chain 'G' and (resid 5 through 33 or (resid 34 and (name N or name CA or name C \ or name O or name CB )) or resid 35 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 108)) } 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=0.00 max=1.00 mean=0.92 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: 0.760 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: 1.190 Check model and map are aligned: 0.180 Set scattering table: 0.250 Process input model: 67.400 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.100 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4967 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26242 Z= 0.223 Angle : 0.879 15.800 35541 Z= 0.502 Chirality : 0.057 0.843 4111 Planarity : 0.006 0.085 4712 Dihedral : 9.765 75.860 9817 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.03 % Favored : 91.76 % Rotamer: Outliers : 0.70 % Allowed : 2.57 % Favored : 96.73 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.03 % 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: -4.57 (0.11), residues: 3373 helix: -2.95 (0.10), residues: 1172 sheet: -1.61 (0.31), residues: 233 loop : -3.42 (0.11), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C1276 HIS 0.015 0.001 HIS C1023 PHE 0.022 0.002 PHE D 620 TYR 0.022 0.001 TYR C 215 ARG 0.006 0.000 ARG C 592 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 742 time to evaluate : 3.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 330 HIS cc_start: 0.5248 (m-70) cc_final: 0.5042 (m-70) REVERT: C 611 GLU cc_start: 0.5726 (pt0) cc_final: 0.5400 (pp20) REVERT: C 704 MET cc_start: 0.5480 (mmp) cc_final: 0.4783 (ppp) REVERT: C 735 LYS cc_start: 0.8768 (ttpp) cc_final: 0.8559 (tptm) REVERT: C 755 LYS cc_start: 0.7620 (mtpp) cc_final: 0.7143 (mtpp) REVERT: C 767 GLN cc_start: 0.7252 (mm110) cc_final: 0.6915 (mm-40) REVERT: C 782 VAL cc_start: 0.7528 (p) cc_final: 0.7325 (m) REVERT: D 29 MET cc_start: 0.7671 (ttp) cc_final: 0.7410 (tpp) REVERT: D 475 GLU cc_start: 0.7058 (pm20) cc_final: 0.6810 (mp0) REVERT: F 38 HIS cc_start: 0.6427 (m-70) cc_final: 0.6082 (m90) REVERT: G 5 MET cc_start: 0.3567 (mmp) cc_final: 0.3000 (mmt) outliers start: 19 outliers final: 4 residues processed: 754 average time/residue: 0.3815 time to fit residues: 428.3567 Evaluate side-chains 387 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 383 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 885 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 285 optimal weight: 40.0000 chunk 256 optimal weight: 10.0000 chunk 142 optimal weight: 0.1980 chunk 87 optimal weight: 9.9990 chunk 172 optimal weight: 0.8980 chunk 136 optimal weight: 5.9990 chunk 264 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 197 optimal weight: 6.9990 chunk 306 optimal weight: 5.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- 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: