Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 15:09:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlm_22248/04_2023/6xlm_22248_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlm_22248/04_2023/6xlm_22248.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlm_22248/04_2023/6xlm_22248.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlm_22248/04_2023/6xlm_22248.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlm_22248/04_2023/6xlm_22248_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlm_22248/04_2023/6xlm_22248_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.003 sd= 0.100 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 40 5.49 5 Mg 1 5.21 5 S 118 5.16 5 C 17594 2.51 5 N 4990 2.21 5 O 5499 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 91": "NH1" <-> "NH2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A GLU 204": "OE1" <-> "OE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A ASP 233": "OD1" <-> "OD2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B ASP 199": "OD1" <-> "OD2" Residue "C TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 175": "NH1" <-> "NH2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C ASP 185": "OD1" <-> "OD2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 200": "NH1" <-> "NH2" Residue "C ASP 222": "OD1" <-> "OD2" Residue "C PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 240": "OE1" <-> "OE2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "C ASP 254": "OD1" <-> "OD2" Residue "C TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ASP 280": "OD1" <-> "OD2" Residue "C ASP 281": "OD1" <-> "OD2" Residue "C GLU 304": "OE1" <-> "OE2" Residue "C GLU 308": "OE1" <-> "OE2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ASP 358": "OD1" <-> "OD2" Residue "C TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 392": "OE1" <-> "OE2" Residue "C TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 412": "OE1" <-> "OE2" Residue "C ARG 470": "NH1" <-> "NH2" Residue "C ASP 516": "OD1" <-> "OD2" Residue "C ARG 529": "NH1" <-> "NH2" Residue "C PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C ASP 549": "OD1" <-> "OD2" Residue "C TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 601": "OD1" <-> "OD2" Residue "C GLU 631": "OE1" <-> "OE2" Residue "C PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 738": "OE1" <-> "OE2" Residue "C TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 853": "OD1" <-> "OD2" Residue "C GLU 876": "OE1" <-> "OE2" Residue "C GLU 898": "OE1" <-> "OE2" Residue "C GLU 899": "OE1" <-> "OE2" Residue "C PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 908": "OE1" <-> "OE2" Residue "C ASP 937": "OD1" <-> "OD2" Residue "C GLU 987": "OE1" <-> "OE2" Residue "C ASP 1004": "OD1" <-> "OD2" Residue "C TYR 1053": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1059": "NH1" <-> "NH2" Residue "C GLU 1083": "OE1" <-> "OE2" Residue "C ASP 1126": "OD1" <-> "OD2" Residue "C GLU 1192": "OE1" <-> "OE2" Residue "C ASP 1203": "OD1" <-> "OD2" Residue "C TYR 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1240": "OD1" <-> "OD2" Residue "C TYR 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1341": "OD1" <-> "OD2" Residue "D ASP 18": "OD1" <-> "OD2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D GLU 52": "OE1" <-> "OE2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D GLU 86": "OE1" <-> "OE2" Residue "D ASP 129": "OD1" <-> "OD2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 162": "OE1" <-> "OE2" Residue "D ASP 167": "OD1" <-> "OD2" Residue "D ASP 267": "OD1" <-> "OD2" Residue "D ASP 304": "OD1" <-> "OD2" Residue "D ASP 329": "OD1" <-> "OD2" Residue "D GLU 386": "OE1" <-> "OE2" Residue "D ARG 388": "NH1" <-> "NH2" Residue "D GLU 404": "OE1" <-> "OE2" Residue "D ARG 431": "NH1" <-> "NH2" Residue "D PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 497": "OE1" <-> "OE2" Residue "D GLU 532": "OE1" <-> "OE2" Residue "D TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 660": "OE1" <-> "OE2" Residue "D ASP 710": "OD1" <-> "OD2" Residue "D GLU 827": "OE1" <-> "OE2" Residue "D ASP 855": "OD1" <-> "OD2" Residue "D GLU 873": "OE1" <-> "OE2" Residue "D GLU 981": "OE1" <-> "OE2" Residue "D GLU 1015": "OE1" <-> "OE2" Residue "D PHE 1034": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1094": "OD1" <-> "OD2" Residue "D TYR 1099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1110": "OE1" <-> "OE2" Residue "D ASP 1119": "OD1" <-> "OD2" Residue "D GLU 1188": "OE1" <-> "OE2" Residue "D GLU 1200": "OE1" <-> "OE2" Residue "D ASP 1208": "OD1" <-> "OD2" Residue "D ASP 1273": "OD1" <-> "OD2" Residue "D GLU 1327": "OE1" <-> "OE2" Residue "D GLU 1334": "OE1" <-> "OE2" Residue "D GLU 1343": "OE1" <-> "OE2" Residue "E GLU 11": "OE1" <-> "OE2" Residue "E GLU 41": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E ASP 65": "OD1" <-> "OD2" Residue "F GLU 136": "OE1" <-> "OE2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "F GLU 146": "OE1" <-> "OE2" Residue "F ARG 150": "NH1" <-> "NH2" Residue "F ARG 157": "NH1" <-> "NH2" Residue "F ASP 213": "OD1" <-> "OD2" Residue "F PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 223": "OE1" <-> "OE2" Residue "F GLU 248": "OE1" <-> "OE2" Residue "F GLU 254": "OE1" <-> "OE2" Residue "F PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 332": "OD1" <-> "OD2" Residue "F GLU 369": "OE1" <-> "OE2" Residue "F ASP 403": "OD1" <-> "OD2" Residue "F GLU 420": "OE1" <-> "OE2" Residue "F ASP 445": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 28244 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1793 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain: "B" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1711 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 213} Chain breaks: 1 Chain: "C" Number of atoms: 10560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1339, 10560 Classifications: {'peptide': 1339} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1282} Chain: "D" Number of atoms: 10387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10387 Classifications: {'peptide': 1336} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1280} Chain breaks: 2 Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2282 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 5, 'TRANS': 272} Chain breaks: 3 Chain: "N" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 290 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "T" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 346 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "R" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 193 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna3p': 8} Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'1N7': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14513 SG CYS D 70 103.224 40.598 87.204 1.00132.18 S ATOM 14527 SG CYS D 72 103.186 37.316 86.584 1.00134.99 S ATOM 14635 SG CYS D 85 105.452 39.414 85.002 1.00135.60 S ATOM 14659 SG CYS D 88 101.783 39.714 84.276 1.00136.35 S ATOM 20347 SG CYS D 814 90.767 106.035 90.888 1.00103.46 S ATOM 20912 SG CYS D 888 88.983 103.035 91.034 1.00107.74 S ATOM 20963 SG CYS D 895 90.275 104.458 93.797 1.00 97.39 S ATOM 20984 SG CYS D 898 87.792 106.194 92.401 1.00100.12 S Time building chain proxies: 16.40, per 1000 atoms: 0.58 Number of scatterers: 28244 At special positions: 0 Unit cell: (141.298, 151.962, 179.955, 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 118 16.00 P 40 15.00 Mg 1 11.99 O 5499 8.00 N 4990 7.00 C 17594 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: 12.37 Conformation dependent library (CDL) restraints added in 4.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " Number of angles added : 12 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6456 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 121 helices and 38 sheets defined 36.8% alpha, 12.6% beta 15 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 11.66 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.777A pdb=" N SER A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 87 removed outlier: 3.941A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 155 through 160 removed outlier: 4.666A pdb=" N HIS A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 227 Processing helix chain 'A' and resid 229 through 233 Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 78 through 86 Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 213 through 230 removed outlier: 4.000A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 39 Processing helix chain 'C' and resid 49 through 56 removed outlier: 3.511A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 207 through 212 Processing helix chain 'C' and resid 217 through 224 Processing helix chain 'C' and resid 243 through 246 removed outlier: 3.503A pdb=" N LEU C 246 " --> pdb=" O PRO C 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 243 through 246' Processing helix chain 'C' and resid 271 through 280 Processing helix chain 'C' and resid 289 through 291 No H-bonds generated for 'chain 'C' and resid 289 through 291' Processing helix chain 'C' and resid 319 through 327 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 359 through 370 Processing helix chain 'C' and resid 378 through 389 removed outlier: 3.980A pdb=" N SER C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 408 Processing helix chain 'C' and resid 422 through 436 Processing helix chain 'C' and resid 456 through 480 removed outlier: 3.725A pdb=" N GLU C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 485 No H-bonds generated for 'chain 'C' and resid 483 through 485' Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 520 through 527 Processing helix chain 'C' and resid 552 through 554 No H-bonds generated for 'chain 'C' and resid 552 through 554' Processing helix chain 'C' and resid 610 through 613 No H-bonds generated for 'chain 'C' and resid 610 through 613' Processing helix chain 'C' and resid 657 through 659 No H-bonds generated for 'chain 'C' and resid 657 through 659' Processing helix chain 'C' and resid 665 through 667 No H-bonds generated for 'chain 'C' and resid 665 through 667' Processing helix chain 'C' and resid 671 through 673 No H-bonds generated for 'chain 'C' and resid 671 through 673' Processing helix chain 'C' and resid 676 through 685 removed outlier: 3.678A pdb=" N MET C 681 " --> pdb=" O ASN C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 711 Processing helix chain 'C' and resid 820 through 824 removed outlier: 3.586A pdb=" N GLN C 824 " --> pdb=" O ARG C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 863 No H-bonds generated for 'chain 'C' and resid 861 through 863' Processing helix chain 'C' and resid 897 through 905 Processing helix chain 'C' and resid 943 through 980 Processing helix chain 'C' and resid 986 through 989 No H-bonds generated for 'chain 'C' and resid 986 through 989' Processing helix chain 'C' and resid 994 through 998 removed outlier: 3.978A pdb=" N LEU C 998 " --> pdb=" O ARG C 994 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 994 through 998' Processing helix chain 'C' and resid 1007 through 1036 removed outlier: 4.064A pdb=" N LYS C1027 " --> pdb=" O HIS C1023 " (cutoff:3.500A) Processing helix chain 'C' and resid 1082 through 1084 No H-bonds generated for 'chain 'C' and resid 1082 through 1084' Processing helix chain 'C' and resid 1100 through 1102 No H-bonds generated for 'chain 'C' and resid 1100 through 1102' Processing helix chain 'C' and resid 1109 through 1133 removed outlier: 4.068A pdb=" N LEU C1113 " --> pdb=" O GLY C1110 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU C1114 " --> pdb=" O GLN C1111 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU C1117 " --> pdb=" O GLU C1114 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY C1118 " --> pdb=" O THR C1115 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASP C1126 " --> pdb=" O GLY C1123 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN C1129 " --> pdb=" O ASP C1126 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU C1132 " --> pdb=" O ASN C1129 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1149 Processing helix chain 'C' and resid 1166 through 1178 removed outlier: 5.335A pdb=" N LYS C1178 " --> pdb=" O GLU C1174 " (cutoff:3.500A) Processing helix chain 'C' and resid 1192 through 1201 Processing helix chain 'C' and resid 1239 through 1241 No H-bonds generated for 'chain 'C' and resid 1239 through 1241' Processing helix chain 'C' and resid 1272 through 1281 removed outlier: 3.533A 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 1300 through 1308 Processing helix chain 'C' and resid 1321 through 1331 Processing helix chain 'D' and resid 27 through 33 Processing helix chain 'D' and resid 59 through 62 No H-bonds generated for 'chain 'D' and resid 59 through 62' Processing helix chain 'D' and resid 78 through 80 No H-bonds generated for 'chain 'D' and resid 78 through 80' Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 114 through 118 Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 132 through 139 removed outlier: 3.575A pdb=" N ARG D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 172 removed outlier: 3.584A pdb=" N LEU D 166 " --> pdb=" O GLU D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 191 Processing helix chain 'D' and resid 194 through 205 removed outlier: 3.667A pdb=" N GLU D 203 " --> pdb=" O GLU D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 229 removed outlier: 3.566A pdb=" N VAL D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 264 through 285 removed outlier: 3.786A pdb=" N ARG D 275 " --> pdb=" O ARG D 271 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 307 removed outlier: 3.916A pdb=" N ASN D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 removed outlier: 3.591A pdb=" N ILE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 327 through 331' Processing helix chain 'D' and resid 337 through 340 No H-bonds generated for 'chain 'D' and resid 337 through 340' Processing helix chain 'D' and resid 370 through 376 removed outlier: 3.825A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 387 Processing helix chain 'D' and resid 394 through 403 Processing helix chain 'D' and resid 406 through 415 removed outlier: 4.186A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 433 No H-bonds generated for 'chain 'D' and resid 431 through 433' Processing helix chain 'D' and resid 451 through 457 removed outlier: 3.757A pdb=" N ALA D 455 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 482 Processing helix chain 'D' and resid 486 through 488 No H-bonds generated for 'chain 'D' and resid 486 through 488' Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 530 through 538 Processing helix chain 'D' and resid 574 through 582 removed outlier: 3.844A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 612 Processing helix chain 'D' and resid 614 through 635 Processing helix chain 'D' and resid 648 through 669 removed outlier: 3.649A pdb=" N HIS D 651 " --> pdb=" O GLU D 648 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE D 653 " --> pdb=" O LYS D 650 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE D 654 " --> pdb=" O HIS D 651 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU D 658 " --> pdb=" O SER D 655 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL D 661 " --> pdb=" O GLU D 658 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA D 662 " --> pdb=" O ALA D 659 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLN D 665 " --> pdb=" O ALA D 662 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU D 666 " --> pdb=" O GLU D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 701 removed outlier: 3.676A pdb=" N ALA D 689 " --> pdb=" O ILE D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 727 Processing helix chain 'D' and resid 734 through 741 Processing helix chain 'D' and resid 769 through 803 removed outlier: 3.734A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 839 Processing helix chain 'D' and resid 866 through 874 Processing helix chain 'D' and resid 885 through 887 No H-bonds generated for 'chain 'D' and resid 885 through 887' Processing helix chain 'D' and resid 896 through 899 No H-bonds generated for 'chain 'D' and resid 896 through 899' Processing helix chain 'D' and resid 915 through 924 Processing helix chain 'D' and resid 926 through 929 Processing helix chain 'D' and resid 1138 through 1145 Processing helix chain 'D' and resid 1217 through 1241 removed outlier: 7.392A pdb=" N VAL D1226 " --> pdb=" O ARG D1222 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N HIS D1227 " --> pdb=" O LEU D1223 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA D1228 " --> pdb=" O ARG D1224 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1260 removed outlier: 4.050A pdb=" N VAL D1255 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG D1258 " --> pdb=" O VAL D1255 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1294 Processing helix chain 'D' and resid 1309 through 1314 Processing helix chain 'D' and resid 1319 through 1323 Processing helix chain 'D' and resid 1328 through 1337 Processing helix chain 'D' and resid 1347 through 1352 Processing helix chain 'D' and resid 1360 through 1373 removed outlier: 4.134A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP D1368 " --> pdb=" O ALA D1364 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG D1373 " --> pdb=" O ARG D1369 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 12 removed outlier: 3.593A pdb=" N GLU E 11 " --> pdb=" O GLN E 7 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 7 through 12' Processing helix chain 'E' and resid 16 through 31 removed outlier: 3.930A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 61 through 77 Processing helix chain 'F' and resid 114 through 136 removed outlier: 3.805A pdb=" N GLU F 136 " --> pdb=" O CYS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 152 removed outlier: 3.678A pdb=" N ASP F 149 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 233 Processing helix chain 'F' and resid 242 through 258 removed outlier: 3.536A pdb=" N GLN F 246 " --> pdb=" O HIS F 242 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU F 248 " --> pdb=" O THR F 244 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 291 removed outlier: 3.762A pdb=" N VAL F 280 " --> pdb=" O MET F 276 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN F 283 " --> pdb=" O ARG F 279 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 308 removed outlier: 4.538A pdb=" N THR F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 332 removed outlier: 4.193A pdb=" N LEU F 330 " --> pdb=" O SER F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 350 Processing helix chain 'F' and resid 355 through 382 removed outlier: 3.888A pdb=" N GLU F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 397 removed outlier: 5.629A pdb=" N ASN F 396 " --> pdb=" O LYS F 392 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ARG F 397 " --> pdb=" O LYS F 393 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 417 removed outlier: 4.380A pdb=" N GLN F 406 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP F 417 " --> pdb=" O MET F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 423 No H-bonds generated for 'chain 'F' and resid 421 through 423' Processing helix chain 'F' and resid 427 through 445 removed outlier: 4.703A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN F 437 " --> pdb=" O TRP F 433 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG F 441 " --> pdb=" O GLN F 437 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA F 444 " --> pdb=" O THR F 440 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 12 through 17 removed outlier: 6.572A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 90 through 92 Processing sheet with id= C, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.587A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 108 through 111 Processing sheet with id= E, first strand: chain 'B' and resid 13 through 20 removed outlier: 6.468A pdb=" N HIS B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 90 through 92 Processing sheet with id= G, first strand: chain 'B' and resid 97 through 106 removed outlier: 4.128A pdb=" N ALA B 138 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU B 58 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 108 through 111 Processing sheet with id= I, first strand: chain 'C' and resid 93 through 95 Processing sheet with id= J, first strand: chain 'C' and resid 136 through 138 Processing sheet with id= K, first strand: chain 'C' and resid 148 through 151 Processing sheet with id= L, first strand: chain 'C' and resid 154 through 158 Processing sheet with id= M, first strand: chain 'C' and resid 227 through 231 Processing sheet with id= N, first strand: chain 'C' and resid 529 through 531 Processing sheet with id= O, first strand: chain 'C' and resid 603 through 606 Processing sheet with id= P, first strand: chain 'C' and resid 633 through 637 Processing sheet with id= Q, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.092A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 1227 through 1232 removed outlier: 6.503A pdb=" N ILE C1096 " --> pdb=" O ALA C 803 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 887 through 889 Processing sheet with id= T, first strand: chain 'C' and resid 1065 through 1067 removed outlier: 7.319A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 66 through 75 removed outlier: 6.497A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 301 through 303 removed outlier: 5.605A pdb=" N ASP C 303 " --> pdb=" O LEU C 309 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU C 309 " --> pdb=" O ASP C 303 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.568A pdb=" N THR C 830 " --> pdb=" O ARG C1058 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 103 through 106 Processing sheet with id= Y, first strand: chain 'D' and resid 350 through 354 Processing sheet with id= Z, first strand: chain 'D' and resid 547 through 557 Processing sheet with id= AA, first strand: chain 'D' and resid 706 through 709 Processing sheet with id= AB, first strand: chain 'D' and resid 821 through 823 Processing sheet with id= AC, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.925A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 965 through 967 Processing sheet with id= AE, first strand: chain 'D' and resid 1024 through 1026 Processing sheet with id= AF, first strand: chain 'D' and resid 1034 through 1038 Processing sheet with id= AG, first strand: chain 'D' and resid 1046 through 1050 Processing sheet with id= AH, first strand: chain 'D' and resid 1173 through 1176 Processing sheet with id= AI, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.711A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'D' and resid 145 through 148 removed outlier: 6.989A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'D' and resid 825 through 827 removed outlier: 3.542A pdb=" N VAL D 825 " --> pdb=" O GLU D 833 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU D 833 " --> pdb=" O VAL D 825 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLU D 827 " --> pdb=" O VAL D 831 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL D 831 " --> pdb=" O GLU D 827 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'F' and resid 162 through 165 removed outlier: 6.874A pdb=" N ARG F 260 " --> pdb=" O THR F 163 " (cutoff:3.500A) 980 hydrogen bonds defined for protein. 2742 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 11.34 Time building geometry restraints manager: 13.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8285 1.33 - 1.45: 4530 1.45 - 1.57: 15647 1.57 - 1.70: 77 1.70 - 1.82: 205 Bond restraints: 28744 Sorted by residual: bond pdb=" N ARG F 374 " pdb=" CA ARG F 374 " ideal model delta sigma weight residual 1.459 1.423 0.036 1.17e-02 7.31e+03 9.54e+00 bond pdb=" CA GLU C 825 " pdb=" C GLU C 825 " ideal model delta sigma weight residual 1.523 1.481 0.041 1.41e-02 5.03e+03 8.50e+00 bond pdb=" CA ASN B 208 " pdb=" C ASN B 208 " ideal model delta sigma weight residual 1.524 1.478 0.046 1.66e-02 3.63e+03 7.65e+00 bond pdb=" CB THR D 890 " pdb=" OG1 THR D 890 " ideal model delta sigma weight residual 1.433 1.392 0.041 1.60e-02 3.91e+03 6.60e+00 bond pdb=" CB THR D 816 " pdb=" OG1 THR D 816 " ideal model delta sigma weight residual 1.433 1.397 0.036 1.60e-02 3.91e+03 5.06e+00 ... (remaining 28739 not shown) Histogram of bond angle deviations from ideal: 98.36 - 105.52: 697 105.52 - 112.68: 15585 112.68 - 119.83: 9687 119.83 - 126.99: 12705 126.99 - 134.15: 311 Bond angle restraints: 38985 Sorted by residual: angle pdb=" CA ASP D 460 " pdb=" CB ASP D 460 " pdb=" CG ASP D 460 " ideal model delta sigma weight residual 112.60 119.01 -6.41 1.00e+00 1.00e+00 4.10e+01 angle pdb=" C LYS D 40 " pdb=" N PRO D 41 " pdb=" CA PRO D 41 " ideal model delta sigma weight residual 119.56 125.10 -5.54 1.01e+00 9.80e-01 3.01e+01 angle pdb=" CA ASP D 462 " pdb=" CB ASP D 462 " pdb=" CG ASP D 462 " ideal model delta sigma weight residual 112.60 117.23 -4.63 1.00e+00 1.00e+00 2.14e+01 angle pdb=" N ARG F 374 " pdb=" CA ARG F 374 " pdb=" C ARG F 374 " ideal model delta sigma weight residual 110.97 106.01 4.96 1.09e+00 8.42e-01 2.07e+01 angle pdb=" N GLY C 597 " pdb=" CA GLY C 597 " pdb=" C GLY C 597 " ideal model delta sigma weight residual 115.59 109.89 5.70 1.32e+00 5.74e-01 1.86e+01 ... (remaining 38980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 15566 18.00 - 36.00: 1607 36.00 - 53.99: 295 53.99 - 71.99: 66 71.99 - 89.99: 18 Dihedral angle restraints: 17552 sinusoidal: 7529 harmonic: 10023 Sorted by residual: dihedral pdb=" CA LYS F 296 " pdb=" C LYS F 296 " pdb=" N MET F 297 " pdb=" CA MET F 297 " ideal model delta harmonic sigma weight residual -180.00 -151.30 -28.70 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA LYS C 227 " pdb=" C LYS C 227 " pdb=" N VAL C 228 " pdb=" CA VAL C 228 " ideal model delta harmonic sigma weight residual 180.00 155.11 24.89 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA SER D 503 " pdb=" C SER D 503 " pdb=" N GLN D 504 " pdb=" CA GLN D 504 " ideal model delta harmonic sigma weight residual -180.00 -155.50 -24.50 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 17549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3060 0.046 - 0.091: 1063 0.091 - 0.137: 296 0.137 - 0.182: 31 0.182 - 0.228: 11 Chirality restraints: 4461 Sorted by residual: chirality pdb=" CA HIS D1366 " pdb=" N HIS D1366 " pdb=" C HIS D1366 " pdb=" CB HIS D1366 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA ASP D 462 " pdb=" N ASP D 462 " pdb=" C ASP D 462 " pdb=" CB ASP D 462 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB ILE B 183 " pdb=" CA ILE B 183 " pdb=" CG1 ILE B 183 " pdb=" CG2 ILE B 183 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 4458 not shown) Planarity restraints: 4950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 75 " 0.063 2.00e-02 2.50e+03 3.34e-02 2.24e+01 pdb=" CG TYR D 75 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR D 75 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR D 75 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR D 75 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR D 75 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR D 75 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 75 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 886 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.34e+00 pdb=" C VAL D 886 " 0.053 2.00e-02 2.50e+03 pdb=" O VAL D 886 " -0.020 2.00e-02 2.50e+03 pdb=" N SER D 887 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 461 " 0.015 2.00e-02 2.50e+03 1.85e-02 5.96e+00 pdb=" CG PHE D 461 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 PHE D 461 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE D 461 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE D 461 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 461 " -0.018 2.00e-02 2.50e+03 pdb=" CZ PHE D 461 " 0.033 2.00e-02 2.50e+03 ... (remaining 4947 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 296 2.56 - 3.14: 23130 3.14 - 3.73: 44846 3.73 - 4.31: 63369 4.31 - 4.90: 104537 Nonbonded interactions: 236178 Sorted by model distance: nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1501 " model vdw 1.972 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 1.995 2.170 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1501 " model vdw 2.104 2.170 nonbonded pdb=" O ILE C 11 " pdb=" OH TYR C1149 " model vdw 2.197 2.440 nonbonded pdb=" OG SER C 348 " pdb=" OE2 GLU C 349 " model vdw 2.209 2.440 ... (remaining 236173 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 159 or resid 169 through 234)) selection = (chain 'B' and resid 5 through 234) } 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: 0.790 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: 0.020 Extract box with map and model: 6.350 Check model and map are aligned: 0.470 Set scattering table: 0.270 Process input model: 85.730 Find NCS groups from input model: 1.020 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: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 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 : 0.008 0.069 28744 Z= 0.519 Angle : 0.795 9.173 38985 Z= 0.476 Chirality : 0.049 0.228 4461 Planarity : 0.004 0.049 4950 Dihedral : 14.944 89.988 11096 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 0.69 % Favored : 99.28 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.52 (0.12), residues: 3461 helix: -1.71 (0.12), residues: 1291 sheet: -1.72 (0.22), residues: 426 loop : -1.53 (0.13), residues: 1744 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 230 time to evaluate : 3.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 232 average time/residue: 0.5184 time to fit residues: 178.5975 Evaluate side-chains 153 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 3.611 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 293 optimal weight: 0.7980 chunk 263 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 271 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 202 optimal weight: 9.9990 chunk 315 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 117 HIS ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 ASN B 132 HIS B 137 ASN C 41 GLN C 46 GLN C 193 ASN C 330 HIS C 618 GLN C 620 ASN ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 GLN C1209 GLN C1244 HIS C1268 GLN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN D 158 GLN D 206 ASN D 232 ASN D 266 ASN D 274 ASN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D 365 GLN D 488 ASN D 712 GLN ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 GLN D1244 GLN D1367 GLN E 72 GLN F 301 ASN F 323 ASN F 400 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 28744 Z= 0.214 Angle : 0.510 8.193 38985 Z= 0.267 Chirality : 0.041 0.150 4461 Planarity : 0.004 0.041 4950 Dihedral : 9.526 67.018 4230 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.29 (0.14), residues: 3461 helix: -0.30 (0.14), residues: 1287 sheet: -1.42 (0.22), residues: 451 loop : -1.04 (0.14), residues: 1723 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 170 time to evaluate : 3.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 188 average time/residue: 0.4277 time to fit residues: 130.4772 Evaluate side-chains 164 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 153 time to evaluate : 3.710 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2863 time to fit residues: 11.1203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 175 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 chunk 262 optimal weight: 8.9990 chunk 214 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 315 optimal weight: 3.9990 chunk 341 optimal weight: 20.0000 chunk 281 optimal weight: 3.9990 chunk 313 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 253 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 GLN C1061 GLN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1279 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 28744 Z= 0.172 Angle : 0.475 13.663 38985 Z= 0.248 Chirality : 0.040 0.194 4461 Planarity : 0.003 0.068 4950 Dihedral : 9.220 65.086 4230 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.66 (0.14), residues: 3461 helix: 0.31 (0.15), residues: 1288 sheet: -1.18 (0.23), residues: 452 loop : -0.71 (0.15), residues: 1721 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 170 time to evaluate : 3.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 3 residues processed: 190 average time/residue: 0.4048 time to fit residues: 127.0633 Evaluate side-chains 152 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 149 time to evaluate : 3.579 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2601 time to fit residues: 6.2039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 311 optimal weight: 0.9980 chunk 237 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 chunk 316 optimal weight: 4.9990 chunk 335 optimal weight: 0.9990 chunk 165 optimal weight: 6.9990 chunk 300 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN C 580 GLN C 628 HIS ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 28744 Z= 0.304 Angle : 0.526 9.920 38985 Z= 0.272 Chirality : 0.042 0.179 4461 Planarity : 0.004 0.059 4950 Dihedral : 9.213 65.291 4230 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.47 (0.14), residues: 3461 helix: 0.44 (0.15), residues: 1299 sheet: -1.02 (0.24), residues: 443 loop : -0.61 (0.15), residues: 1719 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 154 time to evaluate : 3.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 20 residues processed: 178 average time/residue: 0.4033 time to fit residues: 118.5750 Evaluate side-chains 165 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 145 time to evaluate : 3.740 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2748 time to fit residues: 15.2261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 279 optimal weight: 0.0370 chunk 190 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 249 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 286 optimal weight: 20.0000 chunk 231 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 171 optimal weight: 5.9990 chunk 301 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 overall best weight: 4.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.075 28744 Z= 0.503 Angle : 0.625 11.667 38985 Z= 0.322 Chirality : 0.045 0.178 4461 Planarity : 0.004 0.077 4950 Dihedral : 9.447 64.395 4230 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.61 (0.14), residues: 3461 helix: 0.29 (0.14), residues: 1298 sheet: -1.06 (0.24), residues: 440 loop : -0.67 (0.15), residues: 1723 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 147 time to evaluate : 3.538 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 22 residues processed: 185 average time/residue: 0.4106 time to fit residues: 125.2192 Evaluate side-chains 162 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 140 time to evaluate : 3.786 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2780 time to fit residues: 16.0416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 112 optimal weight: 0.6980 chunk 302 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 196 optimal weight: 8.9990 chunk 82 optimal weight: 0.0020 chunk 335 optimal weight: 9.9990 chunk 278 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 176 optimal weight: 0.0870 overall best weight: 0.4966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 28744 Z= 0.133 Angle : 0.476 11.384 38985 Z= 0.245 Chirality : 0.040 0.180 4461 Planarity : 0.003 0.061 4950 Dihedral : 9.018 66.495 4230 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.13 (0.14), residues: 3461 helix: 0.78 (0.15), residues: 1288 sheet: -0.65 (0.24), residues: 447 loop : -0.51 (0.15), residues: 1726 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 156 time to evaluate : 3.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 171 average time/residue: 0.4352 time to fit residues: 122.5040 Evaluate side-chains 153 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 144 time to evaluate : 3.498 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2640 time to fit residues: 9.2789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 323 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 191 optimal weight: 9.9990 chunk 245 optimal weight: 7.9990 chunk 189 optimal weight: 8.9990 chunk 282 optimal weight: 8.9990 chunk 187 optimal weight: 8.9990 chunk 334 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 GLN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 28744 Z= 0.403 Angle : 0.578 11.626 38985 Z= 0.294 Chirality : 0.043 0.166 4461 Planarity : 0.004 0.061 4950 Dihedral : 9.095 64.945 4230 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.29 (0.14), residues: 3461 helix: 0.61 (0.15), residues: 1302 sheet: -0.83 (0.25), residues: 433 loop : -0.55 (0.15), residues: 1726 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 145 time to evaluate : 3.585 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 10 residues processed: 163 average time/residue: 0.4345 time to fit residues: 117.1703 Evaluate side-chains 151 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 141 time to evaluate : 3.420 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2801 time to fit residues: 9.8189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 206 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 199 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 212 optimal weight: 0.9990 chunk 227 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 262 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN C 276 GLN ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 GLN C1157 GLN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 28744 Z= 0.162 Angle : 0.487 11.655 38985 Z= 0.249 Chirality : 0.041 0.229 4461 Planarity : 0.003 0.057 4950 Dihedral : 8.842 66.182 4230 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.09 (0.14), residues: 3461 helix: 0.82 (0.15), residues: 1304 sheet: -0.64 (0.25), residues: 434 loop : -0.51 (0.15), residues: 1723 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 157 time to evaluate : 3.678 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 3 residues processed: 166 average time/residue: 0.4297 time to fit residues: 117.7124 Evaluate side-chains 147 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 3.564 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2894 time to fit residues: 6.3447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 304 optimal weight: 3.9990 chunk 320 optimal weight: 6.9990 chunk 292 optimal weight: 6.9990 chunk 311 optimal weight: 0.9990 chunk 187 optimal weight: 8.9990 chunk 135 optimal weight: 0.0040 chunk 244 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 281 optimal weight: 30.0000 chunk 294 optimal weight: 9.9990 chunk 310 optimal weight: 4.9990 overall best weight: 3.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN C1013 GLN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 28744 Z= 0.366 Angle : 0.573 12.451 38985 Z= 0.291 Chirality : 0.043 0.188 4461 Planarity : 0.004 0.085 4950 Dihedral : 9.015 64.661 4230 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.14 (0.15), residues: 3461 helix: 0.74 (0.15), residues: 1300 sheet: -0.72 (0.25), residues: 435 loop : -0.48 (0.16), residues: 1726 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 149 time to evaluate : 3.338 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 154 average time/residue: 0.4469 time to fit residues: 112.3142 Evaluate side-chains 149 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 145 time to evaluate : 3.848 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3196 time to fit residues: 7.0032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 204 optimal weight: 5.9990 chunk 329 optimal weight: 5.9990 chunk 201 optimal weight: 0.6980 chunk 156 optimal weight: 0.7980 chunk 229 optimal weight: 1.9990 chunk 345 optimal weight: 20.0000 chunk 318 optimal weight: 30.0000 chunk 275 optimal weight: 40.0000 chunk 28 optimal weight: 9.9990 chunk 212 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 28744 Z= 0.186 Angle : 0.504 11.941 38985 Z= 0.256 Chirality : 0.041 0.198 4461 Planarity : 0.003 0.076 4950 Dihedral : 8.836 65.251 4230 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.04 (0.15), residues: 3461 helix: 0.87 (0.15), residues: 1310 sheet: -0.69 (0.25), residues: 438 loop : -0.47 (0.16), residues: 1713 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 3.825 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 150 average time/residue: 0.4472 time to fit residues: 109.1354 Evaluate side-chains 147 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 3.454 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2896 time to fit residues: 6.2764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 218 optimal weight: 3.9990 chunk 293 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 253 optimal weight: 0.0770 chunk 40 optimal weight: 5.9990 chunk 76 optimal weight: 0.0970 chunk 275 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 283 optimal weight: 30.0000 chunk 34 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 overall best weight: 1.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.099850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.065500 restraints weight = 67056.786| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.92 r_work: 0.2947 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 28744 Z= 0.216 Angle : 0.512 12.068 38985 Z= 0.259 Chirality : 0.041 0.192 4461 Planarity : 0.003 0.074 4950 Dihedral : 8.799 64.899 4230 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.01 (0.15), residues: 3461 helix: 0.89 (0.15), residues: 1311 sheet: -0.62 (0.25), residues: 435 loop : -0.44 (0.15), residues: 1715 =============================================================================== Job complete usr+sys time: 4984.00 seconds wall clock time: 92 minutes 21.73 seconds (5541.73 seconds total)