Starting phenix.real_space_refine on Thu Feb 15 02:51:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkd_36368/02_2024/8jkd_36368.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkd_36368/02_2024/8jkd_36368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkd_36368/02_2024/8jkd_36368.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkd_36368/02_2024/8jkd_36368.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkd_36368/02_2024/8jkd_36368.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkd_36368/02_2024/8jkd_36368.pdb" } resolution = 2.6 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= 0.099 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 104 5.16 5 C 6883 2.51 5 N 1858 2.21 5 O 2115 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 1243": "OE1" <-> "OE2" Residue "A TYR 1359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1534": "OE1" <-> "OE2" Residue "B PHE 1221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1243": "OE1" <-> "OE2" Residue "B GLU 1250": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10960 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3688 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 19, 'TRANS': 452} Chain breaks: 2 Chain: "B" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3629 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 19, 'TRANS': 444} Chain breaks: 2 Chain: "C" Number of atoms: 3643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3643 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 19, 'TRANS': 447} Chain breaks: 3 Time building chain proxies: 6.13, per 1000 atoms: 0.56 Number of scatterers: 10960 At special positions: 0 Unit cell: (90.25, 90.25, 141.55, 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 104 16.00 O 2115 8.00 N 1858 7.00 C 6883 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A1165 " - pdb=" SG CYS A1198 " distance=2.03 Simple disulfide: pdb=" SG CYS A1169 " - pdb=" SG CYS A1205 " distance=2.03 Simple disulfide: pdb=" SG CYS A1173 " - pdb=" SG CYS A1207 " distance=2.03 Simple disulfide: pdb=" SG CYS A1175 " - pdb=" SG CYS A1180 " distance=2.03 Simple disulfide: pdb=" SG CYS A1193 " - pdb=" SG CYS A1360 " distance=2.03 Simple disulfide: pdb=" SG CYS A1208 " - pdb=" SG CYS A1368 " distance=2.03 Simple disulfide: pdb=" SG CYS A1236 " - pdb=" SG CYS A1246 " distance=2.03 Simple disulfide: pdb=" SG CYS A1305 " - pdb=" SG CYS A1310 " distance=2.03 Simple disulfide: pdb=" SG CYS A1452 " - pdb=" SG CYS A1464 " distance=2.03 Simple disulfide: pdb=" SG CYS A1455 " - pdb=" SG CYS A1458 " distance=2.03 Simple disulfide: pdb=" SG CYS A1519 " - pdb=" SG CYS A1539 " distance=2.04 Simple disulfide: pdb=" SG CYS A1528 " - pdb=" SG CYS A1531 " distance=2.03 Simple disulfide: pdb=" SG CYS B1165 " - pdb=" SG CYS B1198 " distance=2.03 Simple disulfide: pdb=" SG CYS B1169 " - pdb=" SG CYS B1205 " distance=2.03 Simple disulfide: pdb=" SG CYS B1173 " - pdb=" SG CYS B1207 " distance=2.03 Simple disulfide: pdb=" SG CYS B1175 " - pdb=" SG CYS B1180 " distance=2.03 Simple disulfide: pdb=" SG CYS B1193 " - pdb=" SG CYS B1360 " distance=2.02 Simple disulfide: pdb=" SG CYS B1208 " - pdb=" SG CYS B1368 " distance=2.03 Simple disulfide: pdb=" SG CYS B1236 " - pdb=" SG CYS B1246 " distance=2.03 Simple disulfide: pdb=" SG CYS B1305 " - pdb=" SG CYS B1310 " distance=2.03 Simple disulfide: pdb=" SG CYS B1452 " - pdb=" SG CYS B1464 " distance=2.03 Simple disulfide: pdb=" SG CYS B1455 " - pdb=" SG CYS B1458 " distance=2.03 Simple disulfide: pdb=" SG CYS B1519 " - pdb=" SG CYS B1539 " distance=2.04 Simple disulfide: pdb=" SG CYS B1528 " - pdb=" SG CYS B1531 " distance=2.03 Simple disulfide: pdb=" SG CYS C1169 " - pdb=" SG CYS C1205 " distance=2.03 Simple disulfide: pdb=" SG CYS C1173 " - pdb=" SG CYS C1207 " distance=2.03 Simple disulfide: pdb=" SG CYS C1175 " - pdb=" SG CYS C1180 " distance=2.03 Simple disulfide: pdb=" SG CYS C1193 " - pdb=" SG CYS C1360 " distance=2.03 Simple disulfide: pdb=" SG CYS C1208 " - pdb=" SG CYS C1368 " distance=2.03 Simple disulfide: pdb=" SG CYS C1236 " - pdb=" SG CYS C1246 " distance=2.03 Simple disulfide: pdb=" SG CYS C1305 " - pdb=" SG CYS C1310 " distance=2.03 Simple disulfide: pdb=" SG CYS C1452 " - pdb=" SG CYS C1464 " distance=2.03 Simple disulfide: pdb=" SG CYS C1455 " - pdb=" SG CYS C1458 " distance=2.03 Simple disulfide: pdb=" SG CYS C1519 " - pdb=" SG CYS C1539 " distance=2.03 Simple disulfide: pdb=" SG CYS C1528 " - pdb=" SG CYS C1531 " distance=2.04 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: 4.04 Conformation dependent library (CDL) restraints added in 2.1 seconds 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2626 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 23 sheets defined 5.4% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 1095 through 1099 removed outlier: 3.702A pdb=" N ASN A1098 " --> pdb=" O HIS A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1388 Processing helix chain 'A' and resid 1390 through 1394 removed outlier: 3.929A pdb=" N ASN A1394 " --> pdb=" O ASP A1390 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1390 through 1394' Processing helix chain 'A' and resid 1524 through 1528 Processing helix chain 'B' and resid 1095 through 1099 removed outlier: 3.727A pdb=" N ASN B1098 " --> pdb=" O HIS B1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 1377 through 1388 Processing helix chain 'B' and resid 1390 through 1394 removed outlier: 3.943A pdb=" N ASN B1394 " --> pdb=" O ASP B1390 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1390 through 1394' Processing helix chain 'B' and resid 1524 through 1528 Processing helix chain 'C' and resid 1095 through 1099 removed outlier: 3.791A pdb=" N ASN C1098 " --> pdb=" O HIS C1095 " (cutoff:3.500A) Processing helix chain 'C' and resid 1377 through 1388 Processing helix chain 'C' and resid 1524 through 1528 Processing sheet with id=AA1, first strand: chain 'A' and resid 1080 through 1081 removed outlier: 6.235A pdb=" N THR A1080 " --> pdb=" O GLY A1117 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N SER A1119 " --> pdb=" O THR A1080 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR A1116 " --> pdb=" O VAL A1137 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS A1131 " --> pdb=" O LEU A1122 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL A1135 " --> pdb=" O GLU A1238 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLU A1238 " --> pdb=" O VAL A1135 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL A1137 " --> pdb=" O CYS A1236 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N CYS A1236 " --> pdb=" O VAL A1137 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP A1139 " --> pdb=" O ILE A1234 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS A1230 " --> pdb=" O MET A1143 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1245 through 1248 current: chain 'A' and resid 1409 through 1417 Processing sheet with id=AA2, first strand: chain 'A' and resid 1086 through 1093 removed outlier: 3.582A pdb=" N THR A1253 " --> pdb=" O LEU A1264 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1147 through 1153 removed outlier: 5.485A pdb=" N PHE A1148 " --> pdb=" O LYS A1225 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LYS A1225 " --> pdb=" O PHE A1148 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR A1150 " --> pdb=" O LYS A1223 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N MET A1220 " --> pdb=" O HIS A1282 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS A1297 " --> pdb=" O LEU A1281 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1157 through 1163 Processing sheet with id=AA5, first strand: chain 'A' and resid 1318 through 1320 Processing sheet with id=AA6, first strand: chain 'A' and resid 1327 through 1328 Processing sheet with id=AA7, first strand: chain 'A' and resid 1355 through 1359 Processing sheet with id=AA8, first strand: chain 'A' and resid 1446 through 1454 removed outlier: 5.259A pdb=" N PHE A1447 " --> pdb=" O HIS A1469 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N HIS A1469 " --> pdb=" O PHE A1447 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1480 through 1482 Processing sheet with id=AB1, first strand: chain 'B' and resid 1080 through 1082 removed outlier: 6.262A pdb=" N THR B1080 " --> pdb=" O GLY B1117 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N SER B1119 " --> pdb=" O THR B1080 " (cutoff:3.500A) removed outlier: 9.425A pdb=" N SER B1082 " --> pdb=" O SER B1119 " (cutoff:3.500A) removed outlier: 13.398A pdb=" N ASP B1121 " --> pdb=" O SER B1082 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR B1116 " --> pdb=" O VAL B1137 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS B1131 " --> pdb=" O LEU B1122 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N VAL B1135 " --> pdb=" O GLU B1238 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N GLU B1238 " --> pdb=" O VAL B1135 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL B1137 " --> pdb=" O CYS B1236 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N CYS B1236 " --> pdb=" O VAL B1137 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP B1139 " --> pdb=" O ILE B1234 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS B1230 " --> pdb=" O MET B1143 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER B1145 " --> pdb=" O TYR B1228 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR B1228 " --> pdb=" O SER B1145 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL B1147 " --> pdb=" O VAL B1226 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N VAL B1226 " --> pdb=" O VAL B1147 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLU B1149 " --> pdb=" O TRP B1224 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N TRP B1224 " --> pdb=" O GLU B1149 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU B1151 " --> pdb=" O VAL B1222 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B1222 " --> pdb=" O LEU B1151 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY B1153 " --> pdb=" O MET B1220 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N MET B1220 " --> pdb=" O GLY B1153 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1245 through 1248 current: chain 'B' and resid 1297 through 1300 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1297 through 1300 current: chain 'B' and resid 1409 through 1417 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1409 through 1417 current: chain 'B' and resid 1494 through 1496 Processing sheet with id=AB2, first strand: chain 'B' and resid 1086 through 1093 removed outlier: 3.613A pdb=" N THR B1253 " --> pdb=" O LEU B1264 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1157 through 1163 Processing sheet with id=AB4, first strand: chain 'B' and resid 1318 through 1320 Processing sheet with id=AB5, first strand: chain 'B' and resid 1355 through 1359 Processing sheet with id=AB6, first strand: chain 'B' and resid 1446 through 1454 removed outlier: 5.042A pdb=" N PHE B1447 " --> pdb=" O HIS B1469 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N HIS B1469 " --> pdb=" O PHE B1447 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1480 through 1482 Processing sheet with id=AB8, first strand: chain 'C' and resid 1080 through 1082 removed outlier: 6.257A pdb=" N THR C1080 " --> pdb=" O GLY C1117 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N SER C1119 " --> pdb=" O THR C1080 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N SER C1082 " --> pdb=" O SER C1119 " (cutoff:3.500A) removed outlier: 13.513A pdb=" N ASP C1121 " --> pdb=" O SER C1082 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR C1116 " --> pdb=" O VAL C1137 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N VAL C1135 " --> pdb=" O GLU C1238 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N GLU C1238 " --> pdb=" O VAL C1135 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N VAL C1137 " --> pdb=" O CYS C1236 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N CYS C1236 " --> pdb=" O VAL C1137 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASP C1139 " --> pdb=" O ILE C1234 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS C1230 " --> pdb=" O MET C1143 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N SER C1145 " --> pdb=" O TYR C1228 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TYR C1228 " --> pdb=" O SER C1145 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL C1147 " --> pdb=" O VAL C1226 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL C1226 " --> pdb=" O VAL C1147 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLU C1149 " --> pdb=" O TRP C1224 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N TRP C1224 " --> pdb=" O GLU C1149 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU C1151 " --> pdb=" O VAL C1222 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL C1222 " --> pdb=" O LEU C1151 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY C1153 " --> pdb=" O MET C1220 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET C1220 " --> pdb=" O GLY C1153 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 1245 through 1248 current: chain 'C' and resid 1297 through 1300 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 1297 through 1300 current: chain 'C' and resid 1409 through 1417 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 1409 through 1417 current: chain 'C' and resid 1462 through 1469 Processing sheet with id=AB9, first strand: chain 'C' and resid 1086 through 1093 Processing sheet with id=AC1, first strand: chain 'C' and resid 1157 through 1163 Processing sheet with id=AC2, first strand: chain 'C' and resid 1289 through 1291 removed outlier: 3.661A pdb=" N LYS C1331 " --> pdb=" O LYS C1328 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 1318 through 1320 Processing sheet with id=AC4, first strand: chain 'C' and resid 1355 through 1359 removed outlier: 3.694A pdb=" N TYR C1359 " --> pdb=" O SER C1367 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER C1367 " --> pdb=" O TYR C1359 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 1480 through 1482 258 hydrogen bonds defined for protein. 684 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: 3.28 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3562 1.34 - 1.47: 2635 1.47 - 1.59: 4872 1.59 - 1.71: 0 1.71 - 1.83: 134 Bond restraints: 11203 Sorted by residual: bond pdb=" CB CYS B1539 " pdb=" SG CYS B1539 " ideal model delta sigma weight residual 1.808 1.766 0.042 3.30e-02 9.18e+02 1.65e+00 bond pdb=" CB ASP B1317 " pdb=" CG ASP B1317 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.20e+00 bond pdb=" CB CYS A1519 " pdb=" SG CYS A1519 " ideal model delta sigma weight residual 1.808 1.773 0.035 3.30e-02 9.18e+02 1.10e+00 bond pdb=" CB CYS A1539 " pdb=" SG CYS A1539 " ideal model delta sigma weight residual 1.808 1.774 0.034 3.30e-02 9.18e+02 1.07e+00 bond pdb=" CB CYS B1519 " pdb=" SG CYS B1519 " ideal model delta sigma weight residual 1.808 1.775 0.033 3.30e-02 9.18e+02 1.03e+00 ... (remaining 11198 not shown) Histogram of bond angle deviations from ideal: 100.00 - 106.84: 345 106.84 - 113.67: 6343 113.67 - 120.50: 3920 120.50 - 127.33: 4424 127.33 - 134.16: 153 Bond angle restraints: 15185 Sorted by residual: angle pdb=" CA CYS B1519 " pdb=" CB CYS B1519 " pdb=" SG CYS B1519 " ideal model delta sigma weight residual 114.40 120.76 -6.36 2.30e+00 1.89e-01 7.65e+00 angle pdb=" C LEU A1518 " pdb=" N CYS A1519 " pdb=" CA CYS A1519 " ideal model delta sigma weight residual 121.40 117.20 4.20 1.52e+00 4.33e-01 7.63e+00 angle pdb=" CA LEU A1215 " pdb=" CB LEU A1215 " pdb=" CG LEU A1215 " ideal model delta sigma weight residual 116.30 125.32 -9.02 3.50e+00 8.16e-02 6.65e+00 angle pdb=" C GLY C1406 " pdb=" N ASP C1407 " pdb=" CA ASP C1407 " ideal model delta sigma weight residual 121.54 126.12 -4.58 1.91e+00 2.74e-01 5.74e+00 angle pdb=" CA CYS A1519 " pdb=" CB CYS A1519 " pdb=" SG CYS A1519 " ideal model delta sigma weight residual 114.40 119.88 -5.48 2.30e+00 1.89e-01 5.68e+00 ... (remaining 15180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 6072 17.82 - 35.64: 594 35.64 - 53.46: 110 53.46 - 71.28: 17 71.28 - 89.10: 10 Dihedral angle restraints: 6803 sinusoidal: 2748 harmonic: 4055 Sorted by residual: dihedral pdb=" CB CYS B1528 " pdb=" SG CYS B1528 " pdb=" SG CYS B1531 " pdb=" CB CYS B1531 " ideal model delta sinusoidal sigma weight residual 93.00 179.58 -86.58 1 1.00e+01 1.00e-02 9.03e+01 dihedral pdb=" CB CYS C1455 " pdb=" SG CYS C1455 " pdb=" SG CYS C1458 " pdb=" CB CYS C1458 " ideal model delta sinusoidal sigma weight residual -86.00 -161.36 75.36 1 1.00e+01 1.00e-02 7.17e+01 dihedral pdb=" CB CYS B1455 " pdb=" SG CYS B1455 " pdb=" SG CYS B1458 " pdb=" CB CYS B1458 " ideal model delta sinusoidal sigma weight residual -86.00 -142.32 56.32 1 1.00e+01 1.00e-02 4.28e+01 ... (remaining 6800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1042 0.033 - 0.066: 436 0.066 - 0.100: 142 0.100 - 0.133: 88 0.133 - 0.166: 12 Chirality restraints: 1720 Sorted by residual: chirality pdb=" CA ILE B1468 " pdb=" N ILE B1468 " pdb=" C ILE B1468 " pdb=" CB ILE B1468 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" CA ILE A1552 " pdb=" N ILE A1552 " pdb=" C ILE A1552 " pdb=" CB ILE A1552 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.71e-01 chirality pdb=" CA ILE C1468 " pdb=" N ILE C1468 " pdb=" C ILE C1468 " pdb=" CB ILE C1468 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.09e-01 ... (remaining 1717 not shown) Planarity restraints: 1921 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP C1365 " -0.041 5.00e-02 4.00e+02 6.21e-02 6.18e+00 pdb=" N PRO C1366 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO C1366 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C1366 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1194 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO A1195 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A1195 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A1195 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU C1215 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.42e+00 pdb=" C LEU C1215 " 0.036 2.00e-02 2.50e+03 pdb=" O LEU C1215 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE C1216 " -0.012 2.00e-02 2.50e+03 ... (remaining 1918 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 866 2.75 - 3.28: 9922 3.28 - 3.82: 18268 3.82 - 4.36: 22785 4.36 - 4.90: 39406 Nonbonded interactions: 91247 Sorted by model distance: nonbonded pdb=" OG SER C1302 " pdb=" OE1 GLU C1388 " model vdw 2.206 2.440 nonbonded pdb=" OG SER A1302 " pdb=" OE1 GLU A1388 " model vdw 2.218 2.440 nonbonded pdb=" OE1 GLN C1319 " pdb=" OH TYR C1321 " model vdw 2.234 2.440 nonbonded pdb=" O ARG A1189 " pdb=" N GLY A1202 " model vdw 2.235 2.520 nonbonded pdb=" OG1 THR A1164 " pdb=" O GLY A1167 " model vdw 2.252 2.440 ... (remaining 91242 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 1078 through 1196 or resid 1202 through 1327 or resid 1344 \ through 1559)) selection = (chain 'B' and (resid 1078 through 1125 or resid 1129 through 1196 or resid 1202 \ through 1559)) selection = (chain 'C' and (resid 1078 through 1125 or resid 1129 through 1327 or resid 1344 \ through 1559)) } 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: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.780 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 31.340 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.050 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:12.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 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 0.042 11203 Z= 0.201 Angle : 0.632 9.025 15185 Z= 0.340 Chirality : 0.046 0.166 1720 Planarity : 0.005 0.062 1921 Dihedral : 14.089 89.103 4072 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.71 (0.23), residues: 1383 helix: 0.82 (1.09), residues: 33 sheet: 0.49 (0.22), residues: 638 loop : -1.49 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A1197 HIS 0.004 0.001 HIS C1469 PHE 0.028 0.002 PHE B1447 TYR 0.013 0.001 TYR A1359 ARG 0.004 0.000 ARG B1401 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.312 Fit side-chains revert: symmetry clash REVERT: A 1191 TRP cc_start: 0.6859 (p-90) cc_final: 0.5591 (m-90) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 1.3012 time to fit residues: 233.2682 Evaluate side-chains 122 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1333 ASN A1377 ASN A1378 HIS A1546 GLN B1156 GLN B1375 GLN C1245 GLN C1296 GLN C1394 ASN C1546 GLN C1554 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.074 11203 Z= 0.566 Angle : 0.840 12.807 15185 Z= 0.442 Chirality : 0.055 0.303 1720 Planarity : 0.006 0.057 1921 Dihedral : 6.606 26.990 1477 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 3.34 % Allowed : 9.87 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.88 (0.22), residues: 1383 helix: 0.27 (1.10), residues: 33 sheet: 0.51 (0.22), residues: 609 loop : -1.65 (0.20), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A1197 HIS 0.009 0.002 HIS A1378 PHE 0.022 0.003 PHE A1447 TYR 0.018 0.003 TYR B1359 ARG 0.006 0.001 ARG C1525 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 117 time to evaluate : 1.436 Fit side-chains REVERT: A 1362 MET cc_start: 0.7449 (tpp) cc_final: 0.7198 (ttm) REVERT: A 1387 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8850 (mt) REVERT: A 1412 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7352 (p0) REVERT: B 1401 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7472 (ttm170) REVERT: B 1495 MET cc_start: 0.8272 (tpp) cc_final: 0.8066 (tpp) REVERT: C 1387 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8901 (mp) outliers start: 42 outliers final: 18 residues processed: 145 average time/residue: 1.1695 time to fit residues: 181.9927 Evaluate side-chains 131 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1387 ILE Chi-restraints excluded: chain A residue 1394 ASN Chi-restraints excluded: chain A residue 1412 ASP Chi-restraints excluded: chain A residue 1483 ASP Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain B residue 1184 GLU Chi-restraints excluded: chain B residue 1188 SER Chi-restraints excluded: chain B residue 1215 LEU Chi-restraints excluded: chain B residue 1302 SER Chi-restraints excluded: chain B residue 1394 ASN Chi-restraints excluded: chain B residue 1401 ARG Chi-restraints excluded: chain B residue 1446 LYS Chi-restraints excluded: chain B residue 1483 ASP Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1277 GLU Chi-restraints excluded: chain C residue 1369 THR Chi-restraints excluded: chain C residue 1387 ILE Chi-restraints excluded: chain C residue 1392 THR Chi-restraints excluded: chain C residue 1516 THR Chi-restraints excluded: chain C residue 1531 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1378 HIS A1546 GLN B1156 GLN C1296 GLN C1377 ASN C1546 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 11203 Z= 0.247 Angle : 0.654 16.836 15185 Z= 0.342 Chirality : 0.046 0.238 1720 Planarity : 0.005 0.051 1921 Dihedral : 5.906 24.051 1477 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.63 % Allowed : 13.61 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.78 (0.22), residues: 1383 helix: 0.46 (1.13), residues: 33 sheet: 0.61 (0.22), residues: 616 loop : -1.65 (0.20), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1197 HIS 0.005 0.001 HIS B1322 PHE 0.012 0.002 PHE A1221 TYR 0.015 0.002 TYR B1359 ARG 0.002 0.000 ARG C1284 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 130 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1412 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7167 (p0) REVERT: B 1113 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7407 (mt-10) outliers start: 33 outliers final: 12 residues processed: 153 average time/residue: 1.0372 time to fit residues: 170.1408 Evaluate side-chains 139 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1394 ASN Chi-restraints excluded: chain A residue 1412 ASP Chi-restraints excluded: chain A residue 1483 ASP Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain B residue 1113 GLU Chi-restraints excluded: chain B residue 1131 LYS Chi-restraints excluded: chain B residue 1188 SER Chi-restraints excluded: chain B residue 1215 LEU Chi-restraints excluded: chain B residue 1302 SER Chi-restraints excluded: chain B residue 1394 ASN Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1369 THR Chi-restraints excluded: chain C residue 1392 THR Chi-restraints excluded: chain C residue 1480 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 chunk 66 optimal weight: 0.3980 chunk 120 optimal weight: 0.1980 chunk 36 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1378 HIS A1546 GLN B1156 GLN C1296 GLN C1546 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 11203 Z= 0.206 Angle : 0.609 15.679 15185 Z= 0.317 Chirality : 0.045 0.261 1720 Planarity : 0.004 0.048 1921 Dihedral : 5.481 29.328 1477 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.03 % Allowed : 14.73 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.23), residues: 1383 helix: 0.59 (1.14), residues: 33 sheet: 0.68 (0.22), residues: 619 loop : -1.56 (0.21), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1197 HIS 0.004 0.001 HIS A1378 PHE 0.011 0.002 PHE B1507 TYR 0.017 0.001 TYR A1358 ARG 0.001 0.000 ARG B1401 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 125 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1333 ASN cc_start: 0.7567 (t0) cc_final: 0.7222 (t0) REVERT: B 1113 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7331 (mt-10) REVERT: B 1375 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7554 (tm130) REVERT: B 1495 MET cc_start: 0.8271 (tpp) cc_final: 0.8061 (tpp) REVERT: C 1138 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7641 (ttp) outliers start: 38 outliers final: 19 residues processed: 154 average time/residue: 1.0796 time to fit residues: 178.3894 Evaluate side-chains 142 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 120 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1394 ASN Chi-restraints excluded: chain A residue 1483 ASP Chi-restraints excluded: chain A residue 1539 CYS Chi-restraints excluded: chain A residue 1552 ILE Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain B residue 1113 GLU Chi-restraints excluded: chain B residue 1131 LYS Chi-restraints excluded: chain B residue 1188 SER Chi-restraints excluded: chain B residue 1193 CYS Chi-restraints excluded: chain B residue 1215 LEU Chi-restraints excluded: chain B residue 1302 SER Chi-restraints excluded: chain B residue 1375 GLN Chi-restraints excluded: chain B residue 1394 ASN Chi-restraints excluded: chain B residue 1408 THR Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1138 MET Chi-restraints excluded: chain C residue 1277 GLU Chi-restraints excluded: chain C residue 1369 THR Chi-restraints excluded: chain C residue 1392 THR Chi-restraints excluded: chain C residue 1480 VAL Chi-restraints excluded: chain C residue 1516 THR Chi-restraints excluded: chain C residue 1531 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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: