Starting phenix.real_space_refine on Sat Jul 20 14:23:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkd_36368/07_2024/8jkd_36368.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkd_36368/07_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_36368/07_2024/8jkd_36368.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkd_36368/07_2024/8jkd_36368.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkd_36368/07_2024/8jkd_36368.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkd_36368/07_2024/8jkd_36368.cif" } 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-5388/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: 7.19, per 1000 atoms: 0.66 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: 3.89 Conformation dependent library (CDL) restraints added in 2.2 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: 1.48 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: 3.31 Time building geometry restraints manager: 4.37 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: 5.470 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 33.150 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 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:13.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.950 ------------------------------------------------------------------------------- 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 : 1.233 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: 1.3069 time to fit residues: 234.5326 Evaluate side-chains 122 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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 : 1.244 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: 1.4403 time to fit residues: 223.9010 Evaluate side-chains 131 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 : 1.330 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: 1.3856 time to fit residues: 227.4501 Evaluate side-chains 139 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 1.236 ------------------------------------------------------------------------------- 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 : 1.322 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: 1.3690 time to fit residues: 226.2321 Evaluate side-chains 142 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 120 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1378 HIS A1546 GLN B1156 GLN B1182 HIS C1296 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 11203 Z= 0.408 Angle : 0.747 18.278 15185 Z= 0.391 Chirality : 0.050 0.303 1720 Planarity : 0.005 0.049 1921 Dihedral : 6.146 28.198 1477 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 3.42 % Allowed : 15.92 % Favored : 80.65 % 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: -0.75 (0.22), residues: 1383 helix: 0.31 (1.10), residues: 33 sheet: 0.60 (0.22), residues: 616 loop : -1.58 (0.20), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1197 HIS 0.008 0.001 HIS A1378 PHE 0.018 0.003 PHE C1381 TYR 0.021 0.002 TYR A1358 ARG 0.004 0.000 ARG C1525 *********************** REFINEMENT MACRO_CYCLE 5 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 168 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 125 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1333 ASN cc_start: 0.7727 (t0) cc_final: 0.7419 (t0) REVERT: A 1412 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7271 (p0) REVERT: C 1467 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7013 (mtp85) REVERT: C 1499 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6585 (mp) outliers start: 43 outliers final: 23 residues processed: 157 average time/residue: 1.2383 time to fit residues: 209.8561 Evaluate side-chains 146 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1093 VAL 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 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 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 1394 ASN Chi-restraints excluded: chain B residue 1408 THR Chi-restraints excluded: chain B residue 1483 ASP Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1124 VAL 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 1467 ARG Chi-restraints excluded: chain C residue 1480 VAL Chi-restraints excluded: chain C residue 1499 LEU Chi-restraints excluded: chain C residue 1516 THR Chi-restraints excluded: chain C residue 1529 LYS Chi-restraints excluded: chain C residue 1531 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 78 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 134 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.0270 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 11203 Z= 0.208 Angle : 0.615 16.046 15185 Z= 0.320 Chirality : 0.045 0.285 1720 Planarity : 0.004 0.048 1921 Dihedral : 5.552 26.439 1477 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.18 % Allowed : 17.04 % Favored : 79.78 % 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: -0.67 (0.22), residues: 1383 helix: 0.48 (1.11), residues: 33 sheet: 0.64 (0.22), residues: 613 loop : -1.50 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1197 HIS 0.004 0.001 HIS A1378 PHE 0.012 0.002 PHE B1507 TYR 0.021 0.001 TYR A1358 ARG 0.002 0.000 ARG A1401 *********************** REFINEMENT MACRO_CYCLE 6 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 166 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 126 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1140 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8597 (tp) REVERT: A 1232 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7648 (mt-10) REVERT: A 1333 ASN cc_start: 0.7449 (t0) cc_final: 0.7184 (t0) REVERT: A 1486 ASP cc_start: 0.7261 (m-30) cc_final: 0.6923 (t0) REVERT: B 1495 MET cc_start: 0.8297 (tpp) cc_final: 0.8056 (tpp) REVERT: C 1465 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7694 (mptt) REVERT: C 1499 LEU cc_start: 0.6798 (OUTLIER) cc_final: 0.6452 (mp) outliers start: 40 outliers final: 23 residues processed: 159 average time/residue: 1.3147 time to fit residues: 225.4090 Evaluate side-chains 149 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 122 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1227 GLU Chi-restraints excluded: chain A residue 1232 GLU 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 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 1394 ASN Chi-restraints excluded: chain B residue 1408 THR Chi-restraints excluded: chain B residue 1462 ILE 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 1392 THR Chi-restraints excluded: chain C residue 1465 LYS Chi-restraints excluded: chain C residue 1480 VAL Chi-restraints excluded: chain C residue 1499 LEU Chi-restraints excluded: chain C residue 1516 THR Chi-restraints excluded: chain C residue 1529 LYS Chi-restraints excluded: chain C residue 1531 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 B1375 GLN C1296 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1553 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= 0.235 Angle : 0.638 15.841 15185 Z= 0.330 Chirality : 0.045 0.284 1720 Planarity : 0.004 0.048 1921 Dihedral : 5.551 25.599 1477 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.11 % Allowed : 17.36 % Favored : 79.54 % 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: -0.63 (0.22), residues: 1383 helix: 0.59 (1.13), residues: 33 sheet: 0.65 (0.22), residues: 611 loop : -1.46 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1197 HIS 0.006 0.001 HIS A1378 PHE 0.012 0.002 PHE C1381 TYR 0.023 0.002 TYR A1358 ARG 0.002 0.000 ARG A1401 *********************** REFINEMENT MACRO_CYCLE 7 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 168 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 129 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1227 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7579 (pt0) REVERT: A 1232 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7628 (mt-10) REVERT: A 1333 ASN cc_start: 0.7430 (t0) cc_final: 0.7183 (t0) REVERT: A 1412 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7062 (p0) REVERT: A 1486 ASP cc_start: 0.7159 (m-30) cc_final: 0.6850 (t0) REVERT: B 1306 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7983 (mtpm) REVERT: B 1375 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7668 (tm130) REVERT: C 1465 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7682 (mptt) REVERT: C 1499 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6502 (mp) outliers start: 39 outliers final: 23 residues processed: 160 average time/residue: 1.3135 time to fit residues: 226.1020 Evaluate side-chains 155 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 125 time to evaluate : 1.310 ------------------------------------------------------------------------------- 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 1227 GLU Chi-restraints excluded: chain A residue 1232 GLU 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 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 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 1306 LYS 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 B residue 1462 ILE Chi-restraints excluded: chain B residue 1483 ASP Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1124 VAL 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 1465 LYS Chi-restraints excluded: chain C residue 1480 VAL Chi-restraints excluded: chain C residue 1499 LEU Chi-restraints excluded: chain C residue 1529 LYS Chi-restraints excluded: chain C residue 1531 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 121 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: ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1378 HIS A1546 GLN B1156 GLN B1375 GLN C1296 GLN C1394 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 11203 Z= 0.321 Angle : 0.705 17.726 15185 Z= 0.366 Chirality : 0.048 0.290 1720 Planarity : 0.005 0.051 1921 Dihedral : 5.927 35.334 1477 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 3.26 % Allowed : 17.44 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.68 (0.22), residues: 1383 helix: 0.48 (1.12), residues: 33 sheet: 0.58 (0.22), residues: 617 loop : -1.47 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1197 HIS 0.007 0.001 HIS A1378 PHE 0.015 0.002 PHE C1381 TYR 0.023 0.002 TYR A1358 ARG 0.003 0.000 ARG C1115 *********************** REFINEMENT MACRO_CYCLE 8 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: 41 poor density : 122 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1232 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7640 (mt-10) REVERT: A 1333 ASN cc_start: 0.7538 (t0) cc_final: 0.7251 (t0) REVERT: A 1412 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7214 (p0) REVERT: A 1486 ASP cc_start: 0.7197 (m-30) cc_final: 0.6850 (t0) REVERT: B 1129 GLU cc_start: 0.4175 (OUTLIER) cc_final: 0.3896 (pp20) REVERT: B 1306 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8122 (mtpm) REVERT: C 1465 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7665 (mptt) REVERT: C 1499 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6551 (mp) outliers start: 41 outliers final: 24 residues processed: 155 average time/residue: 1.3728 time to fit residues: 228.3066 Evaluate side-chains 150 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 120 time to evaluate : 1.161 ------------------------------------------------------------------------------- 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 1232 GLU Chi-restraints excluded: chain A residue 1394 ASN Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1412 ASP 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 1129 GLU 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 1306 LYS Chi-restraints excluded: chain B residue 1394 ASN Chi-restraints excluded: chain B residue 1408 THR Chi-restraints excluded: chain B residue 1462 ILE Chi-restraints excluded: chain B residue 1483 ASP Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1124 VAL 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 1465 LYS Chi-restraints excluded: chain C residue 1480 VAL Chi-restraints excluded: chain C residue 1499 LEU Chi-restraints excluded: chain C residue 1529 LYS Chi-restraints excluded: chain C residue 1531 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 B1375 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 11203 Z= 0.247 Angle : 0.659 16.678 15185 Z= 0.341 Chirality : 0.046 0.285 1720 Planarity : 0.005 0.050 1921 Dihedral : 5.704 36.410 1477 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.63 % Allowed : 18.23 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.69 (0.22), residues: 1383 helix: 0.52 (1.12), residues: 33 sheet: 0.56 (0.22), residues: 614 loop : -1.46 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1197 HIS 0.005 0.001 HIS A1378 PHE 0.012 0.002 PHE B1507 TYR 0.024 0.002 TYR A1358 ARG 0.003 0.000 ARG C1115 *********************** REFINEMENT MACRO_CYCLE 9 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 158 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 125 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1129 GLU cc_start: 0.5691 (OUTLIER) cc_final: 0.4622 (pp20) REVERT: A 1232 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7638 (mt-10) REVERT: A 1333 ASN cc_start: 0.7411 (t0) cc_final: 0.7147 (t0) REVERT: A 1486 ASP cc_start: 0.7222 (m-30) cc_final: 0.6895 (t0) REVERT: B 1129 GLU cc_start: 0.4101 (OUTLIER) cc_final: 0.3845 (pp20) REVERT: B 1156 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7134 (mp10) REVERT: B 1306 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8059 (mtpm) REVERT: B 1375 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7662 (tm130) REVERT: C 1465 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7672 (mptt) REVERT: C 1499 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6479 (mp) outliers start: 33 outliers final: 23 residues processed: 151 average time/residue: 1.3517 time to fit residues: 219.3796 Evaluate side-chains 151 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 120 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1129 GLU Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1232 GLU 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 1129 GLU Chi-restraints excluded: chain B residue 1156 GLN 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 1306 LYS 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 B residue 1462 ILE Chi-restraints excluded: chain B residue 1483 ASP Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1124 VAL 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 1465 LYS Chi-restraints excluded: chain C residue 1480 VAL Chi-restraints excluded: chain C residue 1499 LEU Chi-restraints excluded: chain C residue 1529 LYS Chi-restraints excluded: chain C residue 1531 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 11 optimal weight: 0.0670 chunk 85 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 overall best weight: 1.1324 ------------------------------------------------------------------------------- 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 C1296 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 11203 Z= 0.297 Angle : 0.694 17.101 15185 Z= 0.358 Chirality : 0.047 0.287 1720 Planarity : 0.005 0.050 1921 Dihedral : 5.880 36.558 1477 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.55 % Allowed : 18.55 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.67 (0.23), residues: 1383 helix: 0.49 (1.11), residues: 33 sheet: 0.54 (0.22), residues: 620 loop : -1.43 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1197 HIS 0.007 0.001 HIS A1378 PHE 0.015 0.002 PHE B1381 TYR 0.025 0.002 TYR A1358 ARG 0.003 0.000 ARG C1115 ********************** REFINEMENT MACRO_CYCLE 10 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 153 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 121 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1129 GLU cc_start: 0.5710 (OUTLIER) cc_final: 0.4625 (pp20) REVERT: A 1232 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7637 (mt-10) REVERT: A 1333 ASN cc_start: 0.7509 (t0) cc_final: 0.7218 (t0) REVERT: A 1412 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.7077 (p0) REVERT: A 1486 ASP cc_start: 0.7225 (m-30) cc_final: 0.6894 (t0) REVERT: B 1129 GLU cc_start: 0.4153 (OUTLIER) cc_final: 0.3883 (pp20) REVERT: B 1306 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8091 (mtpm) REVERT: C 1465 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7665 (mptt) REVERT: C 1499 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6514 (mp) outliers start: 32 outliers final: 24 residues processed: 146 average time/residue: 1.3584 time to fit residues: 213.2652 Evaluate side-chains 148 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 117 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1129 GLU Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1232 GLU 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 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 1129 GLU 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 1306 LYS Chi-restraints excluded: chain B residue 1394 ASN Chi-restraints excluded: chain B residue 1408 THR Chi-restraints excluded: chain B residue 1462 ILE Chi-restraints excluded: chain B residue 1483 ASP Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1124 VAL 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 1408 THR Chi-restraints excluded: chain C residue 1465 LYS Chi-restraints excluded: chain C residue 1480 VAL Chi-restraints excluded: chain C residue 1499 LEU Chi-restraints excluded: chain C residue 1529 LYS Chi-restraints excluded: chain C residue 1531 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 C1296 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.150049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.118765 restraints weight = 10655.849| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.60 r_work: 0.3168 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 11203 Z= 0.252 Angle : 0.664 16.534 15185 Z= 0.342 Chirality : 0.046 0.278 1720 Planarity : 0.005 0.050 1921 Dihedral : 5.729 36.612 1477 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.87 % Allowed : 18.55 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.68 (0.23), residues: 1383 helix: 0.58 (1.12), residues: 33 sheet: 0.55 (0.22), residues: 616 loop : -1.44 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A1197 HIS 0.006 0.001 HIS A1378 PHE 0.018 0.002 PHE A1216 TYR 0.026 0.002 TYR A1358 ARG 0.005 0.000 ARG C1115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4452.51 seconds wall clock time: 78 minutes 45.41 seconds (4725.41 seconds total)