Starting phenix.real_space_refine on Sat Aug 23 09:24:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jkd_36368/08_2025/8jkd_36368.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jkd_36368/08_2025/8jkd_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 { model { file = "/net/cci-nas-00/data/ceres_data/8jkd_36368/08_2025/8jkd_36368.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jkd_36368/08_2025/8jkd_36368.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jkd_36368/08_2025/8jkd_36368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jkd_36368/08_2025/8jkd_36368.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.67, per 1000 atoms: 0.24 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 - 3.00 Amino acid : True - 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: 1.01 Conformation dependent library (CDL) restraints added in 301.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.37 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: 1.70 Time building geometry restraints manager: 1.34 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: 0.00 - 1.80: 14814 1.80 - 3.61: 326 3.61 - 5.41: 37 5.41 - 7.22: 6 7.22 - 9.02: 2 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 3.040 nonbonded pdb=" OG SER A1302 " pdb=" OE1 GLU A1388 " model vdw 2.218 3.040 nonbonded pdb=" OE1 GLN C1319 " pdb=" OH TYR C1321 " model vdw 2.234 3.040 nonbonded pdb=" O ARG A1189 " pdb=" N GLY A1202 " model vdw 2.235 3.120 nonbonded pdb=" OG1 THR A1164 " pdb=" O GLY A1167 " model vdw 2.252 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 4.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.120 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 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:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.760 ------------------------------------------------------------------------------- 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 11238 Z= 0.136 Angle : 0.639 9.025 15255 Z= 0.343 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 : 7.32 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG B1401 TYR 0.013 0.001 TYR A1359 PHE 0.028 0.002 PHE B1447 TRP 0.031 0.002 TRP A1197 HIS 0.004 0.001 HIS C1469 Details of bonding type rmsd covalent geometry : bond 0.00307 (11203) covalent geometry : angle 0.63158 (15185) SS BOND : bond 0.00306 ( 35) SS BOND : angle 1.57476 ( 70) hydrogen bonds : bond 0.10344 ( 258) hydrogen bonds : angle 6.27023 ( 684) *********************** 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 to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.477 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: 0.6082 time to fit residues: 108.9342 Evaluate side-chains 122 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** A1377 ASN A1378 HIS A1546 GLN B1156 GLN C1245 GLN C1296 GLN C1394 ASN C1546 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.156181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.126361 restraints weight = 11452.345| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.66 r_work: 0.3295 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11238 Z= 0.158 Angle : 0.645 12.475 15255 Z= 0.337 Chirality : 0.047 0.244 1720 Planarity : 0.005 0.051 1921 Dihedral : 5.683 21.348 1477 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 1.99 % Allowed : 8.52 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.23), residues: 1383 helix: 0.68 (1.13), residues: 33 sheet: 0.55 (0.22), residues: 628 loop : -1.53 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1115 TYR 0.016 0.002 TYR B1359 PHE 0.015 0.002 PHE A1216 TRP 0.023 0.002 TRP A1197 HIS 0.004 0.001 HIS B1322 Details of bonding type rmsd covalent geometry : bond 0.00379 (11203) covalent geometry : angle 0.63812 (15185) SS BOND : bond 0.00333 ( 35) SS BOND : angle 1.53221 ( 70) hydrogen bonds : bond 0.03538 ( 258) hydrogen bonds : angle 5.43354 ( 684) *********************** 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 157 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.308 Fit side-chains REVERT: A 1191 TRP cc_start: 0.6817 (p-90) cc_final: 0.5453 (m-90) REVERT: A 1387 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8945 (mt) REVERT: B 1306 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8327 (mtpm) outliers start: 25 outliers final: 5 residues processed: 145 average time/residue: 0.6645 time to fit residues: 102.9340 Evaluate side-chains 127 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1387 ILE Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain B residue 1302 SER Chi-restraints excluded: chain B residue 1306 LYS Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1369 THR Chi-restraints excluded: chain C residue 1392 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 92 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 C1377 ASN C1394 ASN C1554 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.154347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.124513 restraints weight = 11596.014| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.66 r_work: 0.3268 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11238 Z= 0.183 Angle : 0.666 12.232 15255 Z= 0.349 Chirality : 0.047 0.254 1720 Planarity : 0.005 0.049 1921 Dihedral : 5.813 23.395 1477 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.39 % Allowed : 12.02 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.22), residues: 1383 helix: 0.56 (1.13), residues: 33 sheet: 0.63 (0.22), residues: 620 loop : -1.57 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1525 TYR 0.013 0.002 TYR B1150 PHE 0.014 0.002 PHE C1381 TRP 0.021 0.002 TRP A1197 HIS 0.006 0.001 HIS A1378 Details of bonding type rmsd covalent geometry : bond 0.00441 (11203) covalent geometry : angle 0.66078 (15185) SS BOND : bond 0.00425 ( 35) SS BOND : angle 1.42195 ( 70) hydrogen bonds : bond 0.03701 ( 258) hydrogen bonds : angle 5.41035 ( 684) *********************** 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 154 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.464 Fit side-chains REVERT: A 1138 MET cc_start: 0.8492 (mtp) cc_final: 0.8259 (ttm) REVERT: A 1333 ASN cc_start: 0.7983 (m-40) cc_final: 0.7445 (t0) REVERT: A 1387 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8890 (mt) REVERT: A 1412 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7654 (p0) REVERT: B 1306 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8321 (mtpm) REVERT: C 1387 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8866 (mp) outliers start: 30 outliers final: 11 residues processed: 145 average time/residue: 0.6991 time to fit residues: 108.2428 Evaluate side-chains 131 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1387 ILE Chi-restraints excluded: chain A residue 1412 ASP Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain B residue 1131 LYS 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 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 1480 VAL Chi-restraints excluded: chain C residue 1531 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 81 optimal weight: 0.0270 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1194 ASN A1378 HIS A1546 GLN B1156 GLN B1182 HIS C1296 GLN C1394 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.155584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.125892 restraints weight = 11569.370| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.66 r_work: 0.3290 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 11238 Z= 0.146 Angle : 0.620 11.435 15255 Z= 0.323 Chirality : 0.045 0.266 1720 Planarity : 0.005 0.049 1921 Dihedral : 5.574 29.133 1477 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.39 % Allowed : 14.09 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.23), residues: 1383 helix: 0.53 (1.12), residues: 33 sheet: 0.67 (0.22), residues: 618 loop : -1.50 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1115 TYR 0.018 0.002 TYR B1359 PHE 0.012 0.002 PHE B1507 TRP 0.023 0.002 TRP A1197 HIS 0.005 0.001 HIS A1378 Details of bonding type rmsd covalent geometry : bond 0.00352 (11203) covalent geometry : angle 0.61361 (15185) SS BOND : bond 0.00368 ( 35) SS BOND : angle 1.44848 ( 70) hydrogen bonds : bond 0.03323 ( 258) hydrogen bonds : angle 5.22804 ( 684) *********************** 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 155 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.303 Fit side-chains REVERT: A 1232 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: A 1333 ASN cc_start: 0.7864 (t0) cc_final: 0.7373 (t0) REVERT: A 1387 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8877 (mt) REVERT: A 1412 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7554 (p0) REVERT: A 1545 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7779 (mt-10) REVERT: B 1306 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8268 (mtpm) outliers start: 30 outliers final: 11 residues processed: 147 average time/residue: 0.6893 time to fit residues: 108.3851 Evaluate side-chains 137 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1232 GLU Chi-restraints excluded: chain A residue 1387 ILE Chi-restraints excluded: chain A residue 1412 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 1302 SER Chi-restraints excluded: chain B residue 1306 LYS 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 1480 VAL 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 125 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 66 optimal weight: 0.1980 chunk 95 optimal weight: 0.0020 chunk 82 optimal weight: 0.0670 chunk 10 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 overall best weight: 0.3726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1378 HIS A1546 GLN C1296 GLN C1394 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.154007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.121869 restraints weight = 11006.852| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.74 r_work: 0.3212 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 11238 Z= 0.109 Angle : 0.568 11.561 15255 Z= 0.295 Chirality : 0.044 0.262 1720 Planarity : 0.004 0.046 1921 Dihedral : 5.098 26.791 1477 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.15 % Allowed : 15.68 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.23), residues: 1383 helix: 0.60 (1.11), residues: 33 sheet: 0.68 (0.22), residues: 615 loop : -1.37 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B1401 TYR 0.020 0.001 TYR A1358 PHE 0.017 0.002 PHE A1216 TRP 0.025 0.001 TRP A1197 HIS 0.004 0.001 HIS B1322 Details of bonding type rmsd covalent geometry : bond 0.00260 (11203) covalent geometry : angle 0.56069 (15185) SS BOND : bond 0.00385 ( 35) SS BOND : angle 1.43442 ( 70) hydrogen bonds : bond 0.02932 ( 258) hydrogen bonds : angle 4.97908 ( 684) *********************** 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 160 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1232 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8094 (mt-10) REVERT: A 1333 ASN cc_start: 0.7688 (t0) cc_final: 0.7116 (t0) REVERT: A 1545 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7629 (tt0) REVERT: B 1156 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.7642 (mp10) REVERT: B 1306 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8203 (mtpm) outliers start: 27 outliers final: 9 residues processed: 152 average time/residue: 0.6961 time to fit residues: 113.3393 Evaluate side-chains 135 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1232 GLU 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 1156 GLN Chi-restraints excluded: chain B residue 1302 SER Chi-restraints excluded: chain B residue 1306 LYS 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 1531 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 57 optimal weight: 0.4980 chunk 69 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 0.0770 chunk 40 optimal weight: 6.9990 chunk 110 optimal weight: 0.0010 chunk 51 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.4944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1378 HIS A1546 GLN C1296 GLN C1394 ASN C1546 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.158013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.128287 restraints weight = 11565.130| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.67 r_work: 0.3324 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 11238 Z= 0.123 Angle : 0.610 17.672 15255 Z= 0.314 Chirality : 0.044 0.271 1720 Planarity : 0.004 0.046 1921 Dihedral : 5.115 26.220 1477 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.31 % Allowed : 16.64 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.23), residues: 1383 helix: 0.73 (1.12), residues: 33 sheet: 0.70 (0.22), residues: 615 loop : -1.30 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C1115 TYR 0.020 0.001 TYR A1358 PHE 0.012 0.002 PHE A1216 TRP 0.026 0.001 TRP A1197 HIS 0.005 0.001 HIS A1378 Details of bonding type rmsd covalent geometry : bond 0.00302 (11203) covalent geometry : angle 0.59864 (15185) SS BOND : bond 0.00463 ( 35) SS BOND : angle 1.80834 ( 70) hydrogen bonds : bond 0.03058 ( 258) hydrogen bonds : angle 5.04446 ( 684) *********************** 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 159 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1232 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.7998 (mt-10) REVERT: A 1333 ASN cc_start: 0.7643 (t0) cc_final: 0.7195 (t0) REVERT: A 1545 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7763 (tt0) REVERT: B 1156 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.7643 (mp10) REVERT: B 1306 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8233 (mtpm) REVERT: C 1465 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7790 (mptt) outliers start: 29 outliers final: 15 residues processed: 149 average time/residue: 0.6989 time to fit residues: 111.4515 Evaluate side-chains 140 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1232 GLU Chi-restraints excluded: chain A residue 1477 THR 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 1156 GLN Chi-restraints excluded: chain B residue 1193 CYS Chi-restraints excluded: chain B residue 1302 SER Chi-restraints excluded: chain B residue 1306 LYS 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 1531 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 93 optimal weight: 0.0020 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1322 HIS A1378 HIS A1546 GLN C1296 GLN C1394 ASN C1546 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.152005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.119609 restraints weight = 10896.330| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.73 r_work: 0.3179 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 11238 Z= 0.142 Angle : 0.636 16.242 15255 Z= 0.329 Chirality : 0.045 0.260 1720 Planarity : 0.004 0.046 1921 Dihedral : 5.322 26.088 1477 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.63 % Allowed : 16.56 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.23), residues: 1383 helix: 0.73 (1.13), residues: 33 sheet: 0.65 (0.22), residues: 621 loop : -1.31 (0.21), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1525 TYR 0.022 0.002 TYR A1358 PHE 0.013 0.002 PHE C1216 TRP 0.027 0.002 TRP A1197 HIS 0.006 0.001 HIS A1378 Details of bonding type rmsd covalent geometry : bond 0.00348 (11203) covalent geometry : angle 0.62451 (15185) SS BOND : bond 0.00452 ( 35) SS BOND : angle 1.89681 ( 70) hydrogen bonds : bond 0.03256 ( 258) hydrogen bonds : angle 5.12315 ( 684) *********************** 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 159 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1232 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8053 (mt-10) REVERT: A 1333 ASN cc_start: 0.7775 (t0) cc_final: 0.7237 (t0) REVERT: A 1486 ASP cc_start: 0.7680 (m-30) cc_final: 0.7052 (t0) REVERT: A 1545 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7643 (tt0) REVERT: B 1156 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.7686 (mp10) REVERT: B 1306 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8266 (mtpm) REVERT: B 1433 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8625 (mtm) outliers start: 33 outliers final: 14 residues processed: 149 average time/residue: 0.7008 time to fit residues: 111.6016 Evaluate side-chains 141 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1232 GLU 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 1156 GLN Chi-restraints excluded: chain B residue 1193 CYS Chi-restraints excluded: chain B residue 1302 SER Chi-restraints excluded: chain B residue 1306 LYS Chi-restraints excluded: chain B residue 1433 MET 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 1480 VAL 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 118 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 C1394 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.152262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.122662 restraints weight = 11503.547| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.63 r_work: 0.3254 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 11238 Z= 0.314 Angle : 0.834 20.031 15255 Z= 0.434 Chirality : 0.053 0.333 1720 Planarity : 0.005 0.048 1921 Dihedral : 6.265 26.812 1477 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.47 % Allowed : 17.12 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.22), residues: 1383 helix: 0.22 (1.08), residues: 33 sheet: 0.58 (0.22), residues: 612 loop : -1.49 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1525 TYR 0.023 0.003 TYR A1358 PHE 0.022 0.003 PHE C1216 TRP 0.022 0.003 TRP A1197 HIS 0.009 0.002 HIS A1378 Details of bonding type rmsd covalent geometry : bond 0.00770 (11203) covalent geometry : angle 0.81990 (15185) SS BOND : bond 0.00672 ( 35) SS BOND : angle 2.40217 ( 70) hydrogen bonds : bond 0.04246 ( 258) hydrogen bonds : angle 5.49729 ( 684) *********************** 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 149 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 1232 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8028 (mt-10) REVERT: A 1333 ASN cc_start: 0.7999 (t0) cc_final: 0.7508 (t0) REVERT: A 1412 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7797 (p0) REVERT: A 1486 ASP cc_start: 0.7713 (m-30) cc_final: 0.7095 (t0) REVERT: A 1545 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7691 (mt-10) REVERT: B 1433 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8829 (mtm) REVERT: C 1499 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6554 (mp) outliers start: 31 outliers final: 18 residues processed: 143 average time/residue: 0.7183 time to fit residues: 110.1754 Evaluate side-chains 136 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1232 GLU Chi-restraints excluded: chain A residue 1412 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 1156 GLN Chi-restraints excluded: chain B residue 1193 CYS Chi-restraints excluded: chain B residue 1215 LEU Chi-restraints excluded: chain B residue 1220 MET Chi-restraints excluded: chain B residue 1302 SER Chi-restraints excluded: chain B residue 1408 THR Chi-restraints excluded: chain B residue 1433 MET 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 1480 VAL Chi-restraints excluded: chain C residue 1499 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 0.9980 chunk 127 optimal weight: 0.2980 chunk 103 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3766 r_free = 0.3766 target = 0.155792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.126415 restraints weight = 11337.732| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.62 r_work: 0.3306 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 11238 Z= 0.150 Angle : 0.664 17.027 15255 Z= 0.343 Chirality : 0.046 0.279 1720 Planarity : 0.005 0.047 1921 Dihedral : 5.662 26.231 1477 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.99 % Allowed : 17.75 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.23), residues: 1383 helix: 0.47 (1.10), residues: 33 sheet: 0.59 (0.22), residues: 617 loop : -1.47 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1155 TYR 0.025 0.002 TYR A1358 PHE 0.013 0.002 PHE B1507 TRP 0.031 0.002 TRP A1197 HIS 0.005 0.001 HIS A1378 Details of bonding type rmsd covalent geometry : bond 0.00364 (11203) covalent geometry : angle 0.65246 (15185) SS BOND : bond 0.00482 ( 35) SS BOND : angle 1.90923 ( 70) hydrogen bonds : bond 0.03366 ( 258) hydrogen bonds : angle 5.29697 ( 684) *********************** 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 151 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1232 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8000 (mt-10) REVERT: A 1333 ASN cc_start: 0.7774 (t0) cc_final: 0.7260 (t0) REVERT: A 1486 ASP cc_start: 0.7662 (m-30) cc_final: 0.7101 (t0) REVERT: A 1545 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7764 (tt0) REVERT: B 1220 MET cc_start: 0.8796 (ttt) cc_final: 0.8556 (ttp) REVERT: B 1433 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8672 (mtm) REVERT: C 1465 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7816 (mptt) REVERT: C 1499 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6506 (mp) outliers start: 25 outliers final: 16 residues processed: 142 average time/residue: 0.6936 time to fit residues: 105.7603 Evaluate side-chains 138 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1232 GLU 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 1193 CYS Chi-restraints excluded: chain B residue 1215 LEU Chi-restraints excluded: chain B residue 1302 SER Chi-restraints excluded: chain B residue 1433 MET 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 1531 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 131 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 89 optimal weight: 0.1980 chunk 10 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3778 r_free = 0.3778 target = 0.156897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.127526 restraints weight = 11498.757| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.63 r_work: 0.3325 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 11238 Z= 0.136 Angle : 0.643 16.446 15255 Z= 0.331 Chirality : 0.045 0.268 1720 Planarity : 0.004 0.047 1921 Dihedral : 5.423 25.505 1477 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.91 % Allowed : 18.07 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.23), residues: 1383 helix: 0.61 (1.11), residues: 33 sheet: 0.59 (0.22), residues: 618 loop : -1.38 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1115 TYR 0.026 0.002 TYR A1358 PHE 0.013 0.002 PHE B1507 TRP 0.038 0.002 TRP A1197 HIS 0.005 0.001 HIS A1378 Details of bonding type rmsd covalent geometry : bond 0.00331 (11203) covalent geometry : angle 0.63242 (15185) SS BOND : bond 0.00463 ( 35) SS BOND : angle 1.81687 ( 70) hydrogen bonds : bond 0.03233 ( 258) hydrogen bonds : angle 5.17946 ( 684) ********************** 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 144 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1232 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: A 1333 ASN cc_start: 0.7789 (t0) cc_final: 0.7273 (t0) REVERT: A 1486 ASP cc_start: 0.7627 (m-30) cc_final: 0.7100 (t0) REVERT: A 1545 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7735 (mt-10) REVERT: B 1220 MET cc_start: 0.8791 (ttt) cc_final: 0.8537 (ttp) REVERT: C 1465 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7789 (mptt) REVERT: C 1499 LEU cc_start: 0.6904 (OUTLIER) cc_final: 0.6532 (mp) outliers start: 24 outliers final: 15 residues processed: 137 average time/residue: 0.5687 time to fit residues: 83.7281 Evaluate side-chains 134 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1232 GLU 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 1193 CYS Chi-restraints excluded: chain B residue 1215 LEU Chi-restraints excluded: chain B residue 1302 SER 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 1531 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 2 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1378 HIS A1546 GLN C1394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.156396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.126955 restraints weight = 11381.485| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.63 r_work: 0.3314 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 11238 Z= 0.152 Angle : 0.667 16.661 15255 Z= 0.343 Chirality : 0.046 0.272 1720 Planarity : 0.004 0.047 1921 Dihedral : 5.539 25.674 1477 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.99 % Allowed : 18.15 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.23), residues: 1383 helix: 0.59 (1.11), residues: 33 sheet: 0.55 (0.22), residues: 615 loop : -1.32 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1115 TYR 0.026 0.002 TYR A1358 PHE 0.013 0.002 PHE B1507 TRP 0.034 0.002 TRP A1197 HIS 0.006 0.001 HIS A1378 Details of bonding type rmsd covalent geometry : bond 0.00371 (11203) covalent geometry : angle 0.65612 (15185) SS BOND : bond 0.00475 ( 35) SS BOND : angle 1.85748 ( 70) hydrogen bonds : bond 0.03344 ( 258) hydrogen bonds : angle 5.20747 ( 684) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4007.33 seconds wall clock time: 69 minutes 10.45 seconds (4150.45 seconds total)