Starting phenix.real_space_refine on Mon Jul 28 09:07:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fgf_31579/07_2025/7fgf_31579.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fgf_31579/07_2025/7fgf_31579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fgf_31579/07_2025/7fgf_31579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fgf_31579/07_2025/7fgf_31579.map" model { file = "/net/cci-nas-00/data/ceres_data/7fgf_31579/07_2025/7fgf_31579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fgf_31579/07_2025/7fgf_31579.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.096 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 102 5.16 5 C 6375 2.51 5 N 1713 2.21 5 O 1953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10143 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3381 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 18, 'TRANS': 413} Chain breaks: 6 Restraints were copied for chains: C, B Time building chain proxies: 6.50, per 1000 atoms: 0.64 Number of scatterers: 10143 At special positions: 0 Unit cell: (86.62, 84.79, 129.93, 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 102 16.00 O 1953 8.00 N 1713 7.00 C 6375 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 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=2.02 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 C1169 " - pdb=" SG CYS C1205 " distance=2.03 Simple disulfide: pdb=" SG CYS B1169 " - pdb=" SG CYS B1205 " distance=2.03 Simple disulfide: pdb=" SG CYS C1173 " - pdb=" SG CYS C1207 " distance=2.03 Simple disulfide: pdb=" SG CYS B1173 " - pdb=" SG CYS B1207 " distance=2.03 Simple disulfide: pdb=" SG CYS C1175 " - pdb=" SG CYS C1180 " distance=2.03 Simple disulfide: pdb=" SG CYS B1175 " - pdb=" SG CYS B1180 " distance=2.03 Simple disulfide: pdb=" SG CYS C1193 " - pdb=" SG CYS C1360 " distance=2.02 Simple disulfide: pdb=" SG CYS B1193 " - pdb=" SG CYS B1360 " distance=2.02 Simple disulfide: pdb=" SG CYS C1208 " - pdb=" SG CYS C1368 " distance=2.03 Simple disulfide: pdb=" SG CYS B1208 " - pdb=" SG CYS B1368 " distance=2.03 Simple disulfide: pdb=" SG CYS C1236 " - pdb=" SG CYS C1246 " distance=2.03 Simple disulfide: pdb=" SG CYS B1236 " - pdb=" SG CYS B1246 " distance=2.03 Simple disulfide: pdb=" SG CYS C1305 " - pdb=" SG CYS C1310 " distance=2.03 Simple disulfide: pdb=" SG CYS B1305 " - pdb=" SG CYS B1310 " distance=2.03 Simple disulfide: pdb=" SG CYS C1452 " - pdb=" SG CYS C1464 " distance=2.03 Simple disulfide: pdb=" SG CYS B1452 " - pdb=" SG CYS B1464 " distance=2.03 Simple disulfide: pdb=" SG CYS C1455 " - pdb=" SG CYS C1458 " distance=2.03 Simple disulfide: pdb=" SG CYS B1455 " - pdb=" SG CYS B1458 " distance=2.03 Simple disulfide: pdb=" SG CYS C1519 " - pdb=" SG CYS C1539 " distance=2.04 Simple disulfide: pdb=" SG CYS B1519 " - pdb=" SG CYS B1539 " distance=2.04 Simple disulfide: pdb=" SG CYS C1528 " - pdb=" SG CYS C1531 " distance=2.03 Simple disulfide: pdb=" SG CYS B1528 " - pdb=" SG CYS B1531 " distance=2.03 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: 2.54 Conformation dependent library (CDL) restraints added in 1.1 seconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2460 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 24 sheets defined 5.8% alpha, 45.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 1314 through 1318 removed outlier: 4.494A pdb=" N LEU A1318 " --> pdb=" O PRO A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1388 Processing helix chain 'A' and resid 1390 through 1394 removed outlier: 3.983A 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 1526 No H-bonds generated for 'chain 'A' and resid 1524 through 1526' Processing helix chain 'B' and resid 1314 through 1318 removed outlier: 4.494A pdb=" N LEU B1318 " --> pdb=" O PRO B1315 " (cutoff:3.500A) Processing helix chain 'B' and resid 1377 through 1388 Processing helix chain 'B' and resid 1390 through 1394 removed outlier: 3.984A 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 1526 No H-bonds generated for 'chain 'B' and resid 1524 through 1526' Processing helix chain 'C' and resid 1314 through 1318 removed outlier: 4.494A pdb=" N LEU C1318 " --> pdb=" O PRO C1315 " (cutoff:3.500A) Processing helix chain 'C' and resid 1377 through 1388 Processing helix chain 'C' and resid 1390 through 1394 removed outlier: 3.984A pdb=" N ASN C1394 " --> pdb=" O ASP C1390 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1390 through 1394' Processing helix chain 'C' and resid 1524 through 1526 No H-bonds generated for 'chain 'C' and resid 1524 through 1526' Processing sheet with id=AA1, first strand: chain 'A' and resid 1245 through 1248 removed outlier: 4.913A pdb=" N MET A1220 " --> pdb=" O SER A1152 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N SER A1152 " --> pdb=" O MET A1220 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL A1222 " --> pdb=" O TYR A1150 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TYR A1150 " --> pdb=" O VAL A1222 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TRP A1224 " --> pdb=" O PHE A1148 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE A1148 " --> pdb=" O TRP A1224 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL A1226 " --> pdb=" O PRO A1146 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TYR A1228 " --> pdb=" O TYR A1144 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TYR A1144 " --> pdb=" O TYR A1228 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS A1230 " --> pdb=" O GLN A1142 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLN A1142 " --> pdb=" O LYS A1230 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLU A1232 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU A1140 " --> pdb=" O GLU A1232 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE A1234 " --> pdb=" O MET A1138 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LEU A1140 " --> pdb=" O PRO A1417 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU A1413 " --> pdb=" O TYR A1144 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU A1411 " --> pdb=" O PRO A1146 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE A1148 " --> pdb=" O PRO A1409 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLN A1410 " --> pdb=" O VAL A1402 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL A1402 " --> pdb=" O GLN A1410 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASP A1412 " --> pdb=" O LYS A1400 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A1400 " --> pdb=" O ASP A1412 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LYS A1414 " --> pdb=" O HIS A1398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1297 through 1300 removed outlier: 4.439A pdb=" N MET A1220 " --> pdb=" O HIS A1282 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N MET A1220 " --> pdb=" O SER A1152 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N SER A1152 " --> pdb=" O MET A1220 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL A1222 " --> pdb=" O TYR A1150 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TYR A1150 " --> pdb=" O VAL A1222 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TRP A1224 " --> pdb=" O PHE A1148 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE A1148 " --> pdb=" O TRP A1224 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL A1226 " --> pdb=" O PRO A1146 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TYR A1228 " --> pdb=" O TYR A1144 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TYR A1144 " --> pdb=" O TYR A1228 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS A1230 " --> pdb=" O GLN A1142 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLN A1142 " --> pdb=" O LYS A1230 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLU A1232 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU A1140 " --> pdb=" O GLU A1232 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE A1234 " --> pdb=" O MET A1138 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR A1116 " --> pdb=" O VAL A1137 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N THR A1080 " --> pdb=" O GLY A1117 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL A1081 " --> pdb=" O THR A1477 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1086 through 1092 removed outlier: 3.730A pdb=" N GLY A1104 " --> pdb=" O VAL A1430 " (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 1319 through 1320 Processing sheet with id=AA6, first strand: chain 'A' and resid 1355 through 1359 Processing sheet with id=AA7, first strand: chain 'A' and resid 1487 through 1489 removed outlier: 6.735A pdb=" N SER A1463 " --> pdb=" O CYS A1452 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N CYS A1452 " --> pdb=" O SER A1463 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS A1465 " --> pdb=" O LEU A1450 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU A1450 " --> pdb=" O LYS A1465 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG A1467 " --> pdb=" O ALA A1448 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N GLU A1545 " --> pdb=" O CYS A1452 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N GLY A1454 " --> pdb=" O GLU A1545 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1480 through 1482 Processing sheet with id=AA9, first strand: chain 'B' and resid 1245 through 1248 removed outlier: 4.913A pdb=" N MET B1220 " --> pdb=" O SER B1152 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N SER B1152 " --> pdb=" O MET B1220 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL B1222 " --> pdb=" O TYR B1150 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TYR B1150 " --> pdb=" O VAL B1222 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TRP B1224 " --> pdb=" O PHE B1148 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE B1148 " --> pdb=" O TRP B1224 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL B1226 " --> pdb=" O PRO B1146 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N TYR B1228 " --> pdb=" O TYR B1144 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TYR B1144 " --> pdb=" O TYR B1228 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS B1230 " --> pdb=" O GLN B1142 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLN B1142 " --> pdb=" O LYS B1230 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU B1232 " --> pdb=" O LEU B1140 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU B1140 " --> pdb=" O GLU B1232 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE B1234 " --> pdb=" O MET B1138 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LEU B1140 " --> pdb=" O PRO B1417 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU B1413 " --> pdb=" O TYR B1144 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU B1411 " --> pdb=" O PRO B1146 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N PHE B1148 " --> pdb=" O PRO B1409 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN B1410 " --> pdb=" O VAL B1402 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL B1402 " --> pdb=" O GLN B1410 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASP B1412 " --> pdb=" O LYS B1400 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS B1400 " --> pdb=" O ASP B1412 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LYS B1414 " --> pdb=" O HIS B1398 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1297 through 1300 removed outlier: 4.440A pdb=" N MET B1220 " --> pdb=" O HIS B1282 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N MET B1220 " --> pdb=" O SER B1152 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N SER B1152 " --> pdb=" O MET B1220 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL B1222 " --> pdb=" O TYR B1150 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TYR B1150 " --> pdb=" O VAL B1222 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TRP B1224 " --> pdb=" O PHE B1148 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE B1148 " --> pdb=" O TRP B1224 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL B1226 " --> pdb=" O PRO B1146 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N TYR B1228 " --> pdb=" O TYR B1144 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TYR B1144 " --> pdb=" O TYR B1228 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS B1230 " --> pdb=" O GLN B1142 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLN B1142 " --> pdb=" O LYS B1230 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU B1232 " --> pdb=" O LEU B1140 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU B1140 " --> pdb=" O GLU B1232 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE B1234 " --> pdb=" O MET B1138 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR B1116 " --> pdb=" O VAL B1137 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N THR B1080 " --> pdb=" O GLY B1117 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL B1081 " --> pdb=" O THR B1477 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1086 through 1092 removed outlier: 3.730A pdb=" N GLY B1104 " --> pdb=" O VAL B1430 " (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 1319 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 1487 through 1489 removed outlier: 6.735A pdb=" N SER B1463 " --> pdb=" O CYS B1452 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N CYS B1452 " --> pdb=" O SER B1463 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS B1465 " --> pdb=" O LEU B1450 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU B1450 " --> pdb=" O LYS B1465 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG B1467 " --> pdb=" O ALA B1448 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N GLU B1545 " --> pdb=" O CYS B1452 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N GLY B1454 " --> pdb=" O GLU B1545 " (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 1245 through 1248 removed outlier: 4.913A pdb=" N MET C1220 " --> pdb=" O SER C1152 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N SER C1152 " --> pdb=" O MET C1220 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL C1222 " --> pdb=" O TYR C1150 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TYR C1150 " --> pdb=" O VAL C1222 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TRP C1224 " --> pdb=" O PHE C1148 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE C1148 " --> pdb=" O TRP C1224 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL C1226 " --> pdb=" O PRO C1146 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TYR C1228 " --> pdb=" O TYR C1144 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TYR C1144 " --> pdb=" O TYR C1228 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS C1230 " --> pdb=" O GLN C1142 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLN C1142 " --> pdb=" O LYS C1230 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLU C1232 " --> pdb=" O LEU C1140 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU C1140 " --> pdb=" O GLU C1232 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE C1234 " --> pdb=" O MET C1138 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LEU C1140 " --> pdb=" O PRO C1417 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU C1413 " --> pdb=" O TYR C1144 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU C1411 " --> pdb=" O PRO C1146 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE C1148 " --> pdb=" O PRO C1409 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN C1410 " --> pdb=" O VAL C1402 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL C1402 " --> pdb=" O GLN C1410 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASP C1412 " --> pdb=" O LYS C1400 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS C1400 " --> pdb=" O ASP C1412 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS C1414 " --> pdb=" O HIS C1398 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 1297 through 1300 removed outlier: 4.440A pdb=" N MET C1220 " --> pdb=" O HIS C1282 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N MET C1220 " --> pdb=" O SER C1152 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N SER C1152 " --> pdb=" O MET C1220 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL C1222 " --> pdb=" O TYR C1150 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TYR C1150 " --> pdb=" O VAL C1222 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TRP C1224 " --> pdb=" O PHE C1148 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE C1148 " --> pdb=" O TRP C1224 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL C1226 " --> pdb=" O PRO C1146 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TYR C1228 " --> pdb=" O TYR C1144 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TYR C1144 " --> pdb=" O TYR C1228 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS C1230 " --> pdb=" O GLN C1142 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLN C1142 " --> pdb=" O LYS C1230 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLU C1232 " --> pdb=" O LEU C1140 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU C1140 " --> pdb=" O GLU C1232 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE C1234 " --> pdb=" O MET C1138 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR C1116 " --> pdb=" O VAL C1137 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N THR C1080 " --> pdb=" O GLY C1117 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL C1081 " --> pdb=" O THR C1477 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 1086 through 1092 removed outlier: 3.731A pdb=" N GLY C1104 " --> pdb=" O VAL C1430 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 1157 through 1163 Processing sheet with id=AC3, first strand: chain 'C' and resid 1319 through 1320 Processing sheet with id=AC4, first strand: chain 'C' and resid 1355 through 1359 Processing sheet with id=AC5, first strand: chain 'C' and resid 1487 through 1489 removed outlier: 6.734A pdb=" N SER C1463 " --> pdb=" O CYS C1452 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N CYS C1452 " --> pdb=" O SER C1463 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS C1465 " --> pdb=" O LEU C1450 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU C1450 " --> pdb=" O LYS C1465 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG C1467 " --> pdb=" O ALA C1448 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N GLU C1545 " --> pdb=" O CYS C1452 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLY C1454 " --> pdb=" O GLU C1545 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1480 through 1482 297 hydrogen bonds defined for protein. 756 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: 3.18 Time building geometry restraints manager: 3.02 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: 3255 1.34 - 1.46: 2386 1.46 - 1.58: 4580 1.58 - 1.71: 0 1.71 - 1.83: 132 Bond restraints: 10353 Sorted by residual: bond pdb=" CG GLN A1319 " pdb=" CD GLN A1319 " ideal model delta sigma weight residual 1.516 1.472 0.044 2.50e-02 1.60e+03 3.12e+00 bond pdb=" CB ASP C1317 " pdb=" CG ASP C1317 " ideal model delta sigma weight residual 1.516 1.472 0.044 2.50e-02 1.60e+03 3.11e+00 bond pdb=" CG GLN B1319 " pdb=" CD GLN B1319 " ideal model delta sigma weight residual 1.516 1.473 0.043 2.50e-02 1.60e+03 3.01e+00 bond pdb=" CB ASP B1317 " pdb=" CG ASP B1317 " ideal model delta sigma weight residual 1.516 1.473 0.043 2.50e-02 1.60e+03 2.93e+00 bond pdb=" CB ASP A1317 " pdb=" CG ASP A1317 " ideal model delta sigma weight residual 1.516 1.473 0.043 2.50e-02 1.60e+03 2.93e+00 ... (remaining 10348 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 13527 1.87 - 3.73: 408 3.73 - 5.60: 75 5.60 - 7.46: 9 7.46 - 9.33: 3 Bond angle restraints: 14022 Sorted by residual: angle pdb=" C LYS C1538 " pdb=" N CYS C1539 " pdb=" CA CYS C1539 " ideal model delta sigma weight residual 121.72 117.53 4.19 1.54e+00 4.22e-01 7.42e+00 angle pdb=" C LYS A1538 " pdb=" N CYS A1539 " pdb=" CA CYS A1539 " ideal model delta sigma weight residual 121.72 117.55 4.17 1.54e+00 4.22e-01 7.32e+00 angle pdb=" C LYS B1538 " pdb=" N CYS B1539 " pdb=" CA CYS B1539 " ideal model delta sigma weight residual 121.72 117.58 4.14 1.54e+00 4.22e-01 7.24e+00 angle pdb=" CA LEU C1215 " pdb=" CB LEU C1215 " pdb=" CG LEU C1215 " ideal model delta sigma weight residual 116.30 125.63 -9.33 3.50e+00 8.16e-02 7.11e+00 angle pdb=" CA LEU A1215 " pdb=" CB LEU A1215 " pdb=" CG LEU A1215 " ideal model delta sigma weight residual 116.30 125.62 -9.32 3.50e+00 8.16e-02 7.10e+00 ... (remaining 14017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 5570 17.14 - 34.28: 589 34.28 - 51.42: 129 51.42 - 68.56: 24 68.56 - 85.69: 12 Dihedral angle restraints: 6324 sinusoidal: 2553 harmonic: 3771 Sorted by residual: dihedral pdb=" CB CYS A1173 " pdb=" SG CYS A1173 " pdb=" SG CYS A1207 " pdb=" CB CYS A1207 " ideal model delta sinusoidal sigma weight residual 93.00 164.29 -71.29 1 1.00e+01 1.00e-02 6.52e+01 dihedral pdb=" CB CYS B1173 " pdb=" SG CYS B1173 " pdb=" SG CYS B1207 " pdb=" CB CYS B1207 " ideal model delta sinusoidal sigma weight residual 93.00 164.28 -71.28 1 1.00e+01 1.00e-02 6.52e+01 dihedral pdb=" CB CYS C1173 " pdb=" SG CYS C1173 " pdb=" SG CYS C1207 " pdb=" CB CYS C1207 " ideal model delta sinusoidal sigma weight residual 93.00 164.26 -71.26 1 1.00e+01 1.00e-02 6.52e+01 ... (remaining 6321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 843 0.031 - 0.062: 478 0.062 - 0.093: 171 0.093 - 0.124: 93 0.124 - 0.156: 29 Chirality restraints: 1614 Sorted by residual: chirality pdb=" CA PRO A1315 " pdb=" N PRO A1315 " pdb=" C PRO A1315 " pdb=" CB PRO A1315 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CA ILE A1234 " pdb=" N ILE A1234 " pdb=" C ILE A1234 " pdb=" CB ILE A1234 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" CA ILE A1270 " pdb=" N ILE A1270 " pdb=" C ILE A1270 " pdb=" CB ILE A1270 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.98e-01 ... (remaining 1611 not shown) Planarity restraints: 1755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A1447 " 0.007 2.00e-02 2.50e+03 1.73e-02 5.22e+00 pdb=" CG PHE A1447 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A1447 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE A1447 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A1447 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A1447 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A1447 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C1447 " -0.007 2.00e-02 2.50e+03 1.72e-02 5.20e+00 pdb=" CG PHE C1447 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE C1447 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE C1447 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE C1447 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE C1447 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C1447 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B1447 " -0.006 2.00e-02 2.50e+03 1.71e-02 5.13e+00 pdb=" CG PHE B1447 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE B1447 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE B1447 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE B1447 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B1447 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B1447 " 0.003 2.00e-02 2.50e+03 ... (remaining 1752 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2867 2.82 - 3.34: 8236 3.34 - 3.86: 16725 3.86 - 4.38: 20625 4.38 - 4.90: 35822 Nonbonded interactions: 84275 Sorted by model distance: nonbonded pdb=" OG SER C1177 " pdb=" OD2 ASP C1211 " model vdw 2.295 3.040 nonbonded pdb=" OG SER A1103 " pdb=" O VAL A1430 " model vdw 2.300 3.040 nonbonded pdb=" OG SER C1103 " pdb=" O VAL C1430 " model vdw 2.300 3.040 nonbonded pdb=" OG SER B1103 " pdb=" O VAL B1430 " model vdw 2.300 3.040 nonbonded pdb=" OD1 ASN C1361 " pdb=" OG SER C1367 " model vdw 2.306 3.040 ... (remaining 84270 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 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: 0.000 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.550 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 0.006 0.044 10386 Z= 0.241 Angle : 0.786 9.331 14088 Z= 0.418 Chirality : 0.049 0.156 1614 Planarity : 0.005 0.050 1755 Dihedral : 14.364 85.695 3765 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: -1.60 (0.23), residues: 1254 helix: -0.08 (0.95), residues: 33 sheet: -0.63 (0.21), residues: 597 loop : -1.52 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1365 HIS 0.005 0.001 HIS A1312 PHE 0.036 0.004 PHE A1447 TYR 0.010 0.002 TYR B1521 ARG 0.002 0.000 ARG B1254 Details of bonding type rmsd hydrogen bonds : bond 0.11304 ( 288) hydrogen bonds : angle 5.91111 ( 756) SS BOND : bond 0.00485 ( 33) SS BOND : angle 2.42367 ( 66) covalent geometry : bond 0.00589 (10353) covalent geometry : angle 0.77041 (14022) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.105 Fit side-chains REVERT: A 1271 GLN cc_start: 0.8682 (mt0) cc_final: 0.8479 (mt0) REVERT: A 1467 ARG cc_start: 0.6828 (tpt170) cc_final: 0.5873 (tmt170) REVERT: B 1467 ARG cc_start: 0.6867 (tpt170) cc_final: 0.5914 (tmt170) REVERT: C 1467 ARG cc_start: 0.6952 (tpt170) cc_final: 0.5958 (tmt170) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 1.4664 time to fit residues: 245.9698 Evaluate side-chains 120 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1256 ASN A1361 ASN A1396 HIS B1256 ASN B1361 ASN B1375 GLN B1396 HIS C1256 ASN C1361 ASN C1375 GLN C1396 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.160666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.132723 restraints weight = 10072.559| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.76 r_work: 0.3352 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10386 Z= 0.119 Angle : 0.575 6.767 14088 Z= 0.301 Chirality : 0.043 0.153 1614 Planarity : 0.005 0.044 1755 Dihedral : 5.350 23.984 1356 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.71 % Allowed : 10.49 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.23), residues: 1254 helix: 0.01 (1.07), residues: 33 sheet: -0.46 (0.21), residues: 591 loop : -1.45 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1351 HIS 0.003 0.000 HIS B1322 PHE 0.011 0.002 PHE B1221 TYR 0.008 0.001 TYR A1228 ARG 0.002 0.000 ARG C1155 Details of bonding type rmsd hydrogen bonds : bond 0.03179 ( 288) hydrogen bonds : angle 4.92063 ( 756) SS BOND : bond 0.00339 ( 33) SS BOND : angle 1.33086 ( 66) covalent geometry : bond 0.00285 (10353) covalent geometry : angle 0.56947 (14022) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 1.092 Fit side-chains REVERT: A 1159 GLU cc_start: 0.7635 (pm20) cc_final: 0.7282 (pp20) REVERT: A 1549 SER cc_start: 0.8644 (p) cc_final: 0.8342 (m) REVERT: B 1159 GLU cc_start: 0.7611 (pm20) cc_final: 0.7258 (pp20) REVERT: B 1242 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.6801 (mt0) REVERT: B 1254 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7260 (mtt90) REVERT: C 1465 LYS cc_start: 0.8362 (mtmt) cc_final: 0.7346 (mmtm) REVERT: C 1549 SER cc_start: 0.8675 (p) cc_final: 0.8357 (m) outliers start: 20 outliers final: 5 residues processed: 162 average time/residue: 1.3624 time to fit residues: 236.2503 Evaluate side-chains 136 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1277 GLU Chi-restraints excluded: chain B residue 1242 GLN Chi-restraints excluded: chain B residue 1254 ARG Chi-restraints excluded: chain B residue 1277 GLU Chi-restraints excluded: chain C residue 1164 THR Chi-restraints excluded: chain C residue 1277 GLU Chi-restraints excluded: chain C residue 1513 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 121 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 33 optimal weight: 0.0020 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1256 ASN ** A1396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1394 ASN ** B1396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1256 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.155687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.126063 restraints weight = 10242.793| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.68 r_work: 0.3280 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10386 Z= 0.217 Angle : 0.671 6.558 14088 Z= 0.352 Chirality : 0.047 0.165 1614 Planarity : 0.005 0.044 1755 Dihedral : 5.705 24.358 1356 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.73 % Allowed : 14.24 % Favored : 83.03 % 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: -1.49 (0.22), residues: 1254 helix: -0.12 (1.06), residues: 33 sheet: -0.51 (0.22), residues: 564 loop : -1.45 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1351 HIS 0.005 0.001 HIS C1312 PHE 0.018 0.003 PHE C1381 TYR 0.011 0.002 TYR C1358 ARG 0.002 0.000 ARG C1155 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 288) hydrogen bonds : angle 5.14791 ( 756) SS BOND : bond 0.00238 ( 33) SS BOND : angle 1.16405 ( 66) covalent geometry : bond 0.00536 (10353) covalent geometry : angle 0.66778 (14022) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 1.076 Fit side-chains REVERT: A 1159 GLU cc_start: 0.7777 (pm20) cc_final: 0.7543 (pp20) REVERT: B 1159 GLU cc_start: 0.7744 (pm20) cc_final: 0.7542 (pp20) REVERT: B 1254 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7663 (ttp-170) REVERT: C 1465 LYS cc_start: 0.8372 (mtmt) cc_final: 0.7386 (mmtm) outliers start: 32 outliers final: 14 residues processed: 147 average time/residue: 1.3636 time to fit residues: 213.7995 Evaluate side-chains 141 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1277 GLU Chi-restraints excluded: chain A residue 1371 THR Chi-restraints excluded: chain A residue 1506 THR Chi-restraints excluded: chain A residue 1513 MET Chi-restraints excluded: chain A residue 1549 SER Chi-restraints excluded: chain B residue 1254 ARG Chi-restraints excluded: chain B residue 1277 GLU Chi-restraints excluded: chain B residue 1371 THR Chi-restraints excluded: chain B residue 1432 ASP Chi-restraints excluded: chain B residue 1506 THR Chi-restraints excluded: chain C residue 1164 THR Chi-restraints excluded: chain C residue 1254 ARG Chi-restraints excluded: chain C residue 1277 GLU Chi-restraints excluded: chain C residue 1371 THR Chi-restraints excluded: chain C residue 1506 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 12 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1271 GLN A1377 ASN B1377 ASN B1394 ASN C1377 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.157358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.127604 restraints weight = 10016.967| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.71 r_work: 0.3280 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10386 Z= 0.201 Angle : 0.650 6.811 14088 Z= 0.342 Chirality : 0.046 0.161 1614 Planarity : 0.005 0.051 1755 Dihedral : 5.672 24.325 1356 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.75 % Allowed : 15.60 % 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: -1.38 (0.23), residues: 1254 helix: -0.14 (1.06), residues: 33 sheet: -0.41 (0.22), residues: 594 loop : -1.44 (0.22), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1351 HIS 0.005 0.001 HIS A1312 PHE 0.016 0.003 PHE C1381 TYR 0.013 0.002 TYR C1358 ARG 0.001 0.000 ARG C1155 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 288) hydrogen bonds : angle 5.14729 ( 756) SS BOND : bond 0.00307 ( 33) SS BOND : angle 1.21888 ( 66) covalent geometry : bond 0.00494 (10353) covalent geometry : angle 0.64627 (14022) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 131 time to evaluate : 1.141 Fit side-chains REVERT: A 1159 GLU cc_start: 0.7729 (pm20) cc_final: 0.7498 (pp20) REVERT: A 1401 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7920 (ttt180) REVERT: A 1465 LYS cc_start: 0.8347 (mtpt) cc_final: 0.7350 (mmtm) REVERT: B 1159 GLU cc_start: 0.7671 (pm20) cc_final: 0.7448 (pp20) REVERT: B 1254 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7217 (mtt90) REVERT: B 1465 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7821 (mtmt) REVERT: C 1465 LYS cc_start: 0.8293 (mtmt) cc_final: 0.7249 (mmtm) REVERT: C 1546 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7832 (tt0) outliers start: 44 outliers final: 23 residues processed: 152 average time/residue: 1.3858 time to fit residues: 224.9254 Evaluate side-chains 153 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1207 CYS Chi-restraints excluded: chain A residue 1247 SER Chi-restraints excluded: chain A residue 1277 GLU Chi-restraints excluded: chain A residue 1371 THR Chi-restraints excluded: chain A residue 1401 ARG Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1506 THR Chi-restraints excluded: chain A residue 1513 MET Chi-restraints excluded: chain A residue 1526 GLU Chi-restraints excluded: chain A residue 1549 SER Chi-restraints excluded: chain B residue 1207 CYS Chi-restraints excluded: chain B residue 1254 ARG Chi-restraints excluded: chain B residue 1277 GLU Chi-restraints excluded: chain B residue 1371 THR Chi-restraints excluded: chain B residue 1408 THR Chi-restraints excluded: chain B residue 1432 ASP Chi-restraints excluded: chain B residue 1465 LYS Chi-restraints excluded: chain B residue 1506 THR Chi-restraints excluded: chain B residue 1549 SER Chi-restraints excluded: chain C residue 1164 THR Chi-restraints excluded: chain C residue 1207 CYS Chi-restraints excluded: chain C residue 1254 ARG Chi-restraints excluded: chain C residue 1277 GLU Chi-restraints excluded: chain C residue 1371 THR Chi-restraints excluded: chain C residue 1408 THR Chi-restraints excluded: chain C residue 1506 THR Chi-restraints excluded: chain C residue 1546 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 0.0050 chunk 109 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.160548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.133961 restraints weight = 10142.635| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.60 r_work: 0.3356 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10386 Z= 0.119 Angle : 0.557 7.251 14088 Z= 0.291 Chirality : 0.043 0.151 1614 Planarity : 0.005 0.046 1755 Dihedral : 5.142 23.459 1356 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.56 % Allowed : 17.56 % Favored : 79.88 % 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: -1.25 (0.23), residues: 1254 helix: 0.06 (1.09), residues: 33 sheet: -0.32 (0.23), residues: 564 loop : -1.32 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1351 HIS 0.003 0.001 HIS A1312 PHE 0.011 0.002 PHE B1381 TYR 0.013 0.001 TYR C1358 ARG 0.001 0.000 ARG A1105 Details of bonding type rmsd hydrogen bonds : bond 0.02902 ( 288) hydrogen bonds : angle 4.76217 ( 756) SS BOND : bond 0.00241 ( 33) SS BOND : angle 0.89509 ( 66) covalent geometry : bond 0.00286 (10353) covalent geometry : angle 0.55446 (14022) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 1.136 Fit side-chains REVERT: A 1159 GLU cc_start: 0.7737 (pm20) cc_final: 0.7450 (pp20) REVERT: A 1465 LYS cc_start: 0.8347 (mtpt) cc_final: 0.7432 (mmtm) REVERT: A 1549 SER cc_start: 0.8657 (OUTLIER) cc_final: 0.8377 (m) REVERT: B 1159 GLU cc_start: 0.7656 (pm20) cc_final: 0.7260 (pp20) REVERT: B 1254 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7313 (mtt90) REVERT: B 1465 LYS cc_start: 0.8316 (mtmt) cc_final: 0.7446 (mmtm) REVERT: C 1254 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7316 (mtt90) REVERT: C 1465 LYS cc_start: 0.8342 (mtmt) cc_final: 0.7387 (mmtm) REVERT: C 1546 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7800 (tt0) outliers start: 30 outliers final: 17 residues processed: 153 average time/residue: 1.4594 time to fit residues: 238.0493 Evaluate side-chains 149 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1207 CYS Chi-restraints excluded: chain A residue 1247 SER Chi-restraints excluded: chain A residue 1277 GLU Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1513 MET Chi-restraints excluded: chain A residue 1526 GLU Chi-restraints excluded: chain A residue 1549 SER Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain B residue 1207 CYS Chi-restraints excluded: chain B residue 1254 ARG Chi-restraints excluded: chain B residue 1277 GLU Chi-restraints excluded: chain B residue 1408 THR Chi-restraints excluded: chain B residue 1432 ASP Chi-restraints excluded: chain B residue 1513 MET Chi-restraints excluded: chain B residue 1549 SER Chi-restraints excluded: chain C residue 1207 CYS Chi-restraints excluded: chain C residue 1247 SER Chi-restraints excluded: chain C residue 1254 ARG Chi-restraints excluded: chain C residue 1277 GLU Chi-restraints excluded: chain C residue 1408 THR Chi-restraints excluded: chain C residue 1546 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 23 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1394 ASN C1256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.154294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.124245 restraints weight = 10202.055| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.72 r_work: 0.3234 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 10386 Z= 0.322 Angle : 0.772 7.349 14088 Z= 0.404 Chirality : 0.051 0.175 1614 Planarity : 0.006 0.047 1755 Dihedral : 5.991 24.421 1356 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.92 % Allowed : 18.76 % Favored : 77.32 % 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: -1.46 (0.22), residues: 1254 helix: -0.28 (1.02), residues: 33 sheet: -0.43 (0.22), residues: 561 loop : -1.47 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1351 HIS 0.007 0.001 HIS A1312 PHE 0.021 0.004 PHE C1381 TYR 0.017 0.002 TYR C1358 ARG 0.002 0.000 ARG C1401 Details of bonding type rmsd hydrogen bonds : bond 0.04224 ( 288) hydrogen bonds : angle 5.32825 ( 756) SS BOND : bond 0.00301 ( 33) SS BOND : angle 1.26883 ( 66) covalent geometry : bond 0.00796 (10353) covalent geometry : angle 0.76854 (14022) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 130 time to evaluate : 1.052 Fit side-chains REVERT: A 1159 GLU cc_start: 0.7763 (pm20) cc_final: 0.7516 (pp20) REVERT: A 1401 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7970 (ttt180) REVERT: A 1465 LYS cc_start: 0.8379 (mtpt) cc_final: 0.7382 (mmtm) REVERT: A 1495 MET cc_start: 0.8802 (tpp) cc_final: 0.8428 (ttt) REVERT: B 1159 GLU cc_start: 0.7713 (pm20) cc_final: 0.7468 (pp20) REVERT: B 1254 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7746 (ttp-170) REVERT: B 1465 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7796 (mtmt) REVERT: C 1465 LYS cc_start: 0.8318 (mtmt) cc_final: 0.7261 (mmtm) outliers start: 46 outliers final: 25 residues processed: 152 average time/residue: 1.3087 time to fit residues: 213.0381 Evaluate side-chains 151 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1207 CYS Chi-restraints excluded: chain A residue 1247 SER Chi-restraints excluded: chain A residue 1277 GLU Chi-restraints excluded: chain A residue 1401 ARG Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1513 MET Chi-restraints excluded: chain A residue 1526 GLU Chi-restraints excluded: chain A residue 1549 SER Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain B residue 1207 CYS Chi-restraints excluded: chain B residue 1254 ARG Chi-restraints excluded: chain B residue 1277 GLU Chi-restraints excluded: chain B residue 1345 ASN Chi-restraints excluded: chain B residue 1408 THR Chi-restraints excluded: chain B residue 1432 ASP Chi-restraints excluded: chain B residue 1465 LYS Chi-restraints excluded: chain B residue 1506 THR Chi-restraints excluded: chain B residue 1549 SER Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain C residue 1164 THR Chi-restraints excluded: chain C residue 1207 CYS Chi-restraints excluded: chain C residue 1247 SER Chi-restraints excluded: chain C residue 1254 ARG Chi-restraints excluded: chain C residue 1277 GLU Chi-restraints excluded: chain C residue 1408 THR Chi-restraints excluded: chain C residue 1506 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 124 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.155317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.125241 restraints weight = 10153.464| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.73 r_work: 0.3250 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 10386 Z= 0.257 Angle : 0.721 6.999 14088 Z= 0.379 Chirality : 0.048 0.159 1614 Planarity : 0.005 0.048 1755 Dihedral : 5.966 24.428 1356 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.58 % Allowed : 19.35 % Favored : 77.07 % 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: -1.45 (0.23), residues: 1254 helix: -0.24 (1.04), residues: 33 sheet: -0.43 (0.21), residues: 591 loop : -1.51 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1351 HIS 0.006 0.001 HIS A1312 PHE 0.018 0.003 PHE C1381 TYR 0.014 0.002 TYR C1358 ARG 0.001 0.000 ARG C1401 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 288) hydrogen bonds : angle 5.32266 ( 756) SS BOND : bond 0.00374 ( 33) SS BOND : angle 1.39449 ( 66) covalent geometry : bond 0.00634 (10353) covalent geometry : angle 0.71629 (14022) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 124 time to evaluate : 1.171 Fit side-chains REVERT: A 1159 GLU cc_start: 0.7762 (pm20) cc_final: 0.7544 (pp20) REVERT: A 1401 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7902 (ttt180) REVERT: A 1465 LYS cc_start: 0.8368 (mtpt) cc_final: 0.7369 (mmtm) REVERT: B 1159 GLU cc_start: 0.7678 (pm20) cc_final: 0.7355 (pp20) REVERT: B 1254 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7642 (ttp-170) REVERT: B 1465 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7800 (mtmt) REVERT: C 1465 LYS cc_start: 0.8318 (mtmt) cc_final: 0.7266 (mmtm) REVERT: C 1546 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7984 (mt0) outliers start: 42 outliers final: 26 residues processed: 145 average time/residue: 1.4906 time to fit residues: 231.1280 Evaluate side-chains 150 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1207 CYS Chi-restraints excluded: chain A residue 1247 SER Chi-restraints excluded: chain A residue 1277 GLU Chi-restraints excluded: chain A residue 1401 ARG Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1432 ASP Chi-restraints excluded: chain A residue 1513 MET Chi-restraints excluded: chain A residue 1526 GLU Chi-restraints excluded: chain A residue 1549 SER Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain B residue 1207 CYS Chi-restraints excluded: chain B residue 1254 ARG Chi-restraints excluded: chain B residue 1277 GLU Chi-restraints excluded: chain B residue 1408 THR Chi-restraints excluded: chain B residue 1432 ASP Chi-restraints excluded: chain B residue 1465 LYS Chi-restraints excluded: chain B residue 1506 THR Chi-restraints excluded: chain B residue 1549 SER Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain C residue 1164 THR Chi-restraints excluded: chain C residue 1207 CYS Chi-restraints excluded: chain C residue 1247 SER Chi-restraints excluded: chain C residue 1254 ARG Chi-restraints excluded: chain C residue 1277 GLU Chi-restraints excluded: chain C residue 1371 THR Chi-restraints excluded: chain C residue 1408 THR Chi-restraints excluded: chain C residue 1462 ILE Chi-restraints excluded: chain C residue 1506 THR Chi-restraints excluded: chain C residue 1546 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 114 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 113 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.159198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.129596 restraints weight = 10228.286| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.73 r_work: 0.3313 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10386 Z= 0.140 Angle : 0.605 7.110 14088 Z= 0.318 Chirality : 0.044 0.151 1614 Planarity : 0.005 0.049 1755 Dihedral : 5.485 23.884 1356 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.30 % Allowed : 21.14 % Favored : 76.56 % 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: -1.31 (0.23), residues: 1254 helix: 0.02 (1.07), residues: 33 sheet: -0.38 (0.22), residues: 564 loop : -1.34 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1160 HIS 0.003 0.001 HIS A1312 PHE 0.011 0.002 PHE B1221 TYR 0.013 0.001 TYR C1358 ARG 0.001 0.000 ARG C1467 Details of bonding type rmsd hydrogen bonds : bond 0.03169 ( 288) hydrogen bonds : angle 4.96963 ( 756) SS BOND : bond 0.00336 ( 33) SS BOND : angle 1.30497 ( 66) covalent geometry : bond 0.00337 (10353) covalent geometry : angle 0.59994 (14022) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 1.177 Fit side-chains REVERT: A 1159 GLU cc_start: 0.7707 (pm20) cc_final: 0.7459 (pp20) REVERT: A 1465 LYS cc_start: 0.8323 (mtpt) cc_final: 0.7329 (mmtm) REVERT: A 1549 SER cc_start: 0.8704 (OUTLIER) cc_final: 0.8414 (m) REVERT: B 1254 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7238 (mtt90) REVERT: B 1465 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7306 (mmtm) REVERT: C 1254 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7864 (ttm170) REVERT: C 1465 LYS cc_start: 0.8279 (mtmt) cc_final: 0.7240 (mmtm) outliers start: 27 outliers final: 17 residues processed: 133 average time/residue: 1.5272 time to fit residues: 216.9196 Evaluate side-chains 136 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1207 CYS Chi-restraints excluded: chain A residue 1277 GLU Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1462 ILE Chi-restraints excluded: chain A residue 1513 MET Chi-restraints excluded: chain A residue 1549 SER Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain B residue 1207 CYS Chi-restraints excluded: chain B residue 1254 ARG Chi-restraints excluded: chain B residue 1277 GLU Chi-restraints excluded: chain B residue 1408 THR Chi-restraints excluded: chain B residue 1462 ILE Chi-restraints excluded: chain B residue 1465 LYS Chi-restraints excluded: chain B residue 1549 SER Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain C residue 1207 CYS Chi-restraints excluded: chain C residue 1254 ARG Chi-restraints excluded: chain C residue 1277 GLU Chi-restraints excluded: chain C residue 1408 THR Chi-restraints excluded: chain C residue 1462 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 37 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 53 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.155692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.125739 restraints weight = 10157.988| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.72 r_work: 0.3256 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 10386 Z= 0.256 Angle : 0.718 7.039 14088 Z= 0.377 Chirality : 0.048 0.156 1614 Planarity : 0.005 0.049 1755 Dihedral : 5.945 24.297 1356 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.73 % Allowed : 20.29 % Favored : 76.98 % 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: -1.44 (0.23), residues: 1254 helix: -0.17 (1.04), residues: 33 sheet: -0.45 (0.22), residues: 561 loop : -1.43 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B1160 HIS 0.006 0.001 HIS C1312 PHE 0.018 0.003 PHE C1381 TYR 0.015 0.002 TYR C1358 ARG 0.001 0.000 ARG C1155 Details of bonding type rmsd hydrogen bonds : bond 0.03903 ( 288) hydrogen bonds : angle 5.25552 ( 756) SS BOND : bond 0.00410 ( 33) SS BOND : angle 1.44364 ( 66) covalent geometry : bond 0.00633 (10353) covalent geometry : angle 0.71257 (14022) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 1.218 Fit side-chains REVERT: A 1159 GLU cc_start: 0.7763 (pm20) cc_final: 0.7552 (pp20) REVERT: A 1465 LYS cc_start: 0.8367 (mtpt) cc_final: 0.7371 (mmtm) REVERT: B 1159 GLU cc_start: 0.7652 (pm20) cc_final: 0.7263 (pp20) REVERT: B 1254 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7664 (ttp-170) REVERT: B 1465 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7802 (mtmt) REVERT: C 1465 LYS cc_start: 0.8298 (mtmt) cc_final: 0.7270 (mmtm) outliers start: 32 outliers final: 23 residues processed: 137 average time/residue: 1.4565 time to fit residues: 214.0494 Evaluate side-chains 144 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1207 CYS Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1277 GLU Chi-restraints excluded: chain A residue 1371 THR Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1513 MET Chi-restraints excluded: chain A residue 1549 SER Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain B residue 1207 CYS Chi-restraints excluded: chain B residue 1254 ARG Chi-restraints excluded: chain B residue 1277 GLU Chi-restraints excluded: chain B residue 1408 THR Chi-restraints excluded: chain B residue 1465 LYS Chi-restraints excluded: chain B residue 1506 THR Chi-restraints excluded: chain B residue 1549 SER Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain C residue 1207 CYS Chi-restraints excluded: chain C residue 1247 SER Chi-restraints excluded: chain C residue 1254 ARG Chi-restraints excluded: chain C residue 1277 GLU Chi-restraints excluded: chain C residue 1408 THR Chi-restraints excluded: chain C residue 1462 ILE Chi-restraints excluded: chain C residue 1480 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 97 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.161701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.132293 restraints weight = 10114.668| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.73 r_work: 0.3337 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10386 Z= 0.117 Angle : 0.575 7.373 14088 Z= 0.302 Chirality : 0.043 0.147 1614 Planarity : 0.005 0.051 1755 Dihedral : 5.258 23.548 1356 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.71 % Allowed : 21.14 % Favored : 77.15 % 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: -1.10 (0.24), residues: 1254 helix: 0.12 (1.08), residues: 33 sheet: -0.19 (0.22), residues: 588 loop : -1.26 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1160 HIS 0.003 0.001 HIS B1322 PHE 0.012 0.002 PHE B1221 TYR 0.015 0.001 TYR C1358 ARG 0.001 0.000 ARG B1105 Details of bonding type rmsd hydrogen bonds : bond 0.02972 ( 288) hydrogen bonds : angle 4.80359 ( 756) SS BOND : bond 0.00293 ( 33) SS BOND : angle 1.08215 ( 66) covalent geometry : bond 0.00278 (10353) covalent geometry : angle 0.57125 (14022) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.612 Fit side-chains REVERT: A 1159 GLU cc_start: 0.7690 (pm20) cc_final: 0.7395 (pp20) REVERT: A 1465 LYS cc_start: 0.8315 (mtpt) cc_final: 0.7326 (mmtm) REVERT: A 1467 ARG cc_start: 0.7531 (tpt170) cc_final: 0.7196 (mmt180) REVERT: A 1549 SER cc_start: 0.8692 (OUTLIER) cc_final: 0.8400 (m) REVERT: B 1254 ARG cc_start: 0.8177 (ttp-170) cc_final: 0.7262 (mtt90) REVERT: B 1465 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7312 (mmtm) REVERT: C 1254 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7293 (mtt90) REVERT: C 1465 LYS cc_start: 0.8272 (mtmt) cc_final: 0.7252 (mmtm) outliers start: 20 outliers final: 17 residues processed: 129 average time/residue: 1.4510 time to fit residues: 199.9101 Evaluate side-chains 136 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1207 CYS Chi-restraints excluded: chain A residue 1277 GLU Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1462 ILE Chi-restraints excluded: chain A residue 1513 MET Chi-restraints excluded: chain A residue 1549 SER Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain B residue 1207 CYS Chi-restraints excluded: chain B residue 1277 GLU Chi-restraints excluded: chain B residue 1408 THR Chi-restraints excluded: chain B residue 1465 LYS Chi-restraints excluded: chain B residue 1549 SER Chi-restraints excluded: chain C residue 1207 CYS Chi-restraints excluded: chain C residue 1247 SER Chi-restraints excluded: chain C residue 1254 ARG Chi-restraints excluded: chain C residue 1277 GLU Chi-restraints excluded: chain C residue 1408 THR Chi-restraints excluded: chain C residue 1462 ILE Chi-restraints excluded: chain C residue 1480 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 22 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 117 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 73 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.157620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.127661 restraints weight = 10119.887| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.73 r_work: 0.3269 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10386 Z= 0.220 Angle : 0.677 6.783 14088 Z= 0.356 Chirality : 0.047 0.155 1614 Planarity : 0.005 0.049 1755 Dihedral : 5.742 23.954 1356 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.73 % Allowed : 20.55 % Favored : 76.73 % 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: -1.30 (0.23), residues: 1254 helix: -0.07 (1.05), residues: 33 sheet: -0.42 (0.22), residues: 564 loop : -1.27 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B1160 HIS 0.006 0.001 HIS A1312 PHE 0.016 0.003 PHE C1381 TYR 0.016 0.002 TYR C1358 ARG 0.001 0.000 ARG C1467 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 288) hydrogen bonds : angle 5.13523 ( 756) SS BOND : bond 0.00383 ( 33) SS BOND : angle 1.27923 ( 66) covalent geometry : bond 0.00542 (10353) covalent geometry : angle 0.67319 (14022) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7435.41 seconds wall clock time: 128 minutes 45.07 seconds (7725.07 seconds total)