Starting phenix.real_space_refine on Wed Mar 4 02:36:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fgf_31579/03_2026/7fgf_31579.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fgf_31579/03_2026/7fgf_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 { model { file = "/net/cci-nas-00/data/ceres_data/7fgf_31579/03_2026/7fgf_31579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fgf_31579/03_2026/7fgf_31579.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fgf_31579/03_2026/7fgf_31579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fgf_31579/03_2026/7fgf_31579.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: B, C Time building chain proxies: 2.37, per 1000 atoms: 0.23 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 B1169 " - pdb=" SG CYS B1205 " distance=2.03 Simple disulfide: pdb=" SG CYS C1169 " - pdb=" SG CYS C1205 " distance=2.03 Simple disulfide: pdb=" SG CYS B1173 " - pdb=" SG CYS B1207 " distance=2.03 Simple disulfide: pdb=" SG CYS C1173 " - pdb=" SG CYS C1207 " distance=2.03 Simple disulfide: pdb=" SG CYS B1175 " - pdb=" SG CYS B1180 " distance=2.03 Simple disulfide: pdb=" SG CYS C1175 " - pdb=" SG CYS C1180 " distance=2.03 Simple disulfide: pdb=" SG CYS B1193 " - pdb=" SG CYS B1360 " distance=2.02 Simple disulfide: pdb=" SG CYS C1193 " - pdb=" SG CYS C1360 " distance=2.02 Simple disulfide: pdb=" SG CYS B1208 " - pdb=" SG CYS B1368 " distance=2.03 Simple disulfide: pdb=" SG CYS C1208 " - pdb=" SG CYS C1368 " distance=2.03 Simple disulfide: pdb=" SG CYS B1236 " - pdb=" SG CYS B1246 " distance=2.03 Simple disulfide: pdb=" SG CYS C1236 " - pdb=" SG CYS C1246 " distance=2.03 Simple disulfide: pdb=" SG CYS B1305 " - pdb=" SG CYS B1310 " distance=2.03 Simple disulfide: pdb=" SG CYS C1305 " - pdb=" SG CYS C1310 " distance=2.03 Simple disulfide: pdb=" SG CYS B1452 " - pdb=" SG CYS B1464 " distance=2.03 Simple disulfide: pdb=" SG CYS C1452 " - pdb=" SG CYS C1464 " distance=2.03 Simple disulfide: pdb=" SG CYS B1455 " - pdb=" SG CYS B1458 " distance=2.03 Simple disulfide: pdb=" SG CYS C1455 " - pdb=" SG CYS C1458 " distance=2.03 Simple disulfide: pdb=" SG CYS B1519 " - pdb=" SG CYS B1539 " distance=2.04 Simple disulfide: pdb=" SG CYS C1519 " - pdb=" SG CYS C1539 " distance=2.04 Simple disulfide: pdb=" SG CYS B1528 " - pdb=" SG CYS B1531 " distance=2.03 Simple disulfide: pdb=" SG CYS C1528 " - pdb=" SG CYS C1531 " 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: 0.77 Conformation dependent library (CDL) restraints added in 481.0 milliseconds 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: 0.34 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: 1.44 Time building geometry restraints manager: 1.08 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 3.540 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: 0.190 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.460 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.080 ------------------------------------------------------------------------------- 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 : 7.84 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG B1254 TYR 0.010 0.002 TYR B1521 PHE 0.036 0.004 PHE A1447 TRP 0.011 0.001 TRP A1365 HIS 0.005 0.001 HIS A1312 Details of bonding type rmsd covalent geometry : bond 0.00589 (10353) covalent geometry : angle 0.77041 (14022) SS BOND : bond 0.00485 ( 33) SS BOND : angle 2.42367 ( 66) hydrogen bonds : bond 0.11304 ( 288) hydrogen bonds : angle 5.91111 ( 756) *********************** 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 : 0.417 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: 0.6875 time to fit residues: 115.0595 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 : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.0970 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.160789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.132827 restraints weight = 10137.094| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.75 r_work: 0.3359 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1184 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= 0.116 Angle : 0.573 6.748 14088 Z= 0.300 Chirality : 0.043 0.153 1614 Planarity : 0.005 0.044 1755 Dihedral : 5.348 23.989 1356 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.53 % Allowed : 10.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG A1155 TYR 0.008 0.001 TYR A1228 PHE 0.011 0.002 PHE B1221 TRP 0.007 0.001 TRP A1351 HIS 0.003 0.000 HIS B1322 Details of bonding type rmsd covalent geometry : bond 0.00275 (10353) covalent geometry : angle 0.56745 (14022) SS BOND : bond 0.00310 ( 33) SS BOND : angle 1.32103 ( 66) hydrogen bonds : bond 0.03147 ( 288) hydrogen bonds : angle 4.93876 ( 756) *********************** 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 172 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.317 Fit side-chains REVERT: A 1109 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8620 (mm) REVERT: A 1159 GLU cc_start: 0.7653 (pm20) cc_final: 0.7293 (pp20) REVERT: A 1549 SER cc_start: 0.8645 (p) cc_final: 0.8339 (m) REVERT: B 1159 GLU cc_start: 0.7622 (pm20) cc_final: 0.7276 (pp20) REVERT: B 1242 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.6821 (mt0) REVERT: B 1254 ARG cc_start: 0.8141 (ttp-170) cc_final: 0.7257 (mtt90) REVERT: C 1109 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8609 (mm) REVERT: C 1465 LYS cc_start: 0.8360 (mtmt) cc_final: 0.7322 (mmtm) REVERT: C 1549 SER cc_start: 0.8674 (p) cc_final: 0.8355 (m) outliers start: 18 outliers final: 5 residues processed: 161 average time/residue: 0.6450 time to fit residues: 110.6105 Evaluate side-chains 136 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1277 GLU Chi-restraints excluded: chain B residue 1242 GLN Chi-restraints excluded: chain B residue 1277 GLU Chi-restraints excluded: chain C residue 1109 ILE 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 98 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 7 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 117 optimal weight: 0.0670 chunk 45 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 overall best weight: 1.1120 ------------------------------------------------------------------------------- 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 C1256 ASN ** C1396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.158269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.128650 restraints weight = 10174.471| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.73 r_work: 0.3318 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10386 Z= 0.137 Angle : 0.579 6.766 14088 Z= 0.303 Chirality : 0.044 0.157 1614 Planarity : 0.004 0.042 1755 Dihedral : 5.232 23.365 1356 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.53 % Allowed : 14.49 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.23), residues: 1254 helix: -0.04 (1.07), residues: 33 sheet: -0.52 (0.22), residues: 570 loop : -1.41 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1115 TYR 0.010 0.001 TYR C1358 PHE 0.013 0.002 PHE C1381 TRP 0.008 0.001 TRP C1351 HIS 0.003 0.001 HIS C1312 Details of bonding type rmsd covalent geometry : bond 0.00335 (10353) covalent geometry : angle 0.57703 (14022) SS BOND : bond 0.00187 ( 33) SS BOND : angle 0.94518 ( 66) hydrogen bonds : bond 0.03073 ( 288) hydrogen bonds : angle 4.82686 ( 756) *********************** 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 160 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.405 Fit side-chains REVERT: A 1159 GLU cc_start: 0.7643 (pm20) cc_final: 0.7379 (pp20) REVERT: B 1159 GLU cc_start: 0.7644 (pm20) cc_final: 0.7388 (pp20) REVERT: B 1254 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7288 (mtt90) REVERT: B 1465 LYS cc_start: 0.8299 (mtmt) cc_final: 0.7370 (mmtm) REVERT: B 1546 GLN cc_start: 0.8191 (mt0) cc_final: 0.7822 (tt0) REVERT: C 1109 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8601 (mm) REVERT: C 1254 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7307 (mtt90) REVERT: C 1465 LYS cc_start: 0.8313 (mtmt) cc_final: 0.7287 (mmtm) outliers start: 18 outliers final: 7 residues processed: 148 average time/residue: 0.6846 time to fit residues: 107.6962 Evaluate side-chains 138 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1277 GLU Chi-restraints excluded: chain A residue 1513 MET Chi-restraints excluded: chain A residue 1526 GLU Chi-restraints excluded: chain B residue 1254 ARG Chi-restraints excluded: chain B residue 1277 GLU Chi-restraints excluded: chain B residue 1432 ASP Chi-restraints excluded: chain C residue 1109 ILE Chi-restraints excluded: chain C residue 1254 ARG Chi-restraints excluded: chain C residue 1277 GLU Chi-restraints excluded: chain C residue 1513 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 71 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 83 optimal weight: 0.0970 chunk 116 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 chunk 67 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1256 ASN A1271 GLN A1377 ASN ** A1396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1256 ASN B1394 ASN ** B1396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1256 ASN C1377 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.155403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.125433 restraints weight = 10139.141| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.71 r_work: 0.3255 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 10386 Z= 0.277 Angle : 0.727 6.976 14088 Z= 0.382 Chirality : 0.049 0.168 1614 Planarity : 0.005 0.054 1755 Dihedral : 5.921 24.542 1356 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.92 % Allowed : 15.69 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.23), residues: 1254 helix: -0.22 (1.04), residues: 33 sheet: -0.48 (0.22), residues: 564 loop : -1.45 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C1401 TYR 0.014 0.002 TYR C1358 PHE 0.020 0.003 PHE C1381 TRP 0.009 0.002 TRP A1351 HIS 0.006 0.001 HIS C1312 Details of bonding type rmsd covalent geometry : bond 0.00685 (10353) covalent geometry : angle 0.72320 (14022) SS BOND : bond 0.00327 ( 33) SS BOND : angle 1.28793 ( 66) hydrogen bonds : bond 0.03967 ( 288) hydrogen bonds : angle 5.29077 ( 756) *********************** 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 176 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 130 time to evaluate : 0.420 Fit side-chains REVERT: A 1159 GLU cc_start: 0.7739 (pm20) cc_final: 0.7516 (pp20) REVERT: A 1401 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7987 (ttt180) REVERT: A 1465 LYS cc_start: 0.8413 (mtmm) cc_final: 0.7449 (mmtm) REVERT: B 1159 GLU cc_start: 0.7705 (pm20) cc_final: 0.7471 (pp20) REVERT: B 1465 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7823 (mtmt) REVERT: C 1109 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8647 (mm) REVERT: C 1465 LYS cc_start: 0.8320 (mtmt) cc_final: 0.7275 (mmtm) outliers start: 46 outliers final: 20 residues processed: 155 average time/residue: 0.6474 time to fit residues: 106.9012 Evaluate side-chains 148 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 1513 MET Chi-restraints excluded: chain A residue 1549 SER 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 1432 ASP Chi-restraints excluded: chain B residue 1465 LYS Chi-restraints excluded: chain B residue 1506 THR Chi-restraints excluded: chain B residue 1513 MET Chi-restraints excluded: chain B residue 1549 SER Chi-restraints excluded: chain C residue 1109 ILE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 47 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1377 ASN B1394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.157675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.127901 restraints weight = 10175.533| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.72 r_work: 0.3288 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10386 Z= 0.182 Angle : 0.627 6.847 14088 Z= 0.330 Chirality : 0.045 0.158 1614 Planarity : 0.005 0.047 1755 Dihedral : 5.573 24.368 1356 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.90 % Allowed : 17.48 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.23), residues: 1254 helix: -0.11 (1.06), residues: 33 sheet: -0.39 (0.22), residues: 564 loop : -1.40 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C1401 TYR 0.014 0.002 TYR C1358 PHE 0.014 0.002 PHE C1381 TRP 0.009 0.001 TRP A1351 HIS 0.005 0.001 HIS A1312 Details of bonding type rmsd covalent geometry : bond 0.00447 (10353) covalent geometry : angle 0.62490 (14022) SS BOND : bond 0.00246 ( 33) SS BOND : angle 1.01125 ( 66) hydrogen bonds : bond 0.03417 ( 288) hydrogen bonds : angle 5.04751 ( 756) *********************** 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 160 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.318 Fit side-chains REVERT: A 1159 GLU cc_start: 0.7715 (pm20) cc_final: 0.7503 (pp20) REVERT: A 1465 LYS cc_start: 0.8417 (mtmm) cc_final: 0.7469 (mmtm) REVERT: A 1467 ARG cc_start: 0.7566 (tpt170) cc_final: 0.7186 (mmt180) REVERT: B 1159 GLU cc_start: 0.7673 (pm20) cc_final: 0.7401 (pp20) REVERT: B 1465 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7811 (mtmt) REVERT: C 1109 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8589 (mm) REVERT: C 1254 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7833 (ttm170) REVERT: C 1465 LYS cc_start: 0.8283 (mtmt) cc_final: 0.7233 (mmtm) REVERT: C 1546 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7830 (tt0) outliers start: 34 outliers final: 17 residues processed: 142 average time/residue: 0.6457 time to fit residues: 97.6277 Evaluate side-chains 143 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 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 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 1513 MET Chi-restraints excluded: chain B residue 1549 SER Chi-restraints excluded: chain C residue 1109 ILE 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 1408 THR Chi-restraints excluded: chain C residue 1506 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 70 optimal weight: 0.0050 chunk 10 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.158855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.129668 restraints weight = 10244.067| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.67 r_work: 0.3325 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10386 Z= 0.135 Angle : 0.578 7.162 14088 Z= 0.303 Chirality : 0.043 0.152 1614 Planarity : 0.005 0.047 1755 Dihedral : 5.263 23.894 1356 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.64 % Allowed : 18.07 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.23), residues: 1254 helix: -0.01 (1.08), residues: 33 sheet: -0.32 (0.22), residues: 564 loop : -1.33 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B1105 TYR 0.014 0.001 TYR C1358 PHE 0.012 0.002 PHE C1381 TRP 0.008 0.001 TRP A1351 HIS 0.003 0.001 HIS A1312 Details of bonding type rmsd covalent geometry : bond 0.00327 (10353) covalent geometry : angle 0.57563 (14022) SS BOND : bond 0.00200 ( 33) SS BOND : angle 0.96238 ( 66) hydrogen bonds : bond 0.03065 ( 288) hydrogen bonds : angle 4.86066 ( 756) *********************** 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 161 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.454 Fit side-chains REVERT: A 1159 GLU cc_start: 0.7728 (pm20) cc_final: 0.7447 (pp20) REVERT: A 1465 LYS cc_start: 0.8442 (mtmm) cc_final: 0.7538 (mmtm) REVERT: A 1467 ARG cc_start: 0.7562 (tpt170) cc_final: 0.7216 (mmt180) REVERT: A 1549 SER cc_start: 0.8686 (OUTLIER) cc_final: 0.8396 (m) REVERT: B 1159 GLU cc_start: 0.7662 (pm20) cc_final: 0.7300 (pp20) REVERT: B 1465 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7401 (mmtm) REVERT: C 1109 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8550 (mm) REVERT: C 1254 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7324 (mtt90) REVERT: C 1465 LYS cc_start: 0.8314 (mtmt) cc_final: 0.7334 (mmtm) REVERT: C 1546 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7825 (tt0) outliers start: 31 outliers final: 17 residues processed: 146 average time/residue: 0.6527 time to fit residues: 101.4566 Evaluate side-chains 144 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 1462 ILE 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 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 1513 MET Chi-restraints excluded: chain B residue 1549 SER Chi-restraints excluded: chain C residue 1109 ILE 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 1408 THR Chi-restraints excluded: chain C residue 1462 ILE Chi-restraints excluded: chain C residue 1546 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 11 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 101 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1271 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.152344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.122323 restraints weight = 10233.315| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.72 r_work: 0.3217 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.073 10386 Z= 0.398 Angle : 0.852 8.158 14088 Z= 0.447 Chirality : 0.055 0.203 1614 Planarity : 0.006 0.051 1755 Dihedral : 6.286 24.815 1356 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 4.18 % Allowed : 18.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.23), residues: 1254 helix: -0.41 (1.01), residues: 33 sheet: -0.56 (0.21), residues: 597 loop : -1.49 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1401 TYR 0.018 0.002 TYR C1358 PHE 0.023 0.004 PHE A1381 TRP 0.009 0.002 TRP A1351 HIS 0.008 0.001 HIS A1312 Details of bonding type rmsd covalent geometry : bond 0.00990 (10353) covalent geometry : angle 0.84642 (14022) SS BOND : bond 0.00498 ( 33) SS BOND : angle 1.69318 ( 66) hydrogen bonds : bond 0.04673 ( 288) hydrogen bonds : angle 5.57028 ( 756) *********************** 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 178 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 129 time to evaluate : 0.368 Fit side-chains REVERT: A 1159 GLU cc_start: 0.7778 (pm20) cc_final: 0.7538 (pp20) REVERT: A 1401 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7999 (ttt180) REVERT: B 1159 GLU cc_start: 0.7722 (pm20) cc_final: 0.7459 (pp20) REVERT: B 1254 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7714 (ttp-170) REVERT: C 1109 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8690 (mm) REVERT: C 1465 LYS cc_start: 0.8359 (mtmt) cc_final: 0.7291 (mmtm) outliers start: 49 outliers final: 27 residues processed: 154 average time/residue: 0.5990 time to fit residues: 98.7157 Evaluate side-chains 153 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 1371 THR Chi-restraints excluded: chain A residue 1401 ARG Chi-restraints excluded: chain A residue 1432 ASP 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 1506 THR Chi-restraints excluded: chain B residue 1549 SER Chi-restraints excluded: chain C residue 1109 ILE 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 1345 ASN Chi-restraints excluded: chain C residue 1371 THR Chi-restraints excluded: chain C residue 1401 ARG Chi-restraints excluded: chain C residue 1408 THR Chi-restraints excluded: chain C residue 1506 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 104 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 chunk 112 optimal weight: 0.4980 chunk 6 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.159419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.130152 restraints weight = 10162.198| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.73 r_work: 0.3334 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10386 Z= 0.108 Angle : 0.561 7.517 14088 Z= 0.296 Chirality : 0.043 0.149 1614 Planarity : 0.005 0.051 1755 Dihedral : 5.267 23.627 1356 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.79 % Allowed : 21.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.24), residues: 1254 helix: 0.05 (1.10), residues: 33 sheet: -0.21 (0.22), residues: 606 loop : -1.43 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C1254 TYR 0.012 0.001 TYR C1358 PHE 0.012 0.002 PHE B1221 TRP 0.009 0.001 TRP B1160 HIS 0.003 0.000 HIS A1322 Details of bonding type rmsd covalent geometry : bond 0.00253 (10353) covalent geometry : angle 0.55825 (14022) SS BOND : bond 0.00202 ( 33) SS BOND : angle 1.00175 ( 66) hydrogen bonds : bond 0.02872 ( 288) hydrogen bonds : angle 4.83803 ( 756) *********************** 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 142 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.380 Fit side-chains REVERT: A 1159 GLU cc_start: 0.7644 (pm20) cc_final: 0.7289 (pp20) REVERT: A 1465 LYS cc_start: 0.8352 (mtmm) cc_final: 0.7503 (mmtm) REVERT: A 1467 ARG cc_start: 0.7511 (tpt170) cc_final: 0.7176 (mmt180) REVERT: A 1549 SER cc_start: 0.8662 (OUTLIER) cc_final: 0.8393 (m) REVERT: B 1465 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7337 (mmtm) REVERT: C 1254 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7301 (mtt90) REVERT: C 1465 LYS cc_start: 0.8262 (mtmt) cc_final: 0.7247 (mmtm) REVERT: C 1549 SER cc_start: 0.8690 (p) cc_final: 0.8392 (m) outliers start: 21 outliers final: 14 residues processed: 131 average time/residue: 0.6620 time to fit residues: 92.4024 Evaluate side-chains 135 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 1462 ILE 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 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 1506 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 1462 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 82 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.154619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.124713 restraints weight = 10170.841| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.73 r_work: 0.3257 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10386 Z= 0.217 Angle : 0.671 6.838 14088 Z= 0.353 Chirality : 0.046 0.155 1614 Planarity : 0.005 0.048 1755 Dihedral : 5.705 24.040 1356 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.13 % Allowed : 20.97 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.23), residues: 1254 helix: -0.07 (1.07), residues: 33 sheet: -0.42 (0.22), residues: 564 loop : -1.33 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B1525 TYR 0.015 0.002 TYR C1358 PHE 0.016 0.003 PHE C1381 TRP 0.010 0.001 TRP B1160 HIS 0.005 0.001 HIS A1312 Details of bonding type rmsd covalent geometry : bond 0.00533 (10353) covalent geometry : angle 0.66740 (14022) SS BOND : bond 0.00337 ( 33) SS BOND : angle 1.21862 ( 66) hydrogen bonds : bond 0.03640 ( 288) hydrogen bonds : angle 5.11636 ( 756) *********************** 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 140 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.424 Fit side-chains REVERT: A 1159 GLU cc_start: 0.7686 (pm20) cc_final: 0.7468 (pp20) REVERT: A 1465 LYS cc_start: 0.8333 (mtmm) cc_final: 0.7477 (mmtm) REVERT: A 1467 ARG cc_start: 0.7543 (tpt170) cc_final: 0.7152 (mmt180) REVERT: B 1465 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7285 (mmtm) REVERT: C 1109 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8592 (mm) REVERT: C 1254 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7854 (ttm170) REVERT: C 1465 LYS cc_start: 0.8296 (mtmt) cc_final: 0.7259 (mmtm) outliers start: 25 outliers final: 17 residues processed: 129 average time/residue: 0.6304 time to fit residues: 86.8662 Evaluate side-chains 135 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 1549 SER Chi-restraints excluded: chain B residue 1137 VAL 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 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 1109 ILE 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 1462 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 89 optimal weight: 0.5980 chunk 123 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 76 optimal weight: 0.3980 chunk 103 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 82 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.162503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.133494 restraints weight = 9965.202| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.70 r_work: 0.3355 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10386 Z= 0.110 Angle : 0.558 7.617 14088 Z= 0.292 Chirality : 0.042 0.147 1614 Planarity : 0.005 0.051 1755 Dihedral : 5.094 23.189 1356 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.71 % Allowed : 21.40 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.24), residues: 1254 helix: 0.03 (1.09), residues: 33 sheet: -0.21 (0.22), residues: 600 loop : -1.37 (0.23), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B1105 TYR 0.015 0.001 TYR C1358 PHE 0.011 0.002 PHE B1221 TRP 0.009 0.001 TRP B1160 HIS 0.003 0.001 HIS B1322 Details of bonding type rmsd covalent geometry : bond 0.00260 (10353) covalent geometry : angle 0.55561 (14022) SS BOND : bond 0.00252 ( 33) SS BOND : angle 0.93989 ( 66) hydrogen bonds : bond 0.02883 ( 288) hydrogen bonds : angle 4.72499 ( 756) ********************** 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 142 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.391 Fit side-chains REVERT: A 1159 GLU cc_start: 0.7657 (pm20) cc_final: 0.7239 (pp20) REVERT: A 1465 LYS cc_start: 0.8314 (mtmm) cc_final: 0.7463 (mmtm) REVERT: A 1467 ARG cc_start: 0.7510 (tpt170) cc_final: 0.7178 (mmt180) REVERT: A 1549 SER cc_start: 0.8645 (OUTLIER) cc_final: 0.8373 (m) REVERT: B 1465 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7288 (mmtm) REVERT: C 1254 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7300 (mtt90) REVERT: C 1465 LYS cc_start: 0.8270 (mtmt) cc_final: 0.7250 (mmtm) outliers start: 20 outliers final: 14 residues processed: 134 average time/residue: 0.6460 time to fit residues: 92.1891 Evaluate side-chains 137 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 1549 SER Chi-restraints excluded: chain B residue 1137 VAL 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 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 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 65 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 27 optimal weight: 0.0170 chunk 126 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 overall best weight: 1.3822 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.157172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.127513 restraints weight = 10097.570| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.72 r_work: 0.3298 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10386 Z= 0.154 Angle : 0.605 7.009 14088 Z= 0.318 Chirality : 0.044 0.150 1614 Planarity : 0.005 0.048 1755 Dihedral : 5.299 23.266 1356 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.88 % Allowed : 21.23 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.24), residues: 1254 helix: -0.03 (1.07), residues: 33 sheet: -0.19 (0.22), residues: 588 loop : -1.27 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1525 TYR 0.016 0.001 TYR C1358 PHE 0.013 0.002 PHE C1381 TRP 0.009 0.001 TRP C1351 HIS 0.004 0.001 HIS A1312 Details of bonding type rmsd covalent geometry : bond 0.00376 (10353) covalent geometry : angle 0.60225 (14022) SS BOND : bond 0.00285 ( 33) SS BOND : angle 1.03108 ( 66) hydrogen bonds : bond 0.03200 ( 288) hydrogen bonds : angle 4.86858 ( 756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3400.64 seconds wall clock time: 58 minutes 45.89 seconds (3525.89 seconds total)