Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 16:40:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgf_31579/04_2023/7fgf_31579.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgf_31579/04_2023/7fgf_31579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgf_31579/04_2023/7fgf_31579.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgf_31579/04_2023/7fgf_31579.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgf_31579/04_2023/7fgf_31579.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgf_31579/04_2023/7fgf_31579.pdb" } 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 ------------------------------------------------------------------------------- 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 Residue "A GLU 1113": "OE1" <-> "OE2" Residue "A ARG 1115": "NH1" <-> "NH2" Residue "A TYR 1150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1168": "OD1" <-> "OD2" Residue "A GLU 1184": "OE1" <-> "OE2" Residue "A ARG 1192": "NH1" <-> "NH2" Residue "A ASP 1218": "OD1" <-> "OD2" Residue "A PHE 1221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1243": "OE1" <-> "OE2" Residue "A ARG 1244": "NH1" <-> "NH2" Residue "A PHE 1255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1284": "NH1" <-> "NH2" Residue "A PHE 1344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1357": "OD1" <-> "OD2" Residue "A ASP 1364": "OD1" <-> "OD2" Residue "A PHE 1381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1401": "NH1" <-> "NH2" Residue "A ASP 1407": "OD1" <-> "OD2" Residue "A TYR 1456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1474": "OD1" <-> "OD2" Residue "A GLU 1475": "OE1" <-> "OE2" Residue "A ASP 1483": "OD1" <-> "OD2" Residue "A ASP 1486": "OD1" <-> "OD2" Residue "A ARG 1497": "NH1" <-> "NH2" Residue "A PHE 1507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1524": "OE1" <-> "OE2" Residue "A GLU 1533": "OE1" <-> "OE2" Residue "B GLU 1113": "OE1" <-> "OE2" Residue "B ARG 1115": "NH1" <-> "NH2" Residue "B TYR 1150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1168": "OD1" <-> "OD2" Residue "B GLU 1184": "OE1" <-> "OE2" Residue "B ARG 1192": "NH1" <-> "NH2" Residue "B ASP 1218": "OD1" <-> "OD2" Residue "B PHE 1221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1243": "OE1" <-> "OE2" Residue "B ARG 1244": "NH1" <-> "NH2" Residue "B PHE 1255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1284": "NH1" <-> "NH2" Residue "B PHE 1344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1357": "OD1" <-> "OD2" Residue "B ASP 1364": "OD1" <-> "OD2" Residue "B PHE 1381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1401": "NH1" <-> "NH2" Residue "B ASP 1407": "OD1" <-> "OD2" Residue "B TYR 1456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1474": "OD1" <-> "OD2" Residue "B GLU 1475": "OE1" <-> "OE2" Residue "B ASP 1483": "OD1" <-> "OD2" Residue "B ASP 1486": "OD1" <-> "OD2" Residue "B ARG 1497": "NH1" <-> "NH2" Residue "B PHE 1507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1524": "OE1" <-> "OE2" Residue "B GLU 1533": "OE1" <-> "OE2" Residue "C GLU 1113": "OE1" <-> "OE2" Residue "C ARG 1115": "NH1" <-> "NH2" Residue "C TYR 1150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1168": "OD1" <-> "OD2" Residue "C GLU 1184": "OE1" <-> "OE2" Residue "C ARG 1192": "NH1" <-> "NH2" Residue "C ASP 1218": "OD1" <-> "OD2" Residue "C PHE 1221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1243": "OE1" <-> "OE2" Residue "C ARG 1244": "NH1" <-> "NH2" Residue "C PHE 1255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1284": "NH1" <-> "NH2" Residue "C PHE 1344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1357": "OD1" <-> "OD2" Residue "C ASP 1364": "OD1" <-> "OD2" Residue "C PHE 1381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1401": "NH1" <-> "NH2" Residue "C ASP 1407": "OD1" <-> "OD2" Residue "C TYR 1456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1474": "OD1" <-> "OD2" Residue "C GLU 1475": "OE1" <-> "OE2" Residue "C ASP 1483": "OD1" <-> "OD2" Residue "C ASP 1486": "OD1" <-> "OD2" Residue "C ARG 1497": "NH1" <-> "NH2" Residue "C PHE 1507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1524": "OE1" <-> "OE2" Residue "C GLU 1533": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 10143 Number of models: 1 Model: "" Number of chains: 3 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 Chain: "B" 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 Chain: "C" 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 Time building chain proxies: 5.31, per 1000 atoms: 0.52 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 B1173 " - pdb=" SG CYS B1207 " distance=2.03 Simple disulfide: pdb=" SG CYS B1175 " - pdb=" SG CYS B1180 " distance=2.03 Simple disulfide: pdb=" SG CYS B1193 " - pdb=" SG CYS B1360 " distance=2.02 Simple disulfide: pdb=" SG CYS B1208 " - pdb=" SG CYS B1368 " distance=2.03 Simple disulfide: pdb=" SG CYS B1236 " - pdb=" SG CYS B1246 " distance=2.03 Simple disulfide: pdb=" SG CYS B1305 " - pdb=" SG CYS B1310 " distance=2.03 Simple disulfide: pdb=" SG CYS B1452 " - pdb=" SG CYS B1464 " distance=2.03 Simple disulfide: pdb=" SG CYS B1455 " - pdb=" SG CYS B1458 " distance=2.03 Simple disulfide: pdb=" SG CYS B1519 " - pdb=" SG CYS B1539 " distance=2.04 Simple disulfide: pdb=" SG CYS B1528 " - pdb=" SG CYS B1531 " distance=2.03 Simple disulfide: pdb=" SG CYS C1169 " - pdb=" SG CYS C1205 " distance=2.03 Simple disulfide: pdb=" SG CYS C1173 " - pdb=" SG CYS C1207 " distance=2.03 Simple disulfide: pdb=" SG CYS C1175 " - pdb=" SG CYS C1180 " distance=2.03 Simple disulfide: pdb=" SG CYS C1193 " - pdb=" SG CYS C1360 " distance=2.02 Simple disulfide: pdb=" SG CYS C1208 " - pdb=" SG CYS C1368 " distance=2.03 Simple disulfide: pdb=" SG CYS C1236 " - pdb=" SG CYS C1246 " distance=2.03 Simple disulfide: pdb=" SG CYS C1305 " - pdb=" SG CYS C1310 " distance=2.03 Simple disulfide: pdb=" SG CYS C1452 " - pdb=" SG CYS C1464 " distance=2.03 Simple disulfide: pdb=" SG CYS C1455 " - pdb=" SG CYS C1458 " distance=2.03 Simple disulfide: pdb=" SG CYS C1519 " - pdb=" SG CYS C1539 " distance=2.04 Simple disulfide: pdb=" SG CYS C1528 " - pdb=" SG CYS C1531 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.79 Conformation dependent library (CDL) restraints added in 1.7 seconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2460 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 24 sheets defined 5.8% alpha, 45.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 1314 through 1318 removed outlier: 4.494A pdb=" N LEU A1318 " --> pdb=" O PRO A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1388 Processing helix chain 'A' and resid 1390 through 1394 removed outlier: 3.983A pdb=" N ASN A1394 " --> pdb=" O ASP A1390 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1390 through 1394' Processing helix chain 'A' and resid 1524 through 1526 No H-bonds generated for 'chain 'A' and resid 1524 through 1526' Processing helix chain 'B' and resid 1314 through 1318 removed outlier: 4.494A pdb=" N LEU B1318 " --> pdb=" O PRO B1315 " (cutoff:3.500A) Processing helix chain 'B' and resid 1377 through 1388 Processing helix chain 'B' and resid 1390 through 1394 removed outlier: 3.984A pdb=" N ASN B1394 " --> pdb=" O ASP B1390 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1390 through 1394' Processing helix chain 'B' and resid 1524 through 1526 No H-bonds generated for 'chain 'B' and resid 1524 through 1526' Processing helix chain 'C' and resid 1314 through 1318 removed outlier: 4.494A pdb=" N LEU C1318 " --> pdb=" O PRO C1315 " (cutoff:3.500A) Processing helix chain 'C' and resid 1377 through 1388 Processing helix chain 'C' and resid 1390 through 1394 removed outlier: 3.984A pdb=" N ASN C1394 " --> pdb=" O ASP C1390 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1390 through 1394' Processing helix chain 'C' and resid 1524 through 1526 No H-bonds generated for 'chain 'C' and resid 1524 through 1526' Processing sheet with id=AA1, first strand: chain 'A' and resid 1245 through 1248 removed outlier: 4.913A pdb=" N MET A1220 " --> pdb=" O SER A1152 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N SER A1152 " --> pdb=" O MET A1220 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL A1222 " --> pdb=" O TYR A1150 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TYR A1150 " --> pdb=" O VAL A1222 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TRP A1224 " --> pdb=" O PHE A1148 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE A1148 " --> pdb=" O TRP A1224 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL A1226 " --> pdb=" O PRO A1146 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TYR A1228 " --> pdb=" O TYR A1144 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TYR A1144 " --> pdb=" O TYR A1228 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS A1230 " --> pdb=" O GLN A1142 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLN A1142 " --> pdb=" O LYS A1230 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLU A1232 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU A1140 " --> pdb=" O GLU A1232 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE A1234 " --> pdb=" O MET A1138 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LEU A1140 " --> pdb=" O PRO A1417 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU A1413 " --> pdb=" O TYR A1144 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU A1411 " --> pdb=" O PRO A1146 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE A1148 " --> pdb=" O PRO A1409 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLN A1410 " --> pdb=" O VAL A1402 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL A1402 " --> pdb=" O GLN A1410 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASP A1412 " --> pdb=" O LYS A1400 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A1400 " --> pdb=" O ASP A1412 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LYS A1414 " --> pdb=" O HIS A1398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1297 through 1300 removed outlier: 4.439A pdb=" N MET A1220 " --> pdb=" O HIS A1282 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N MET A1220 " --> pdb=" O SER A1152 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N SER A1152 " --> pdb=" O MET A1220 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL A1222 " --> pdb=" O TYR A1150 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TYR A1150 " --> pdb=" O VAL A1222 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TRP A1224 " --> pdb=" O PHE A1148 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE A1148 " --> pdb=" O TRP A1224 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL A1226 " --> pdb=" O PRO A1146 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TYR A1228 " --> pdb=" O TYR A1144 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TYR A1144 " --> pdb=" O TYR A1228 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS A1230 " --> pdb=" O GLN A1142 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLN A1142 " --> pdb=" O LYS A1230 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLU A1232 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU A1140 " --> pdb=" O GLU A1232 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE A1234 " --> pdb=" O MET A1138 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR A1116 " --> pdb=" O VAL A1137 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N THR A1080 " --> pdb=" O GLY A1117 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL A1081 " --> pdb=" O THR A1477 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1086 through 1092 removed outlier: 3.730A pdb=" N GLY A1104 " --> pdb=" O VAL A1430 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1157 through 1163 Processing sheet with id=AA5, first strand: chain 'A' and resid 1319 through 1320 Processing sheet with id=AA6, first strand: chain 'A' and resid 1355 through 1359 Processing sheet with id=AA7, first strand: chain 'A' and resid 1487 through 1489 removed outlier: 6.735A pdb=" N SER A1463 " --> pdb=" O CYS A1452 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N CYS A1452 " --> pdb=" O SER A1463 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS A1465 " --> pdb=" O LEU A1450 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU A1450 " --> pdb=" O LYS A1465 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG A1467 " --> pdb=" O ALA A1448 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N GLU A1545 " --> pdb=" O CYS A1452 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N GLY A1454 " --> pdb=" O GLU A1545 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1480 through 1482 Processing sheet with id=AA9, first strand: chain 'B' and resid 1245 through 1248 removed outlier: 4.913A pdb=" N MET B1220 " --> pdb=" O SER B1152 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N SER B1152 " --> pdb=" O MET B1220 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL B1222 " --> pdb=" O TYR B1150 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TYR B1150 " --> pdb=" O VAL B1222 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TRP B1224 " --> pdb=" O PHE B1148 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE B1148 " --> pdb=" O TRP B1224 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL B1226 " --> pdb=" O PRO B1146 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N TYR B1228 " --> pdb=" O TYR B1144 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TYR B1144 " --> pdb=" O TYR B1228 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS B1230 " --> pdb=" O GLN B1142 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLN B1142 " --> pdb=" O LYS B1230 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU B1232 " --> pdb=" O LEU B1140 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU B1140 " --> pdb=" O GLU B1232 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE B1234 " --> pdb=" O MET B1138 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LEU B1140 " --> pdb=" O PRO B1417 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU B1413 " --> pdb=" O TYR B1144 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU B1411 " --> pdb=" O PRO B1146 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N PHE B1148 " --> pdb=" O PRO B1409 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN B1410 " --> pdb=" O VAL B1402 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL B1402 " --> pdb=" O GLN B1410 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASP B1412 " --> pdb=" O LYS B1400 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS B1400 " --> pdb=" O ASP B1412 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LYS B1414 " --> pdb=" O HIS B1398 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1297 through 1300 removed outlier: 4.440A pdb=" N MET B1220 " --> pdb=" O HIS B1282 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N MET B1220 " --> pdb=" O SER B1152 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N SER B1152 " --> pdb=" O MET B1220 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL B1222 " --> pdb=" O TYR B1150 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TYR B1150 " --> pdb=" O VAL B1222 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TRP B1224 " --> pdb=" O PHE B1148 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE B1148 " --> pdb=" O TRP B1224 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL B1226 " --> pdb=" O PRO B1146 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N TYR B1228 " --> pdb=" O TYR B1144 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TYR B1144 " --> pdb=" O TYR B1228 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS B1230 " --> pdb=" O GLN B1142 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLN B1142 " --> pdb=" O LYS B1230 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU B1232 " --> pdb=" O LEU B1140 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU B1140 " --> pdb=" O GLU B1232 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE B1234 " --> pdb=" O MET B1138 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR B1116 " --> pdb=" O VAL B1137 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N THR B1080 " --> pdb=" O GLY B1117 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL B1081 " --> pdb=" O THR B1477 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1086 through 1092 removed outlier: 3.730A pdb=" N GLY B1104 " --> pdb=" O VAL B1430 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1157 through 1163 Processing sheet with id=AB4, first strand: chain 'B' and resid 1319 through 1320 Processing sheet with id=AB5, first strand: chain 'B' and resid 1355 through 1359 Processing sheet with id=AB6, first strand: chain 'B' and resid 1487 through 1489 removed outlier: 6.735A pdb=" N SER B1463 " --> pdb=" O CYS B1452 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N CYS B1452 " --> pdb=" O SER B1463 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS B1465 " --> pdb=" O LEU B1450 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU B1450 " --> pdb=" O LYS B1465 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG B1467 " --> pdb=" O ALA B1448 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N GLU B1545 " --> pdb=" O CYS B1452 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N GLY B1454 " --> pdb=" O GLU B1545 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1480 through 1482 Processing sheet with id=AB8, first strand: chain 'C' and resid 1245 through 1248 removed outlier: 4.913A pdb=" N MET C1220 " --> pdb=" O SER C1152 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N SER C1152 " --> pdb=" O MET C1220 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL C1222 " --> pdb=" O TYR C1150 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TYR C1150 " --> pdb=" O VAL C1222 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TRP C1224 " --> pdb=" O PHE C1148 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE C1148 " --> pdb=" O TRP C1224 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL C1226 " --> pdb=" O PRO C1146 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TYR C1228 " --> pdb=" O TYR C1144 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TYR C1144 " --> pdb=" O TYR C1228 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS C1230 " --> pdb=" O GLN C1142 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLN C1142 " --> pdb=" O LYS C1230 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLU C1232 " --> pdb=" O LEU C1140 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU C1140 " --> pdb=" O GLU C1232 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE C1234 " --> pdb=" O MET C1138 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LEU C1140 " --> pdb=" O PRO C1417 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU C1413 " --> pdb=" O TYR C1144 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU C1411 " --> pdb=" O PRO C1146 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE C1148 " --> pdb=" O PRO C1409 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN C1410 " --> pdb=" O VAL C1402 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL C1402 " --> pdb=" O GLN C1410 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASP C1412 " --> pdb=" O LYS C1400 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS C1400 " --> pdb=" O ASP C1412 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS C1414 " --> pdb=" O HIS C1398 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 1297 through 1300 removed outlier: 4.440A pdb=" N MET C1220 " --> pdb=" O HIS C1282 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N MET C1220 " --> pdb=" O SER C1152 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N SER C1152 " --> pdb=" O MET C1220 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL C1222 " --> pdb=" O TYR C1150 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TYR C1150 " --> pdb=" O VAL C1222 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TRP C1224 " --> pdb=" O PHE C1148 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE C1148 " --> pdb=" O TRP C1224 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL C1226 " --> pdb=" O PRO C1146 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TYR C1228 " --> pdb=" O TYR C1144 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TYR C1144 " --> pdb=" O TYR C1228 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS C1230 " --> pdb=" O GLN C1142 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLN C1142 " --> pdb=" O LYS C1230 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLU C1232 " --> pdb=" O LEU C1140 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU C1140 " --> pdb=" O GLU C1232 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE C1234 " --> pdb=" O MET C1138 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR C1116 " --> pdb=" O VAL C1137 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N THR C1080 " --> pdb=" O GLY C1117 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL C1081 " --> pdb=" O THR C1477 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 1086 through 1092 removed outlier: 3.731A pdb=" N GLY C1104 " --> pdb=" O VAL C1430 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 1157 through 1163 Processing sheet with id=AC3, first strand: chain 'C' and resid 1319 through 1320 Processing sheet with id=AC4, first strand: chain 'C' and resid 1355 through 1359 Processing sheet with id=AC5, first strand: chain 'C' and resid 1487 through 1489 removed outlier: 6.734A pdb=" N SER C1463 " --> pdb=" O CYS C1452 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N CYS C1452 " --> pdb=" O SER C1463 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS C1465 " --> pdb=" O LEU C1450 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU C1450 " --> pdb=" O LYS C1465 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG C1467 " --> pdb=" O ALA C1448 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N GLU C1545 " --> pdb=" O CYS C1452 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLY C1454 " --> pdb=" O GLU C1545 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1480 through 1482 297 hydrogen bonds defined for protein. 756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.08 Time building geometry restraints manager: 5.05 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: 99.97 - 106.78: 316 106.78 - 113.59: 5951 113.59 - 120.40: 3511 120.40 - 127.21: 4100 127.21 - 134.03: 144 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 2.440 nonbonded pdb=" OG SER A1103 " pdb=" O VAL A1430 " model vdw 2.300 2.440 nonbonded pdb=" OG SER C1103 " pdb=" O VAL C1430 " model vdw 2.300 2.440 nonbonded pdb=" OG SER B1103 " pdb=" O VAL B1430 " model vdw 2.300 2.440 nonbonded pdb=" OD1 ASN C1361 " pdb=" OG SER C1367 " model vdw 2.306 2.440 ... (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 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: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.790 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 30.250 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.360 ------------------------------------------------------------------------------- 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 10353 Z= 0.388 Angle : 0.770 9.331 14022 Z= 0.411 Chirality : 0.049 0.156 1614 Planarity : 0.005 0.050 1755 Dihedral : 14.364 85.695 3765 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.23), residues: 1254 helix: -0.08 (0.95), residues: 33 sheet: -0.63 (0.21), residues: 597 loop : -1.52 (0.23), residues: 624 *********************** 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 fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.312 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 1.4844 time to fit residues: 250.2291 Evaluate side-chains 123 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.198 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1256 ASN A1271 GLN A1396 HIS B1256 ASN B1375 GLN B1396 HIS C1256 ASN C1375 GLN C1396 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 10353 Z= 0.285 Angle : 0.636 6.540 14022 Z= 0.334 Chirality : 0.046 0.162 1614 Planarity : 0.005 0.041 1755 Dihedral : 5.719 24.577 1356 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.23), residues: 1254 helix: -0.12 (1.04), residues: 33 sheet: -0.55 (0.21), residues: 594 loop : -1.46 (0.23), residues: 627 *********************** 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 168 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 1.281 Fit side-chains outliers start: 27 outliers final: 7 residues processed: 152 average time/residue: 1.4032 time to fit residues: 228.2672 Evaluate side-chains 134 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 127 time to evaluate : 1.261 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 1 residues processed: 6 average time/residue: 0.8854 time to fit residues: 7.5580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 0.0970 chunk 97 optimal weight: 6.9990 chunk 79 optimal weight: 0.0270 chunk 32 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 94 optimal weight: 6.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1256 ASN C1256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 10353 Z= 0.147 Angle : 0.520 7.016 14022 Z= 0.272 Chirality : 0.042 0.150 1614 Planarity : 0.004 0.040 1755 Dihedral : 4.888 23.149 1356 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.23), residues: 1254 helix: 0.20 (1.11), residues: 33 sheet: -0.41 (0.22), residues: 597 loop : -1.34 (0.23), residues: 624 *********************** 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 168 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 152 time to evaluate : 1.108 Fit side-chains outliers start: 16 outliers final: 4 residues processed: 158 average time/residue: 1.3867 time to fit residues: 234.4768 Evaluate side-chains 135 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 131 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 3 average time/residue: 1.7202 time to fit residues: 7.0596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 60 optimal weight: 0.1980 chunk 12 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1256 ASN B1546 GLN C1256 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 10353 Z= 0.376 Angle : 0.675 6.344 14022 Z= 0.355 Chirality : 0.048 0.166 1614 Planarity : 0.005 0.044 1755 Dihedral : 5.636 23.998 1356 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer Outliers : 3.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.23), residues: 1254 helix: -0.17 (1.03), residues: 33 sheet: -0.44 (0.22), residues: 567 loop : -1.44 (0.21), residues: 654 *********************** 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 182 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 137 time to evaluate : 1.340 Fit side-chains outliers start: 45 outliers final: 23 residues processed: 161 average time/residue: 1.3537 time to fit residues: 233.5961 Evaluate side-chains 154 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 1.343 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 11 residues processed: 12 average time/residue: 0.2409 time to fit residues: 5.6713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1256 ASN A1377 ASN B1377 ASN C1377 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 10353 Z= 0.168 Angle : 0.541 7.135 14022 Z= 0.283 Chirality : 0.043 0.150 1614 Planarity : 0.004 0.045 1755 Dihedral : 4.985 23.440 1356 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.23), residues: 1254 helix: 0.12 (1.09), residues: 33 sheet: -0.31 (0.22), residues: 561 loop : -1.31 (0.22), residues: 660 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 139 time to evaluate : 1.296 Fit side-chains outliers start: 32 outliers final: 12 residues processed: 157 average time/residue: 1.4513 time to fit residues: 243.7833 Evaluate side-chains 145 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 133 time to evaluate : 1.328 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 4 average time/residue: 1.1440 time to fit residues: 6.8420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1256 ASN A1271 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.058 10353 Z= 0.516 Angle : 0.761 7.562 14022 Z= 0.400 Chirality : 0.051 0.166 1614 Planarity : 0.005 0.047 1755 Dihedral : 5.923 24.449 1356 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer Outliers : 3.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.22), residues: 1254 helix: -0.31 (1.01), residues: 33 sheet: -0.55 (0.22), residues: 573 loop : -1.43 (0.22), residues: 648 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 138 time to evaluate : 1.265 Fit side-chains outliers start: 38 outliers final: 20 residues processed: 160 average time/residue: 1.3412 time to fit residues: 230.4747 Evaluate side-chains 157 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 1.259 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 11 residues processed: 9 average time/residue: 0.1295 time to fit residues: 3.6512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 105 optimal weight: 0.4980 chunk 69 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 10353 Z= 0.172 Angle : 0.546 7.390 14022 Z= 0.287 Chirality : 0.043 0.150 1614 Planarity : 0.005 0.048 1755 Dihedral : 5.038 23.162 1356 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.23), residues: 1254 helix: 0.20 (1.10), residues: 33 sheet: -0.32 (0.22), residues: 579 loop : -1.38 (0.22), residues: 642 *********************** 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 155 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 1.155 Fit side-chains outliers start: 20 outliers final: 14 residues processed: 149 average time/residue: 1.4088 time to fit residues: 224.8407 Evaluate side-chains 142 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 1.238 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 1.6945 time to fit residues: 7.0290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 10.0000 chunk 74 optimal weight: 0.0670 chunk 37 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 0.0070 chunk 97 optimal weight: 0.0270 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 10353 Z= 0.171 Angle : 0.544 7.137 14022 Z= 0.285 Chirality : 0.043 0.153 1614 Planarity : 0.004 0.047 1755 Dihedral : 4.919 22.797 1356 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.23), residues: 1254 helix: 0.27 (1.09), residues: 33 sheet: -0.30 (0.22), residues: 567 loop : -1.26 (0.22), residues: 654 *********************** 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 150 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 129 time to evaluate : 1.276 Fit side-chains outliers start: 21 outliers final: 16 residues processed: 142 average time/residue: 1.3389 time to fit residues: 204.0265 Evaluate side-chains 141 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 1.385 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 0.7071 time to fit residues: 4.9946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 76 optimal weight: 0.4980 chunk 122 optimal weight: 0.2980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 10353 Z= 0.287 Angle : 0.622 7.046 14022 Z= 0.327 Chirality : 0.045 0.162 1614 Planarity : 0.004 0.044 1755 Dihedral : 5.359 23.144 1356 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.23), residues: 1254 helix: 0.05 (1.05), residues: 33 sheet: -0.28 (0.22), residues: 561 loop : -1.30 (0.22), residues: 660 *********************** 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 155 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 1.282 Fit side-chains outliers start: 24 outliers final: 19 residues processed: 144 average time/residue: 1.4007 time to fit residues: 216.0263 Evaluate side-chains 149 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 1.239 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 12 residues processed: 7 average time/residue: 0.8617 time to fit residues: 8.4303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 128 optimal weight: 0.0370 chunk 118 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 10 optimal weight: 20.0000 chunk 79 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 10353 Z= 0.188 Angle : 0.556 7.223 14022 Z= 0.292 Chirality : 0.043 0.154 1614 Planarity : 0.004 0.045 1755 Dihedral : 5.014 22.843 1356 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.23), residues: 1254 helix: 0.16 (1.08), residues: 33 sheet: -0.29 (0.22), residues: 567 loop : -1.23 (0.23), residues: 654 ********************** 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 138 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 126 time to evaluate : 1.413 Fit side-chains outliers start: 12 outliers final: 12 residues processed: 138 average time/residue: 1.4047 time to fit residues: 208.4669 Evaluate side-chains 135 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 1.285 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 1.7559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 0.3980 chunk 94 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.161534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.133024 restraints weight = 10046.460| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.60 r_work: 0.3366 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 10353 Z= 0.194 Angle : 0.560 7.286 14022 Z= 0.293 Chirality : 0.043 0.155 1614 Planarity : 0.004 0.045 1755 Dihedral : 4.980 22.503 1356 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.23), residues: 1254 helix: 0.19 (1.07), residues: 33 sheet: -0.27 (0.22), residues: 570 loop : -1.22 (0.23), residues: 651 =============================================================================== Job complete usr+sys time: 4145.23 seconds wall clock time: 74 minutes 21.26 seconds (4461.26 seconds total)