Starting phenix.real_space_refine on Fri Sep 11 18:25:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wxr_21962/09_2026/6wxr_21962.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wxr_21962/09_2026/6wxr_21962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wxr_21962/09_2026/6wxr_21962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wxr_21962/09_2026/6wxr_21962.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wxr_21962/09_2026/6wxr_21962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wxr_21962/09_2026/6wxr_21962.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6wxr_21962/09_2026/6wxr_21962.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wxr_21962/09_2026/6wxr_21962.cif" } resolution = 3.2 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= 0.011 sd= 0.091 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: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 P 2 5.49 5 S 42 5.16 5 C 6775 2.51 5 N 1776 2.21 5 O 1812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10409 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1075, 8409 Classifications: {'peptide': 1075} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 70, 'TRANS': 1004} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 12, 'ARG:plan': 7, 'GLU:plan': 17, 'ASN:plan1': 4, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 194 Chain: "B" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1744 Classifications: {'peptide': 228} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 11, 'TRANS': 216} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 181 Unusual residues: {'FAD': 1, 'HEM': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.24, per 1000 atoms: 0.22 Number of scatterers: 10409 At special positions: 0 Unit cell: (89.64, 99.36, 155.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 S 42 16.00 P 2 15.00 O 1812 8.00 N 1776 7.00 C 6775 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A1165 " distance=2.04 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 565 " distance=2.04 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 579 " distance=2.03 Simple disulfide: pdb=" SG CYS B 167 " - pdb=" SG CYS B 234 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " MAN C 4 " - " MAN C 5 " ALPHA1-6 " BMA C 3 " - " MAN C 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG A1602 " - " ASN A 94 " " NAG A1603 " - " ASN A 342 " " NAG A1604 " - " ASN A 534 " " NAG B 406 " - " ASN B 84 " " NAG C 1 " - " ASN B 109 " Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 501.2 milliseconds 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2412 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 8 sheets defined 47.7% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 74 through 83 removed outlier: 3.671A pdb=" N ASN A 80 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG A 81 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 111 removed outlier: 3.704A pdb=" N VAL A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 108 " --> pdb=" O TYR A 104 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 110 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 267 removed outlier: 4.075A pdb=" N LEU A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 300 removed outlier: 3.787A pdb=" N LEU A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Proline residue: A 297 - end of helix Processing helix chain 'A' and resid 319 through 331 removed outlier: 3.526A pdb=" N VAL A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 389 Processing helix chain 'A' and resid 401 through 406 Processing helix chain 'A' and resid 419 through 430 removed outlier: 3.584A pdb=" N LEU A 424 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 453 Processing helix chain 'A' and resid 462 through 472 removed outlier: 3.626A pdb=" N GLU A 466 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 467 " --> pdb=" O THR A 463 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 487 Processing helix chain 'A' and resid 494 through 511 removed outlier: 3.818A pdb=" N THR A 499 " --> pdb=" O PRO A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 533 Processing helix chain 'A' and resid 536 through 546 removed outlier: 3.618A pdb=" N ILE A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 604 Processing helix chain 'A' and resid 604 through 621 removed outlier: 4.039A pdb=" N VAL A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1041 Processing helix chain 'A' and resid 1041 through 1068 removed outlier: 3.648A pdb=" N PHE A1068 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1104 removed outlier: 4.295A pdb=" N ALA A1091 " --> pdb=" O ARG A1087 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A1092 " --> pdb=" O GLY A1088 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET A1104 " --> pdb=" O ILE A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1113 removed outlier: 3.583A pdb=" N ILE A1109 " --> pdb=" O CYS A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1156 Processing helix chain 'A' and resid 1159 through 1164 Processing helix chain 'A' and resid 1181 through 1188 removed outlier: 3.536A pdb=" N TRP A1185 " --> pdb=" O LYS A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1208 Processing helix chain 'A' and resid 1210 through 1215 removed outlier: 3.708A pdb=" N ARG A1215 " --> pdb=" O HIS A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1225 removed outlier: 3.514A pdb=" N HIS A1225 " --> pdb=" O PHE A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1240 removed outlier: 3.896A pdb=" N ILE A1236 " --> pdb=" O TYR A1232 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY A1239 " --> pdb=" O LEU A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1253 removed outlier: 3.572A pdb=" N PHE A1252 " --> pdb=" O ARG A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1253 through 1270 removed outlier: 3.945A pdb=" N ARG A1270 " --> pdb=" O VAL A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1287 removed outlier: 4.101A pdb=" N GLY A1286 " --> pdb=" O LEU A1283 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A1287 " --> pdb=" O PRO A1284 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1283 through 1287' Processing helix chain 'A' and resid 1340 through 1350 Processing helix chain 'A' and resid 1375 through 1379 removed outlier: 3.639A pdb=" N LYS A1379 " --> pdb=" O GLU A1376 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1393 removed outlier: 3.519A pdb=" N THR A1393 " --> pdb=" O ILE A1390 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1390 through 1393' Processing helix chain 'A' and resid 1394 through 1410 removed outlier: 3.741A pdb=" N CYS A1410 " --> pdb=" O SER A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1443 Processing helix chain 'A' and resid 1497 through 1509 removed outlier: 3.685A pdb=" N PHE A1501 " --> pdb=" O PRO A1497 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE A1502 " --> pdb=" O PHE A1498 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASN A1503 " --> pdb=" O GLU A1499 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A1507 " --> pdb=" O ASN A1503 " (cutoff:3.500A) Processing helix chain 'A' and resid 1522 through 1538 removed outlier: 3.854A pdb=" N ARG A1538 " --> pdb=" O GLN A1534 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 72 Processing helix chain 'B' and resid 137 through 149 removed outlier: 4.049A pdb=" N GLU B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 160 Processing helix chain 'B' and resid 172 through 180 removed outlier: 3.587A pdb=" N ALA B 176 " --> pdb=" O GLN B 172 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 200 removed outlier: 3.825A pdb=" N LEU B 189 " --> pdb=" O TRP B 185 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TRP B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 208 through 219 removed outlier: 3.780A pdb=" N GLY B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.553A pdb=" N SER B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 275 removed outlier: 3.549A pdb=" N TRP B 252 " --> pdb=" O GLY B 248 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 126 Processing sheet with id=AA2, first strand: chain 'A' and resid 337 through 338 Processing sheet with id=AA3, first strand: chain 'A' and resid 1333 through 1336 removed outlier: 3.665A pdb=" N ILE A1336 " --> pdb=" O THR A1288 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1305 through 1308 Processing sheet with id=AA5, first strand: chain 'A' and resid 1449 through 1453 removed outlier: 3.632A pdb=" N TYR A1453 " --> pdb=" O TRP A1421 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1449 through 1453 removed outlier: 3.632A pdb=" N TYR A1453 " --> pdb=" O TRP A1421 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N CYS A1520 " --> pdb=" O VAL A1384 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL A1386 " --> pdb=" O CYS A1520 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 81 through 86 removed outlier: 13.619A pdb=" N TRP B 94 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 12.173A pdb=" N VAL B 117 " --> pdb=" O TRP B 94 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N SER B 96 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 11.146A pdb=" N THR B 111 " --> pdb=" O PHE B 130 " (cutoff:3.500A) removed outlier: 12.312A pdb=" N PHE B 130 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 11.137A pdb=" N THR B 113 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 12.304A pdb=" N GLU B 128 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 11.254A pdb=" N THR B 115 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 11.817A pdb=" N TYR B 126 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N VAL B 117 " --> pdb=" O ILE B 124 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 81 through 86 444 hydrogen bonds defined for protein. 1290 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: 1.87 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 1556 1.30 - 1.44: 3285 1.44 - 1.59: 5823 1.59 - 1.73: 3 1.73 - 1.87: 71 Bond restraints: 10738 Sorted by residual: bond pdb=" C3B HEM A1605 " pdb=" C4B HEM A1605 " ideal model delta sigma weight residual 1.449 1.292 0.157 2.00e-02 2.50e+03 6.17e+01 bond pdb=" C ILE A1237 " pdb=" O ILE A1237 " ideal model delta sigma weight residual 1.237 1.158 0.079 1.23e-02 6.61e+03 4.11e+01 bond pdb=" CAB HEM A1605 " pdb=" CBB HEM A1605 " ideal model delta sigma weight residual 1.337 1.209 0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C3B HEM A1606 " pdb=" C4B HEM A1606 " ideal model delta sigma weight residual 1.449 1.323 0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" C HIS A1238 " pdb=" O HIS A1238 " ideal model delta sigma weight residual 1.237 1.163 0.073 1.17e-02 7.31e+03 3.93e+01 ... (remaining 10733 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 14346 2.77 - 5.53: 262 5.53 - 8.30: 53 8.30 - 11.06: 12 11.06 - 13.83: 5 Bond angle restraints: 14678 Sorted by residual: angle pdb=" N PRO A1352 " pdb=" CA PRO A1352 " pdb=" CB PRO A1352 " ideal model delta sigma weight residual 103.08 110.67 -7.59 9.70e-01 1.06e+00 6.12e+01 angle pdb=" C1C HEM A1605 " pdb=" CHC HEM A1605 " pdb=" C4B HEM A1605 " ideal model delta sigma weight residual 126.00 112.17 13.83 3.00e+00 1.11e-01 2.12e+01 angle pdb=" C SER A1240 " pdb=" N PHE A1241 " pdb=" CA PHE A1241 " ideal model delta sigma weight residual 121.91 130.78 -8.87 2.03e+00 2.43e-01 1.91e+01 angle pdb=" CA ILE A1237 " pdb=" C ILE A1237 " pdb=" N HIS A1238 " ideal model delta sigma weight residual 117.53 122.67 -5.14 1.19e+00 7.06e-01 1.87e+01 angle pdb=" C LEU A1235 " pdb=" N ILE A1236 " pdb=" CA ILE A1236 " ideal model delta sigma weight residual 122.35 117.31 5.04 1.18e+00 7.18e-01 1.82e+01 ... (remaining 14673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5457 17.98 - 35.96: 521 35.96 - 53.94: 81 53.94 - 71.93: 13 71.93 - 89.91: 7 Dihedral angle restraints: 6079 sinusoidal: 2322 harmonic: 3757 Sorted by residual: dihedral pdb=" CA CYS A 118 " pdb=" C CYS A 118 " pdb=" N PRO A 119 " pdb=" CA PRO A 119 " ideal model delta harmonic sigma weight residual 180.00 116.55 63.45 0 5.00e+00 4.00e-02 1.61e+02 dihedral pdb=" CA THR B 115 " pdb=" C THR B 115 " pdb=" N PRO B 116 " pdb=" CA PRO B 116 " ideal model delta harmonic sigma weight residual 180.00 154.40 25.60 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" C2C HEM A1606 " pdb=" C3C HEM A1606 " pdb=" CAC HEM A1606 " pdb=" CBC HEM A1606 " ideal model delta sinusoidal sigma weight residual 180.00 132.40 47.60 2 1.00e+01 1.00e-02 2.62e+01 ... (remaining 6076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1480 0.074 - 0.147: 134 0.147 - 0.221: 3 0.221 - 0.295: 2 0.295 - 0.368: 1 Chirality restraints: 1620 Sorted by residual: chirality pdb=" C1 NAG A1604 " pdb=" ND2 ASN A 534 " pdb=" C2 NAG A1604 " pdb=" O5 NAG A1604 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA PRO A1352 " pdb=" N PRO A1352 " pdb=" C PRO A1352 " pdb=" CB PRO A1352 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1617 not shown) Planarity restraints: 1837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A1235 " -0.026 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" C LEU A1235 " 0.088 2.00e-02 2.50e+03 pdb=" O LEU A1235 " -0.032 2.00e-02 2.50e+03 pdb=" N ILE A1236 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND HEM A1605 " -0.001 2.00e-02 2.50e+03 2.66e-02 1.59e+01 pdb=" C1D HEM A1605 " 0.007 2.00e-02 2.50e+03 pdb=" C2D HEM A1605 " 0.013 2.00e-02 2.50e+03 pdb=" C3D HEM A1605 " -0.061 2.00e-02 2.50e+03 pdb=" C4D HEM A1605 " 0.010 2.00e-02 2.50e+03 pdb=" CAD HEM A1605 " -0.007 2.00e-02 2.50e+03 pdb=" CHA HEM A1605 " 0.025 2.00e-02 2.50e+03 pdb=" CHD HEM A1605 " -0.021 2.00e-02 2.50e+03 pdb=" CMD HEM A1605 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEM A1605 " -0.060 2.00e-02 2.50e+03 2.52e-02 1.43e+01 pdb=" C2A HEM A1605 " 0.003 2.00e-02 2.50e+03 pdb=" C3A HEM A1605 " -0.004 2.00e-02 2.50e+03 pdb=" C4A HEM A1605 " 0.031 2.00e-02 2.50e+03 pdb=" CAA HEM A1605 " 0.000 2.00e-02 2.50e+03 pdb=" CHA HEM A1605 " 0.027 2.00e-02 2.50e+03 pdb=" CHB HEM A1605 " -0.016 2.00e-02 2.50e+03 pdb=" CMA HEM A1605 " 0.006 2.00e-02 2.50e+03 pdb=" NA HEM A1605 " 0.013 2.00e-02 2.50e+03 ... (remaining 1834 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.19: 5 2.19 - 2.87: 3824 2.87 - 3.55: 14046 3.55 - 4.22: 23282 4.22 - 4.90: 41624 Nonbonded interactions: 82781 Sorted by model distance: nonbonded pdb=" CE1 HIS A1238 " pdb="FE HEM A1606 " model vdw 1.518 3.220 nonbonded pdb=" O2' FAD A1601 " pdb=" O4' FAD A1601 " model vdw 1.995 3.040 nonbonded pdb=" CE1 HIS A1238 " pdb=" NA HEM A1606 " model vdw 2.027 3.340 nonbonded pdb=" O SER A1240 " pdb=" OG SER A1240 " model vdw 2.040 3.040 nonbonded pdb=" OH TYR A 36 " pdb=" O LEU B 146 " model vdw 2.137 3.040 ... (remaining 82776 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.960 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 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 : 0.011 0.263 10751 Z= 0.433 Angle : 0.971 13.825 14713 Z= 0.486 Chirality : 0.044 0.368 1620 Planarity : 0.005 0.055 1832 Dihedral : 14.151 89.908 3655 Min Nonbonded Distance : 1.518 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.61 % Favored : 93.31 % Rotamer: Outliers : 0.19 % Allowed : 4.96 % Favored : 94.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: -3.63 (0.20), residues: 1285 helix: -1.77 (0.18), residues: 613 sheet: -1.86 (0.47), residues: 110 loop : -3.25 (0.22), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 76 TYR 0.014 0.001 TYR A1099 PHE 0.014 0.001 PHE B 222 TRP 0.027 0.001 TRP A1421 HIS 0.014 0.001 HIS A1238 Details of bonding type rmsd/Z covalent geometry : bond 0.01055 / 0.43 (10738) covalent geometry : angle 0.96274 / 0.48 (14678) SS BOND : bond 0.00422 / 0.21 ( 4) SS BOND : angle 1.76810 / 0.83 ( 8) hydrogen bonds : bond 0.16112 / 10.53 ( 430) hydrogen bonds : angle 6.63273 / 4.81 ( 1290) link_ALPHA1-3 : bond 0.00559 / 0.29 ( 1) link_ALPHA1-3 : angle 4.18883 / 2.16 ( 3) link_ALPHA1-6 : bond 0.00659 / 0.35 ( 1) link_ALPHA1-6 : angle 1.84496 / 1.01 ( 3) link_BETA1-4 : bond 0.01240 / 0.62 ( 2) link_BETA1-4 : angle 1.79217 / 0.97 ( 6) link_NAG-ASN : bond 0.00688 / 0.34 ( 5) link_NAG-ASN : angle 3.26384 / 2.30 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 1495 ARG cc_start: 0.7145 (mmm160) cc_final: 0.6819 (ptp90) REVERT: A 1501 PHE cc_start: 0.7263 (t80) cc_final: 0.6882 (t80) REVERT: B 136 ARG cc_start: 0.7698 (mtp85) cc_final: 0.7304 (mtp180) REVERT: B 197 MET cc_start: 0.7935 (mtt) cc_final: 0.7694 (mtt) outliers start: 2 outliers final: 2 residues processed: 110 average time/residue: 0.1181 time to fit residues: 17.7301 Evaluate side-chains 79 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1236 ILE Chi-restraints excluded: chain A residue 1240 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 ASN A 405 GLN A 504 GLN A1107 ASN A1130 HIS A1212 HIS A1238 HIS A1319 HIS B 71 ASN B 119 GLN B 208 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.154840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.119948 restraints weight = 16534.940| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.22 r_work: 0.3552 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10751 Z= 0.193 Angle : 0.787 17.648 14713 Z= 0.357 Chirality : 0.047 0.419 1620 Planarity : 0.005 0.057 1832 Dihedral : 7.462 87.657 1442 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.32 % Favored : 92.61 % Rotamer: Outliers : 1.53 % Allowed : 8.58 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: -2.42 (0.22), residues: 1285 helix: -0.64 (0.20), residues: 605 sheet: -1.71 (0.45), residues: 116 loop : -2.66 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 362 TYR 0.014 0.002 TYR A1099 PHE 0.015 0.002 PHE A 253 TRP 0.023 0.001 TRP A1421 HIS 0.004 0.001 HIS A1148 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.19 (10738) covalent geometry : angle 0.77954 / 0.36 (14678) SS BOND : bond 0.00384 / 0.19 ( 4) SS BOND : angle 1.43626 / 0.68 ( 8) hydrogen bonds : bond 0.05708 / 3.93 ( 430) hydrogen bonds : angle 4.93598 / 3.58 ( 1290) link_ALPHA1-3 : bond 0.01065 / 0.56 ( 1) link_ALPHA1-3 : angle 3.01924 / 1.52 ( 3) link_ALPHA1-6 : bond 0.00608 / 0.32 ( 1) link_ALPHA1-6 : angle 2.22226 / 1.19 ( 3) link_BETA1-4 : bond 0.01192 / 0.57 ( 2) link_BETA1-4 : angle 2.27664 / 1.29 ( 6) link_NAG-ASN : bond 0.00618 / 0.31 ( 5) link_NAG-ASN : angle 2.52777 / 1.47 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 GLN cc_start: 0.7864 (mp10) cc_final: 0.7232 (mp10) REVERT: A 300 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8212 (pp) REVERT: A 1241 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7368 (m-80) REVERT: A 1288 THR cc_start: 0.9136 (OUTLIER) cc_final: 0.8907 (t) REVERT: A 1365 TYR cc_start: 0.8149 (m-80) cc_final: 0.7855 (m-80) REVERT: A 1374 HIS cc_start: 0.7105 (m-70) cc_final: 0.6852 (m-70) REVERT: A 1495 ARG cc_start: 0.7762 (mmm160) cc_final: 0.6368 (ptp90) REVERT: A 1501 PHE cc_start: 0.7135 (t80) cc_final: 0.6573 (t80) REVERT: B 88 LYS cc_start: 0.7513 (pttp) cc_final: 0.7312 (ptmt) REVERT: B 197 MET cc_start: 0.7943 (mtt) cc_final: 0.7640 (mtp) outliers start: 16 outliers final: 7 residues processed: 97 average time/residue: 0.1077 time to fit residues: 14.9174 Evaluate side-chains 90 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1241 PHE Chi-restraints excluded: chain A residue 1288 THR Chi-restraints excluded: chain A residue 1366 LEU Chi-restraints excluded: chain A residue 1535 LEU Chi-restraints excluded: chain B residue 99 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 8 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 61 optimal weight: 0.0870 chunk 90 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 ASN A1375 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.156343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.120987 restraints weight = 16572.936| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.20 r_work: 0.3567 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10751 Z= 0.167 Angle : 0.710 12.563 14713 Z= 0.333 Chirality : 0.046 0.420 1620 Planarity : 0.005 0.054 1832 Dihedral : 7.374 87.558 1439 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.77 % Favored : 93.15 % Rotamer: Outliers : 2.10 % Allowed : 10.10 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: -1.90 (0.23), residues: 1285 helix: -0.13 (0.21), residues: 602 sheet: -1.58 (0.47), residues: 110 loop : -2.48 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 84 TYR 0.015 0.001 TYR A1099 PHE 0.020 0.001 PHE A1404 TRP 0.018 0.001 TRP A1421 HIS 0.005 0.001 HIS A1144 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (10738) covalent geometry : angle 0.70272 / 0.33 (14678) SS BOND : bond 0.00346 / 0.17 ( 4) SS BOND : angle 1.28876 / 0.61 ( 8) hydrogen bonds : bond 0.05255 / 3.61 ( 430) hydrogen bonds : angle 4.68520 / 3.37 ( 1290) link_ALPHA1-3 : bond 0.01272 / 0.67 ( 1) link_ALPHA1-3 : angle 2.81718 / 1.43 ( 3) link_ALPHA1-6 : bond 0.00639 / 0.34 ( 1) link_ALPHA1-6 : angle 2.02298 / 1.09 ( 3) link_BETA1-4 : bond 0.01096 / 0.53 ( 2) link_BETA1-4 : angle 2.18405 / 1.23 ( 6) link_NAG-ASN : bond 0.00623 / 0.32 ( 5) link_NAG-ASN : angle 2.43694 / 1.44 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 265 GLN cc_start: 0.7860 (mp10) cc_final: 0.7224 (mp10) REVERT: A 300 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8203 (pp) REVERT: A 481 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.6548 (tp) REVERT: A 1241 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.7303 (m-80) REVERT: A 1288 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8883 (t) REVERT: A 1365 TYR cc_start: 0.8220 (m-80) cc_final: 0.7928 (m-80) REVERT: A 1367 ASP cc_start: 0.8618 (t0) cc_final: 0.8361 (t0) REVERT: A 1374 HIS cc_start: 0.7003 (m-70) cc_final: 0.6791 (m-70) REVERT: A 1495 ARG cc_start: 0.7747 (mmm160) cc_final: 0.6370 (ptp90) REVERT: A 1501 PHE cc_start: 0.7134 (t80) cc_final: 0.6644 (t80) REVERT: B 197 MET cc_start: 0.7930 (mtt) cc_final: 0.7608 (mtp) outliers start: 22 outliers final: 8 residues processed: 101 average time/residue: 0.1044 time to fit residues: 15.1609 Evaluate side-chains 91 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1241 PHE Chi-restraints excluded: chain A residue 1275 ILE Chi-restraints excluded: chain A residue 1288 THR Chi-restraints excluded: chain A residue 1366 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 274 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 47 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 121 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1226 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.154645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.119040 restraints weight = 16666.798| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.20 r_work: 0.3525 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 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 : 0.005 0.062 10751 Z= 0.213 Angle : 0.743 12.425 14713 Z= 0.351 Chirality : 0.047 0.408 1620 Planarity : 0.005 0.055 1832 Dihedral : 7.520 86.424 1439 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.32 % Favored : 92.61 % Rotamer: Outliers : 3.05 % Allowed : 11.82 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: -1.78 (0.23), residues: 1285 helix: -0.04 (0.21), residues: 613 sheet: -1.62 (0.47), residues: 112 loop : -2.40 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 362 TYR 0.015 0.002 TYR A1099 PHE 0.016 0.002 PHE A 253 TRP 0.020 0.001 TRP A1421 HIS 0.007 0.001 HIS A1225 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.21 (10738) covalent geometry : angle 0.73598 / 0.35 (14678) SS BOND : bond 0.00344 / 0.17 ( 4) SS BOND : angle 1.34521 / 0.65 ( 8) hydrogen bonds : bond 0.05604 / 3.87 ( 430) hydrogen bonds : angle 4.65291 / 3.33 ( 1290) link_ALPHA1-3 : bond 0.01304 / 0.69 ( 1) link_ALPHA1-3 : angle 2.45217 / 1.23 ( 3) link_ALPHA1-6 : bond 0.00858 / 0.45 ( 1) link_ALPHA1-6 : angle 2.18829 / 1.21 ( 3) link_BETA1-4 : bond 0.01062 / 0.52 ( 2) link_BETA1-4 : angle 2.22298 / 1.26 ( 6) link_NAG-ASN : bond 0.00647 / 0.33 ( 5) link_NAG-ASN : angle 2.39537 / 1.41 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 85 time to evaluate : 0.377 Fit side-chains REVERT: A 265 GLN cc_start: 0.7855 (mp10) cc_final: 0.7248 (mp10) REVERT: A 300 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8229 (pp) REVERT: A 339 TYR cc_start: 0.9121 (OUTLIER) cc_final: 0.8530 (m-10) REVERT: A 481 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.6547 (tp) REVERT: A 569 SER cc_start: 0.8508 (p) cc_final: 0.8261 (m) REVERT: A 1225 HIS cc_start: 0.8551 (OUTLIER) cc_final: 0.7865 (t-90) REVERT: A 1241 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.7145 (m-80) REVERT: A 1288 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8898 (t) REVERT: A 1367 ASP cc_start: 0.8652 (t0) cc_final: 0.8376 (t0) REVERT: A 1495 ARG cc_start: 0.7770 (mmm160) cc_final: 0.6391 (ptp90) REVERT: A 1501 PHE cc_start: 0.7099 (t80) cc_final: 0.6642 (t80) REVERT: B 179 TYR cc_start: 0.8474 (m-10) cc_final: 0.8181 (m-80) REVERT: B 197 MET cc_start: 0.8028 (mtt) cc_final: 0.7738 (mtp) outliers start: 32 outliers final: 14 residues processed: 112 average time/residue: 0.1012 time to fit residues: 16.3301 Evaluate side-chains 97 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1225 HIS Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1241 PHE Chi-restraints excluded: chain A residue 1275 ILE Chi-restraints excluded: chain A residue 1288 THR Chi-restraints excluded: chain A residue 1366 LEU Chi-restraints excluded: chain A residue 1535 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 260 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 64 optimal weight: 5.9990 chunk 100 optimal weight: 0.0470 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.158348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.123780 restraints weight = 16435.696| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.22 r_work: 0.3602 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10751 Z= 0.121 Angle : 0.654 12.739 14713 Z= 0.306 Chirality : 0.044 0.425 1620 Planarity : 0.004 0.053 1832 Dihedral : 7.306 89.003 1439 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.07 % Favored : 93.85 % Rotamer: Outliers : 2.19 % Allowed : 13.35 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: -1.38 (0.23), residues: 1285 helix: 0.27 (0.21), residues: 618 sheet: -1.57 (0.48), residues: 110 loop : -2.16 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1424 TYR 0.014 0.001 TYR A1099 PHE 0.015 0.001 PHE A1370 TRP 0.010 0.001 TRP A1421 HIS 0.004 0.001 HIS A1238 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (10738) covalent geometry : angle 0.64709 / 0.30 (14678) SS BOND : bond 0.00316 / 0.16 ( 4) SS BOND : angle 1.10695 / 0.52 ( 8) hydrogen bonds : bond 0.04442 / 3.03 ( 430) hydrogen bonds : angle 4.39686 / 3.15 ( 1290) link_ALPHA1-3 : bond 0.01002 / 0.53 ( 1) link_ALPHA1-3 : angle 2.86930 / 1.45 ( 3) link_ALPHA1-6 : bond 0.00668 / 0.35 ( 1) link_ALPHA1-6 : angle 1.83485 / 0.92 ( 3) link_BETA1-4 : bond 0.01007 / 0.49 ( 2) link_BETA1-4 : angle 2.16098 / 1.20 ( 6) link_NAG-ASN : bond 0.00581 / 0.29 ( 5) link_NAG-ASN : angle 2.22265 / 1.35 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.369 Fit side-chains REVERT: A 92 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7753 (tt) REVERT: A 265 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7222 (mp10) REVERT: A 300 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8125 (pp) REVERT: A 339 TYR cc_start: 0.9078 (OUTLIER) cc_final: 0.8434 (m-10) REVERT: A 414 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8278 (t80) REVERT: A 481 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6594 (tp) REVERT: A 1241 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.7068 (m-80) REVERT: A 1288 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8819 (t) REVERT: A 1495 ARG cc_start: 0.7648 (mmm160) cc_final: 0.6280 (ptp90) REVERT: A 1501 PHE cc_start: 0.6850 (t80) cc_final: 0.6498 (t80) REVERT: B 136 ARG cc_start: 0.8015 (mtp85) cc_final: 0.7752 (mtm180) REVERT: B 197 MET cc_start: 0.7800 (mtt) cc_final: 0.7500 (mtp) outliers start: 23 outliers final: 8 residues processed: 104 average time/residue: 0.0947 time to fit residues: 14.5614 Evaluate side-chains 96 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1241 PHE Chi-restraints excluded: chain A residue 1275 ILE Chi-restraints excluded: chain A residue 1288 THR Chi-restraints excluded: chain A residue 1366 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 274 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 82 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.156080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.120946 restraints weight = 16553.248| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.23 r_work: 0.3566 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10751 Z= 0.167 Angle : 0.692 12.339 14713 Z= 0.324 Chirality : 0.046 0.410 1620 Planarity : 0.005 0.056 1832 Dihedral : 7.281 89.811 1439 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.15 % Favored : 93.77 % Rotamer: Outliers : 2.57 % Allowed : 14.39 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: -1.26 (0.23), residues: 1285 helix: 0.40 (0.21), residues: 607 sheet: -1.59 (0.46), residues: 116 loop : -2.07 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 362 TYR 0.013 0.001 TYR A1099 PHE 0.015 0.001 PHE A 253 TRP 0.014 0.001 TRP A1421 HIS 0.006 0.001 HIS A1225 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (10738) covalent geometry : angle 0.68510 / 0.32 (14678) SS BOND : bond 0.00354 / 0.18 ( 4) SS BOND : angle 1.38175 / 0.72 ( 8) hydrogen bonds : bond 0.04938 / 3.40 ( 430) hydrogen bonds : angle 4.41760 / 3.16 ( 1290) link_ALPHA1-3 : bond 0.01175 / 0.62 ( 1) link_ALPHA1-3 : angle 2.49498 / 1.25 ( 3) link_ALPHA1-6 : bond 0.00701 / 0.37 ( 1) link_ALPHA1-6 : angle 1.92272 / 1.04 ( 3) link_BETA1-4 : bond 0.01012 / 0.49 ( 2) link_BETA1-4 : angle 2.14925 / 1.20 ( 6) link_NAG-ASN : bond 0.00591 / 0.30 ( 5) link_NAG-ASN : angle 2.21628 / 1.31 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.378 Fit side-chains REVERT: A 92 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7782 (tt) REVERT: A 265 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7282 (mp10) REVERT: A 300 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8162 (pp) REVERT: A 339 TYR cc_start: 0.9108 (OUTLIER) cc_final: 0.8532 (m-10) REVERT: A 414 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8302 (t80) REVERT: A 481 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6566 (tp) REVERT: A 1225 HIS cc_start: 0.8533 (OUTLIER) cc_final: 0.7885 (t-90) REVERT: A 1241 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.7144 (m-80) REVERT: A 1288 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8824 (t) REVERT: A 1402 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7446 (tt) REVERT: A 1495 ARG cc_start: 0.7721 (mmm160) cc_final: 0.6325 (ptp90) REVERT: A 1501 PHE cc_start: 0.6919 (t80) cc_final: 0.6576 (t80) REVERT: B 136 ARG cc_start: 0.8141 (mtp85) cc_final: 0.7885 (mtm180) outliers start: 27 outliers final: 12 residues processed: 105 average time/residue: 0.0997 time to fit residues: 15.2037 Evaluate side-chains 99 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1225 HIS Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1241 PHE Chi-restraints excluded: chain A residue 1275 ILE Chi-restraints excluded: chain A residue 1288 THR Chi-restraints excluded: chain A residue 1366 LEU Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 260 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 47 optimal weight: 2.9990 chunk 54 optimal weight: 0.0870 chunk 88 optimal weight: 6.9990 chunk 115 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 87 optimal weight: 0.0770 chunk 63 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 HIS B 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.159843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.125425 restraints weight = 16304.436| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.20 r_work: 0.3631 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10751 Z= 0.113 Angle : 0.641 12.691 14713 Z= 0.298 Chirality : 0.043 0.424 1620 Planarity : 0.004 0.053 1832 Dihedral : 7.083 89.485 1439 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.68 % Favored : 94.24 % Rotamer: Outliers : 2.76 % Allowed : 14.30 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: -1.02 (0.24), residues: 1285 helix: 0.65 (0.22), residues: 599 sheet: -1.53 (0.47), residues: 116 loop : -1.96 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1424 TYR 0.010 0.001 TYR A1099 PHE 0.014 0.001 PHE A1370 TRP 0.008 0.001 TRP A1421 HIS 0.004 0.001 HIS A1144 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (10738) covalent geometry : angle 0.63306 / 0.30 (14678) SS BOND : bond 0.00425 / 0.22 ( 4) SS BOND : angle 1.83828 / 0.98 ( 8) hydrogen bonds : bond 0.04158 / 2.83 ( 430) hydrogen bonds : angle 4.29362 / 3.08 ( 1290) link_ALPHA1-3 : bond 0.01139 / 0.60 ( 1) link_ALPHA1-3 : angle 2.70751 / 1.36 ( 3) link_ALPHA1-6 : bond 0.00632 / 0.33 ( 1) link_ALPHA1-6 : angle 1.72903 / 0.87 ( 3) link_BETA1-4 : bond 0.00913 / 0.44 ( 2) link_BETA1-4 : angle 2.09214 / 1.16 ( 6) link_NAG-ASN : bond 0.00569 / 0.29 ( 5) link_NAG-ASN : angle 2.18263 / 1.33 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.391 Fit side-chains REVERT: A 92 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7703 (tt) REVERT: A 265 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7251 (mp10) REVERT: A 300 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8120 (pp) REVERT: A 339 TYR cc_start: 0.9120 (OUTLIER) cc_final: 0.8535 (m-10) REVERT: A 414 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.8265 (t80) REVERT: A 481 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6608 (tp) REVERT: A 1058 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8106 (mp) REVERT: A 1225 HIS cc_start: 0.8492 (OUTLIER) cc_final: 0.7879 (t-90) REVERT: A 1288 THR cc_start: 0.8948 (OUTLIER) cc_final: 0.8740 (t) REVERT: A 1418 TYR cc_start: 0.7970 (m-80) cc_final: 0.7713 (m-80) REVERT: A 1495 ARG cc_start: 0.7579 (mmm160) cc_final: 0.6271 (ptp90) REVERT: A 1501 PHE cc_start: 0.6802 (t80) cc_final: 0.6462 (t80) REVERT: B 136 ARG cc_start: 0.8105 (mtp85) cc_final: 0.7789 (mtp180) outliers start: 29 outliers final: 17 residues processed: 112 average time/residue: 0.0911 time to fit residues: 15.0149 Evaluate side-chains 112 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1225 HIS Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1241 PHE Chi-restraints excluded: chain A residue 1275 ILE Chi-restraints excluded: chain A residue 1288 THR Chi-restraints excluded: chain A residue 1366 LEU Chi-restraints excluded: chain A residue 1535 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 274 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 0 optimal weight: 6.9990 chunk 78 optimal weight: 0.5980 chunk 120 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.157498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.122573 restraints weight = 16466.952| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.21 r_work: 0.3586 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10751 Z= 0.155 Angle : 0.676 12.330 14713 Z= 0.318 Chirality : 0.045 0.412 1620 Planarity : 0.005 0.053 1832 Dihedral : 7.092 89.795 1439 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.53 % Favored : 94.40 % Rotamer: Outliers : 3.15 % Allowed : 14.59 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: -1.03 (0.24), residues: 1285 helix: 0.59 (0.22), residues: 608 sheet: -1.52 (0.47), residues: 116 loop : -1.94 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1424 TYR 0.012 0.001 TYR A1099 PHE 0.014 0.001 PHE A 253 TRP 0.012 0.001 TRP A 252 HIS 0.005 0.001 HIS A1225 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.15 (10738) covalent geometry : angle 0.66905 / 0.32 (14678) SS BOND : bond 0.00341 / 0.17 ( 4) SS BOND : angle 1.68571 / 0.83 ( 8) hydrogen bonds : bond 0.04617 / 3.17 ( 430) hydrogen bonds : angle 4.34211 / 3.10 ( 1290) link_ALPHA1-3 : bond 0.01128 / 0.59 ( 1) link_ALPHA1-3 : angle 2.46100 / 1.22 ( 3) link_ALPHA1-6 : bond 0.00681 / 0.36 ( 1) link_ALPHA1-6 : angle 1.84600 / 0.99 ( 3) link_BETA1-4 : bond 0.00949 / 0.46 ( 2) link_BETA1-4 : angle 2.11592 / 1.18 ( 6) link_NAG-ASN : bond 0.00580 / 0.29 ( 5) link_NAG-ASN : angle 2.21303 / 1.31 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 86 time to evaluate : 0.376 Fit side-chains REVERT: A 92 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7763 (tt) REVERT: A 265 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7254 (mp10) REVERT: A 300 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8138 (pp) REVERT: A 339 TYR cc_start: 0.9126 (OUTLIER) cc_final: 0.8505 (m-10) REVERT: A 414 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8349 (t80) REVERT: A 587 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.6421 (m-80) REVERT: A 1058 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8059 (mp) REVERT: A 1225 HIS cc_start: 0.8510 (OUTLIER) cc_final: 0.7870 (t-90) REVERT: A 1288 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8784 (t) REVERT: A 1402 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7548 (tt) REVERT: A 1495 ARG cc_start: 0.7591 (mmm160) cc_final: 0.6174 (ptp90) REVERT: A 1501 PHE cc_start: 0.6794 (t80) cc_final: 0.6461 (t80) REVERT: B 136 ARG cc_start: 0.8115 (mtp85) cc_final: 0.7813 (mtp180) outliers start: 33 outliers final: 19 residues processed: 111 average time/residue: 0.0920 time to fit residues: 15.0302 Evaluate side-chains 113 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1225 HIS Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1241 PHE Chi-restraints excluded: chain A residue 1275 ILE Chi-restraints excluded: chain A residue 1288 THR Chi-restraints excluded: chain A residue 1366 LEU Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1403 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 274 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 60 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 64 optimal weight: 0.1980 chunk 91 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 ASN B 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.159510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.124854 restraints weight = 16362.338| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.21 r_work: 0.3627 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10751 Z= 0.121 Angle : 0.653 12.675 14713 Z= 0.306 Chirality : 0.044 0.422 1620 Planarity : 0.004 0.051 1832 Dihedral : 6.798 88.958 1439 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.68 % Favored : 94.24 % Rotamer: Outliers : 3.34 % Allowed : 14.30 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: -0.84 (0.24), residues: 1285 helix: 0.76 (0.22), residues: 600 sheet: -1.49 (0.48), residues: 116 loop : -1.81 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1424 TYR 0.011 0.001 TYR A1099 PHE 0.014 0.001 PHE A1370 TRP 0.008 0.001 TRP A1421 HIS 0.004 0.001 HIS A1144 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (10738) covalent geometry : angle 0.64658 / 0.30 (14678) SS BOND : bond 0.00331 / 0.17 ( 4) SS BOND : angle 1.44855 / 0.72 ( 8) hydrogen bonds : bond 0.04235 / 2.89 ( 430) hydrogen bonds : angle 4.27386 / 3.06 ( 1290) link_ALPHA1-3 : bond 0.01018 / 0.54 ( 1) link_ALPHA1-3 : angle 2.56332 / 1.28 ( 3) link_ALPHA1-6 : bond 0.00646 / 0.34 ( 1) link_ALPHA1-6 : angle 1.73663 / 0.89 ( 3) link_BETA1-4 : bond 0.00880 / 0.43 ( 2) link_BETA1-4 : angle 2.09701 / 1.16 ( 6) link_NAG-ASN : bond 0.00559 / 0.28 ( 5) link_NAG-ASN : angle 2.17552 / 1.31 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 88 time to evaluate : 0.401 Fit side-chains REVERT: A 92 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7715 (tt) REVERT: A 265 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7216 (mp10) REVERT: A 300 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8117 (pp) REVERT: A 339 TYR cc_start: 0.9116 (OUTLIER) cc_final: 0.8448 (m-10) REVERT: A 414 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8291 (t80) REVERT: A 481 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6546 (tp) REVERT: A 587 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.6408 (m-80) REVERT: A 1058 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8025 (mp) REVERT: A 1225 HIS cc_start: 0.8510 (OUTLIER) cc_final: 0.7876 (t-90) REVERT: A 1288 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8735 (t) REVERT: A 1402 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7531 (tt) REVERT: A 1418 TYR cc_start: 0.7975 (m-80) cc_final: 0.7749 (m-80) REVERT: A 1495 ARG cc_start: 0.7467 (mmm160) cc_final: 0.6092 (ptp90) REVERT: A 1501 PHE cc_start: 0.6757 (t80) cc_final: 0.6465 (t80) REVERT: B 136 ARG cc_start: 0.8115 (mtp85) cc_final: 0.7807 (mtp180) outliers start: 35 outliers final: 19 residues processed: 115 average time/residue: 0.0936 time to fit residues: 15.7595 Evaluate side-chains 117 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1225 HIS Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1241 PHE Chi-restraints excluded: chain A residue 1275 ILE Chi-restraints excluded: chain A residue 1288 THR Chi-restraints excluded: chain A residue 1366 LEU Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1403 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 274 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 128 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 49 optimal weight: 0.0770 chunk 18 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 ASN B 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.159945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.125363 restraints weight = 16231.025| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.20 r_work: 0.3627 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10751 Z= 0.120 Angle : 0.649 12.281 14713 Z= 0.306 Chirality : 0.044 0.417 1620 Planarity : 0.005 0.052 1832 Dihedral : 6.646 89.766 1439 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.60 % Favored : 94.32 % Rotamer: Outliers : 2.96 % Allowed : 14.97 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: -0.75 (0.24), residues: 1285 helix: 0.85 (0.22), residues: 598 sheet: -1.55 (0.47), residues: 118 loop : -1.75 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1424 TYR 0.011 0.001 TYR A1099 PHE 0.012 0.001 PHE A 253 TRP 0.008 0.001 TRP A1421 HIS 0.004 0.001 HIS A1144 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (10738) covalent geometry : angle 0.64236 / 0.30 (14678) SS BOND : bond 0.00310 / 0.16 ( 4) SS BOND : angle 1.39438 / 0.69 ( 8) hydrogen bonds : bond 0.04178 / 2.85 ( 430) hydrogen bonds : angle 4.24502 / 3.04 ( 1290) link_ALPHA1-3 : bond 0.01083 / 0.57 ( 1) link_ALPHA1-3 : angle 2.52530 / 1.25 ( 3) link_ALPHA1-6 : bond 0.00635 / 0.33 ( 1) link_ALPHA1-6 : angle 1.71514 / 0.88 ( 3) link_BETA1-4 : bond 0.00924 / 0.45 ( 2) link_BETA1-4 : angle 2.06363 / 1.14 ( 6) link_NAG-ASN : bond 0.00552 / 0.28 ( 5) link_NAG-ASN : angle 2.13008 / 1.28 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 0.385 Fit side-chains REVERT: A 92 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7716 (tt) REVERT: A 265 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7161 (mp10) REVERT: A 300 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8060 (pp) REVERT: A 339 TYR cc_start: 0.9118 (OUTLIER) cc_final: 0.8474 (m-10) REVERT: A 414 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8287 (t80) REVERT: A 481 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6667 (tp) REVERT: A 587 TYR cc_start: 0.8281 (OUTLIER) cc_final: 0.6391 (m-80) REVERT: A 1058 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8009 (mp) REVERT: A 1225 HIS cc_start: 0.8457 (OUTLIER) cc_final: 0.7838 (t-90) REVERT: A 1288 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8710 (t) REVERT: A 1402 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7510 (tt) REVERT: A 1418 TYR cc_start: 0.7958 (m-80) cc_final: 0.7730 (m-80) REVERT: A 1495 ARG cc_start: 0.7448 (mmm160) cc_final: 0.6079 (ptp90) REVERT: A 1501 PHE cc_start: 0.6748 (t80) cc_final: 0.6462 (t80) REVERT: B 136 ARG cc_start: 0.8109 (mtp85) cc_final: 0.7799 (mtp180) REVERT: B 230 LEU cc_start: 0.7131 (tp) cc_final: 0.6900 (tp) outliers start: 31 outliers final: 17 residues processed: 110 average time/residue: 0.0923 time to fit residues: 15.0258 Evaluate side-chains 110 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1225 HIS Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1241 PHE Chi-restraints excluded: chain A residue 1275 ILE Chi-restraints excluded: chain A residue 1288 THR Chi-restraints excluded: chain A residue 1366 LEU Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 274 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 44 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 15 optimal weight: 0.0770 chunk 100 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.160330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.125558 restraints weight = 16401.626| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.21 r_work: 0.3629 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10751 Z= 0.120 Angle : 0.656 12.481 14713 Z= 0.310 Chirality : 0.045 0.419 1620 Planarity : 0.005 0.066 1832 Dihedral : 6.558 88.428 1439 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.76 % Favored : 94.16 % Rotamer: Outliers : 2.96 % Allowed : 15.16 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: -0.71 (0.24), residues: 1285 helix: 0.87 (0.22), residues: 598 sheet: -1.51 (0.47), residues: 118 loop : -1.73 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1424 TYR 0.010 0.001 TYR A1099 PHE 0.019 0.001 PHE A1370 TRP 0.008 0.001 TRP A1421 HIS 0.004 0.001 HIS A1144 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (10738) covalent geometry : angle 0.64997 / 0.31 (14678) SS BOND : bond 0.00303 / 0.15 ( 4) SS BOND : angle 1.35905 / 0.68 ( 8) hydrogen bonds : bond 0.04143 / 2.83 ( 430) hydrogen bonds : angle 4.25566 / 3.05 ( 1290) link_ALPHA1-3 : bond 0.01088 / 0.57 ( 1) link_ALPHA1-3 : angle 2.49988 / 1.24 ( 3) link_ALPHA1-6 : bond 0.00649 / 0.34 ( 1) link_ALPHA1-6 : angle 1.71190 / 0.88 ( 3) link_BETA1-4 : bond 0.00917 / 0.45 ( 2) link_BETA1-4 : angle 2.07169 / 1.15 ( 6) link_NAG-ASN : bond 0.00547 / 0.28 ( 5) link_NAG-ASN : angle 2.12592 / 1.28 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2650.86 seconds wall clock time: 46 minutes 13.09 seconds (2773.09 seconds total)