Starting phenix.real_space_refine on Wed Mar 4 04:37:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wxr_21962/03_2026/6wxr_21962.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wxr_21962/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6wxr_21962/03_2026/6wxr_21962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wxr_21962/03_2026/6wxr_21962.map" model { file = "/net/cci-nas-00/data/ceres_data/6wxr_21962/03_2026/6wxr_21962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wxr_21962/03_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-dev-5986/lib/python3.9/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 dihedrals: 15 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 dihedrals: 9 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 dihedrals: 3 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: 0.70 Conformation dependent library (CDL) restraints added in 384.8 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: 0.25 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: 1.52 Time building geometry restraints manager: 0.90 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 - 22.68: 5837 22.68 - 45.36: 399 45.36 - 68.04: 51 68.04 - 90.72: 11 90.72 - 113.39: 7 Dihedral angle restraints: 6305 sinusoidal: 2548 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 6302 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: 0.750 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.320 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 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 : 15.608 113.394 3881 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 covalent geometry : bond 0.01055 (10738) covalent geometry : angle 0.96274 (14678) SS BOND : bond 0.00422 ( 4) SS BOND : angle 1.76810 ( 8) hydrogen bonds : bond 0.16112 ( 430) hydrogen bonds : angle 6.63273 ( 1290) link_ALPHA1-3 : bond 0.00559 ( 1) link_ALPHA1-3 : angle 4.18883 ( 3) link_ALPHA1-6 : bond 0.00659 ( 1) link_ALPHA1-6 : angle 1.84496 ( 3) link_BETA1-4 : bond 0.01240 ( 2) link_BETA1-4 : angle 1.79217 ( 6) link_NAG-ASN : bond 0.00688 ( 5) link_NAG-ASN : angle 3.26384 ( 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 : 0.290 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: 0.1189 time to fit residues: 17.7133 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 : 0.276 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 405 GLN A 504 GLN A1107 ASN A1130 HIS A1212 HIS A1226 HIS A1238 HIS A1319 HIS B 71 ASN B 119 GLN B 208 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.154990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.119986 restraints weight = 16529.188| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.22 r_work: 0.3556 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10751 Z= 0.191 Angle : 0.800 18.980 14713 Z= 0.360 Chirality : 0.046 0.304 1620 Planarity : 0.005 0.056 1832 Dihedral : 11.351 88.548 1668 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.32 % Favored : 92.61 % Rotamer: Outliers : 1.53 % Allowed : 9.15 % Favored : 89.32 % 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: -2.38 (0.22), residues: 1285 helix: -0.61 (0.20), residues: 604 sheet: -1.71 (0.45), residues: 116 loop : -2.64 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 362 TYR 0.015 0.002 TYR A1099 PHE 0.015 0.002 PHE A 253 TRP 0.024 0.001 TRP A1421 HIS 0.005 0.001 HIS A1144 Details of bonding type rmsd covalent geometry : bond 0.00451 (10738) covalent geometry : angle 0.78895 (14678) SS BOND : bond 0.00390 ( 4) SS BOND : angle 1.44860 ( 8) hydrogen bonds : bond 0.05592 ( 430) hydrogen bonds : angle 4.90604 ( 1290) link_ALPHA1-3 : bond 0.00711 ( 1) link_ALPHA1-3 : angle 3.78883 ( 3) link_ALPHA1-6 : bond 0.00807 ( 1) link_ALPHA1-6 : angle 1.85491 ( 3) link_BETA1-4 : bond 0.00969 ( 2) link_BETA1-4 : angle 3.42230 ( 6) link_NAG-ASN : bond 0.00378 ( 5) link_NAG-ASN : angle 3.08092 ( 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 : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 GLN cc_start: 0.7876 (mp10) cc_final: 0.7243 (mp10) REVERT: A 300 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8287 (pp) REVERT: A 1241 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7411 (m-80) REVERT: A 1288 THR cc_start: 0.9143 (OUTLIER) cc_final: 0.8909 (t) REVERT: A 1365 TYR cc_start: 0.8136 (m-80) cc_final: 0.7905 (m-80) REVERT: A 1374 HIS cc_start: 0.7105 (m-70) cc_final: 0.6859 (m-70) REVERT: A 1495 ARG cc_start: 0.7763 (mmm160) cc_final: 0.6361 (ptp90) REVERT: A 1501 PHE cc_start: 0.7132 (t80) cc_final: 0.6588 (t80) REVERT: B 197 MET cc_start: 0.7976 (mtt) cc_final: 0.7674 (mtp) outliers start: 16 outliers final: 7 residues processed: 97 average time/residue: 0.0983 time to fit residues: 13.6948 Evaluate side-chains 88 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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: 0.8980 chunk 113 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 61 optimal weight: 0.0970 chunk 90 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4062 r_free = 0.4062 target = 0.159591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.124814 restraints weight = 16510.583| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.09 r_work: 0.3627 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1463 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 : 0.666 12.480 14713 Z= 0.311 Chirality : 0.042 0.292 1620 Planarity : 0.005 0.054 1832 Dihedral : 10.674 89.515 1665 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.91 % Favored : 94.01 % Rotamer: Outliers : 2.00 % Allowed : 10.49 % Favored : 87.51 % 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: -1.67 (0.23), residues: 1285 helix: 0.03 (0.21), residues: 606 sheet: -1.52 (0.47), residues: 110 loop : -2.31 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 84 TYR 0.014 0.001 TYR A1099 PHE 0.020 0.001 PHE A1404 TRP 0.014 0.001 TRP A1421 HIS 0.003 0.001 HIS A1144 Details of bonding type rmsd covalent geometry : bond 0.00274 (10738) covalent geometry : angle 0.65419 (14678) SS BOND : bond 0.00351 ( 4) SS BOND : angle 1.19342 ( 8) hydrogen bonds : bond 0.04678 ( 430) hydrogen bonds : angle 4.56752 ( 1290) link_ALPHA1-3 : bond 0.00763 ( 1) link_ALPHA1-3 : angle 4.11923 ( 3) link_ALPHA1-6 : bond 0.00902 ( 1) link_ALPHA1-6 : angle 1.31168 ( 3) link_BETA1-4 : bond 0.00985 ( 2) link_BETA1-4 : angle 3.37173 ( 6) link_NAG-ASN : bond 0.00227 ( 5) link_NAG-ASN : angle 2.77043 ( 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 111 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 265 GLN cc_start: 0.7792 (mp10) cc_final: 0.7188 (mp10) REVERT: A 300 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8137 (pp) REVERT: A 339 TYR cc_start: 0.9120 (OUTLIER) cc_final: 0.8676 (m-10) REVERT: A 1241 PHE cc_start: 0.7784 (OUTLIER) cc_final: 0.7272 (m-80) REVERT: A 1288 THR cc_start: 0.9072 (OUTLIER) cc_final: 0.8847 (t) REVERT: A 1365 TYR cc_start: 0.8177 (m-80) cc_final: 0.7897 (m-80) REVERT: A 1367 ASP cc_start: 0.8535 (t0) cc_final: 0.8333 (t0) REVERT: A 1495 ARG cc_start: 0.7608 (mmm160) cc_final: 0.6329 (ptp90) REVERT: A 1501 PHE cc_start: 0.7084 (t80) cc_final: 0.6609 (t80) REVERT: B 136 ARG cc_start: 0.7990 (mtp85) cc_final: 0.7728 (mtm180) REVERT: B 197 MET cc_start: 0.7771 (mtt) cc_final: 0.7439 (mtp) REVERT: B 216 PHE cc_start: 0.7945 (m-80) cc_final: 0.7716 (m-80) outliers start: 21 outliers final: 5 residues processed: 105 average time/residue: 0.1099 time to fit residues: 16.2796 Evaluate side-chains 92 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 339 TYR 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 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: 0.8980 chunk 99 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 44 optimal weight: 0.1980 chunk 86 optimal weight: 0.4980 chunk 97 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.160693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.125502 restraints weight = 16479.821| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.19 r_work: 0.3613 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10751 Z= 0.116 Angle : 0.639 12.052 14713 Z= 0.299 Chirality : 0.042 0.296 1620 Planarity : 0.004 0.055 1832 Dihedral : 10.220 87.705 1665 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.84 % Favored : 94.09 % Rotamer: Outliers : 2.67 % Allowed : 11.06 % Favored : 86.27 % 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: -1.26 (0.23), residues: 1285 helix: 0.43 (0.21), residues: 604 sheet: -1.49 (0.45), residues: 116 loop : -2.11 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 174 TYR 0.011 0.001 TYR A1099 PHE 0.013 0.001 PHE A 253 TRP 0.013 0.001 TRP A1421 HIS 0.004 0.001 HIS A1144 Details of bonding type rmsd covalent geometry : bond 0.00266 (10738) covalent geometry : angle 0.62697 (14678) SS BOND : bond 0.00292 ( 4) SS BOND : angle 1.05692 ( 8) hydrogen bonds : bond 0.04356 ( 430) hydrogen bonds : angle 4.36834 ( 1290) link_ALPHA1-3 : bond 0.00723 ( 1) link_ALPHA1-3 : angle 4.17910 ( 3) link_ALPHA1-6 : bond 0.00769 ( 1) link_ALPHA1-6 : angle 1.31488 ( 3) link_BETA1-4 : bond 0.00840 ( 2) link_BETA1-4 : angle 3.53781 ( 6) link_NAG-ASN : bond 0.00245 ( 5) link_NAG-ASN : angle 2.44324 ( 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 123 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 107 LEU cc_start: 0.8418 (mt) cc_final: 0.8172 (mt) REVERT: A 265 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7212 (mp10) REVERT: A 300 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8116 (pp) REVERT: A 339 TYR cc_start: 0.9143 (OUTLIER) cc_final: 0.8624 (m-10) REVERT: A 1241 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7189 (m-80) REVERT: A 1288 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8779 (t) REVERT: A 1365 TYR cc_start: 0.8174 (m-80) cc_final: 0.7862 (m-80) REVERT: A 1416 LYS cc_start: 0.7174 (mmmt) cc_final: 0.6913 (mmmt) REVERT: A 1495 ARG cc_start: 0.7586 (mmm160) cc_final: 0.6282 (ptp90) REVERT: A 1501 PHE cc_start: 0.6890 (t80) cc_final: 0.6506 (t80) REVERT: B 136 ARG cc_start: 0.7987 (mtp85) cc_final: 0.7728 (mtm180) REVERT: B 197 MET cc_start: 0.7803 (mtt) cc_final: 0.7492 (mtp) outliers start: 28 outliers final: 10 residues processed: 114 average time/residue: 0.1045 time to fit residues: 17.0588 Evaluate side-chains 102 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 1345 ARG Chi-restraints excluded: chain A residue 1366 LEU Chi-restraints excluded: chain A residue 1535 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 64 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.153598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.118858 restraints weight = 16633.545| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.21 r_work: 0.3533 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 10751 Z= 0.243 Angle : 0.765 12.317 14713 Z= 0.362 Chirality : 0.047 0.311 1620 Planarity : 0.005 0.051 1832 Dihedral : 10.191 86.797 1665 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.77 % Favored : 93.15 % Rotamer: Outliers : 2.86 % Allowed : 12.58 % Favored : 84.56 % 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: -1.44 (0.23), residues: 1285 helix: 0.18 (0.21), residues: 614 sheet: -1.51 (0.46), residues: 116 loop : -2.14 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 509 TYR 0.014 0.002 TYR A1099 PHE 0.024 0.002 PHE A1370 TRP 0.017 0.002 TRP A1421 HIS 0.008 0.001 HIS A1225 Details of bonding type rmsd covalent geometry : bond 0.00598 (10738) covalent geometry : angle 0.75509 (14678) SS BOND : bond 0.00338 ( 4) SS BOND : angle 1.29618 ( 8) hydrogen bonds : bond 0.05762 ( 430) hydrogen bonds : angle 4.61051 ( 1290) link_ALPHA1-3 : bond 0.00865 ( 1) link_ALPHA1-3 : angle 3.70305 ( 3) link_ALPHA1-6 : bond 0.00737 ( 1) link_ALPHA1-6 : angle 1.69547 ( 3) link_BETA1-4 : bond 0.00890 ( 2) link_BETA1-4 : angle 3.72271 ( 6) link_NAG-ASN : bond 0.00460 ( 5) link_NAG-ASN : angle 2.56091 ( 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 114 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 0.354 Fit side-chains REVERT: A 92 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7817 (tt) REVERT: A 265 GLN cc_start: 0.7868 (mp10) cc_final: 0.7306 (mp10) REVERT: A 300 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8223 (pp) REVERT: A 414 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.8335 (t80) REVERT: A 1225 HIS cc_start: 0.8615 (OUTLIER) cc_final: 0.7910 (t-90) REVERT: A 1241 PHE cc_start: 0.7837 (OUTLIER) cc_final: 0.7241 (m-80) REVERT: A 1288 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8836 (t) REVERT: A 1495 ARG cc_start: 0.7676 (mmm160) cc_final: 0.6322 (ptp90) REVERT: A 1501 PHE cc_start: 0.6970 (t80) cc_final: 0.6595 (t80) REVERT: B 197 MET cc_start: 0.8013 (mtt) cc_final: 0.7696 (mtp) outliers start: 30 outliers final: 12 residues processed: 109 average time/residue: 0.1000 time to fit residues: 15.7202 Evaluate side-chains 99 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 300 LEU Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 414 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 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 260 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 82 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 57 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.158233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.123474 restraints weight = 16468.390| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.22 r_work: 0.3604 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10751 Z= 0.121 Angle : 0.653 12.764 14713 Z= 0.307 Chirality : 0.042 0.292 1620 Planarity : 0.004 0.051 1832 Dihedral : 9.474 86.590 1665 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.60 % Favored : 94.32 % Rotamer: Outliers : 2.76 % Allowed : 12.96 % Favored : 84.27 % 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: -1.17 (0.23), residues: 1285 helix: 0.41 (0.21), residues: 613 sheet: -1.49 (0.48), residues: 110 loop : -1.99 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1424 TYR 0.015 0.001 TYR A1099 PHE 0.013 0.001 PHE A 253 TRP 0.012 0.001 TRP A1421 HIS 0.004 0.001 HIS A1238 Details of bonding type rmsd covalent geometry : bond 0.00280 (10738) covalent geometry : angle 0.64187 (14678) SS BOND : bond 0.00521 ( 4) SS BOND : angle 1.17441 ( 8) hydrogen bonds : bond 0.04519 ( 430) hydrogen bonds : angle 4.36491 ( 1290) link_ALPHA1-3 : bond 0.00774 ( 1) link_ALPHA1-3 : angle 4.12831 ( 3) link_ALPHA1-6 : bond 0.00693 ( 1) link_ALPHA1-6 : angle 1.22033 ( 3) link_BETA1-4 : bond 0.00846 ( 2) link_BETA1-4 : angle 3.72335 ( 6) link_NAG-ASN : bond 0.00239 ( 5) link_NAG-ASN : angle 2.22192 ( 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 115 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.407 Fit side-chains REVERT: A 92 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7733 (tt) REVERT: A 265 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7231 (mp10) REVERT: A 300 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8134 (pp) REVERT: A 339 TYR cc_start: 0.9122 (OUTLIER) cc_final: 0.8596 (m-10) REVERT: A 414 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.8263 (t80) REVERT: A 1241 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.7115 (m-80) REVERT: A 1288 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8797 (t) REVERT: A 1401 ASP cc_start: 0.7441 (t0) cc_final: 0.7222 (t0) REVERT: A 1402 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7510 (tt) REVERT: A 1495 ARG cc_start: 0.7482 (mmm160) cc_final: 0.6078 (ptp90) REVERT: A 1501 PHE cc_start: 0.6860 (t80) cc_final: 0.6521 (t80) REVERT: B 136 ARG cc_start: 0.8112 (mtp85) cc_final: 0.7828 (mtp180) outliers start: 29 outliers final: 15 residues processed: 107 average time/residue: 0.0928 time to fit residues: 14.4560 Evaluate side-chains 104 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 339 TYR Chi-restraints excluded: chain A residue 414 PHE 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 1345 ARG Chi-restraints excluded: chain A residue 1366 LEU Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1457 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 260 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 274 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 47 optimal weight: 3.9990 chunk 54 optimal weight: 0.2980 chunk 88 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 HIS B 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.159859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.124163 restraints weight = 16335.364| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.22 r_work: 0.3613 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2019 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 : 0.651 12.271 14713 Z= 0.305 Chirality : 0.043 0.298 1620 Planarity : 0.004 0.052 1832 Dihedral : 9.075 87.191 1665 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.76 % Favored : 94.16 % Rotamer: Outliers : 2.76 % Allowed : 13.54 % Favored : 83.70 % 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: -1.00 (0.24), residues: 1285 helix: 0.60 (0.22), residues: 605 sheet: -1.44 (0.47), residues: 116 loop : -1.91 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1424 TYR 0.012 0.001 TYR A1099 PHE 0.017 0.001 PHE A1370 TRP 0.012 0.001 TRP A1421 HIS 0.004 0.001 HIS A1144 Details of bonding type rmsd covalent geometry : bond 0.00279 (10738) covalent geometry : angle 0.63877 (14678) SS BOND : bond 0.00407 ( 4) SS BOND : angle 2.15269 ( 8) hydrogen bonds : bond 0.04394 ( 430) hydrogen bonds : angle 4.30280 ( 1290) link_ALPHA1-3 : bond 0.00766 ( 1) link_ALPHA1-3 : angle 4.06088 ( 3) link_ALPHA1-6 : bond 0.00793 ( 1) link_ALPHA1-6 : angle 1.26399 ( 3) link_BETA1-4 : bond 0.00730 ( 2) link_BETA1-4 : angle 3.73864 ( 6) link_NAG-ASN : bond 0.00261 ( 5) link_NAG-ASN : angle 2.15067 ( 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 117 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 0.386 Fit side-chains REVERT: A 92 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7722 (tt) REVERT: A 265 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7236 (mp10) REVERT: A 300 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8120 (pp) REVERT: A 339 TYR cc_start: 0.9107 (OUTLIER) cc_final: 0.8469 (m-10) REVERT: A 414 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8296 (t80) REVERT: A 1225 HIS cc_start: 0.8438 (OUTLIER) cc_final: 0.7705 (t-90) REVERT: A 1288 THR cc_start: 0.9003 (OUTLIER) cc_final: 0.8788 (t) REVERT: A 1402 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7526 (tt) REVERT: A 1495 ARG cc_start: 0.7450 (mmm160) cc_final: 0.6026 (ptp90) REVERT: A 1501 PHE cc_start: 0.6763 (t80) cc_final: 0.6460 (t80) REVERT: B 136 ARG cc_start: 0.8067 (mtp85) cc_final: 0.7788 (mtp180) outliers start: 29 outliers final: 16 residues processed: 112 average time/residue: 0.0931 time to fit residues: 15.2598 Evaluate side-chains 108 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 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 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 263 LEU 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: 0.9980 chunk 120 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.155812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.120561 restraints weight = 16535.040| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.22 r_work: 0.3558 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10751 Z= 0.186 Angle : 0.711 12.409 14713 Z= 0.335 Chirality : 0.045 0.310 1620 Planarity : 0.005 0.051 1832 Dihedral : 8.774 87.453 1665 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.38 % Favored : 93.54 % Rotamer: Outliers : 2.57 % Allowed : 14.11 % Favored : 83.32 % 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: -1.17 (0.23), residues: 1285 helix: 0.45 (0.21), residues: 608 sheet: -1.53 (0.46), residues: 116 loop : -2.01 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 509 TYR 0.014 0.001 TYR A1099 PHE 0.028 0.002 PHE A1404 TRP 0.018 0.001 TRP A1421 HIS 0.006 0.001 HIS A1144 Details of bonding type rmsd covalent geometry : bond 0.00458 (10738) covalent geometry : angle 0.70089 (14678) SS BOND : bond 0.00387 ( 4) SS BOND : angle 1.76180 ( 8) hydrogen bonds : bond 0.05143 ( 430) hydrogen bonds : angle 4.43950 ( 1290) link_ALPHA1-3 : bond 0.00957 ( 1) link_ALPHA1-3 : angle 3.62196 ( 3) link_ALPHA1-6 : bond 0.00914 ( 1) link_ALPHA1-6 : angle 1.51250 ( 3) link_BETA1-4 : bond 0.00785 ( 2) link_BETA1-4 : angle 3.73525 ( 6) link_NAG-ASN : bond 0.00380 ( 5) link_NAG-ASN : angle 2.25753 ( 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 109 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.388 Fit side-chains REVERT: A 92 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7794 (tt) REVERT: A 265 GLN cc_start: 0.7804 (mp10) cc_final: 0.7226 (mp10) REVERT: A 300 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8146 (pp) REVERT: A 339 TYR cc_start: 0.9123 (OUTLIER) cc_final: 0.8568 (m-10) REVERT: A 414 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8304 (t80) REVERT: A 1225 HIS cc_start: 0.8559 (OUTLIER) cc_final: 0.7656 (t-90) REVERT: A 1241 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.7039 (m-80) REVERT: A 1288 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8825 (t) REVERT: A 1402 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7616 (tt) REVERT: A 1495 ARG cc_start: 0.7492 (mmm160) cc_final: 0.6108 (ptp90) REVERT: A 1501 PHE cc_start: 0.6836 (t80) cc_final: 0.6518 (t80) REVERT: B 136 ARG cc_start: 0.8163 (mtp85) cc_final: 0.7861 (mtp180) REVERT: B 144 LYS cc_start: 0.8389 (mtmm) cc_final: 0.8129 (mtmm) outliers start: 27 outliers final: 13 residues processed: 104 average time/residue: 0.0972 time to fit residues: 14.5345 Evaluate side-chains 102 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 300 LEU Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 436 THR 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 171 ASN Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 260 LEU 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: 0.9990 chunk 99 optimal weight: 5.9990 chunk 32 optimal weight: 0.0370 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.154559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.119871 restraints weight = 16511.697| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.18 r_work: 0.3551 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10751 Z= 0.213 Angle : 0.738 12.561 14713 Z= 0.348 Chirality : 0.046 0.313 1620 Planarity : 0.005 0.051 1832 Dihedral : 8.430 87.449 1665 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.77 % Favored : 93.15 % Rotamer: Outliers : 2.57 % Allowed : 14.68 % Favored : 82.75 % 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: -1.30 (0.23), residues: 1285 helix: 0.35 (0.21), residues: 607 sheet: -1.55 (0.48), residues: 110 loop : -2.09 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 509 TYR 0.017 0.002 TYR B 173 PHE 0.024 0.002 PHE A1404 TRP 0.016 0.001 TRP A1421 HIS 0.007 0.001 HIS A1144 Details of bonding type rmsd covalent geometry : bond 0.00528 (10738) covalent geometry : angle 0.72924 (14678) SS BOND : bond 0.00430 ( 4) SS BOND : angle 1.61409 ( 8) hydrogen bonds : bond 0.05373 ( 430) hydrogen bonds : angle 4.49820 ( 1290) link_ALPHA1-3 : bond 0.01039 ( 1) link_ALPHA1-3 : angle 3.41468 ( 3) link_ALPHA1-6 : bond 0.01073 ( 1) link_ALPHA1-6 : angle 1.56608 ( 3) link_BETA1-4 : bond 0.00822 ( 2) link_BETA1-4 : angle 3.55550 ( 6) link_NAG-ASN : bond 0.00358 ( 5) link_NAG-ASN : angle 2.28932 ( 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 107 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.315 Fit side-chains REVERT: A 92 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7789 (tt) REVERT: A 265 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7229 (mp10) REVERT: A 300 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8215 (pp) REVERT: A 339 TYR cc_start: 0.9129 (OUTLIER) cc_final: 0.8575 (m-10) REVERT: A 414 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8313 (t80) REVERT: A 451 GLN cc_start: 0.8915 (tm-30) cc_final: 0.8534 (tm-30) REVERT: A 1225 HIS cc_start: 0.8613 (OUTLIER) cc_final: 0.7621 (t-90) REVERT: A 1241 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.6934 (m-80) REVERT: A 1288 THR cc_start: 0.9084 (OUTLIER) cc_final: 0.8840 (t) REVERT: A 1402 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7596 (tt) REVERT: A 1495 ARG cc_start: 0.7565 (mmm160) cc_final: 0.6196 (ptp90) REVERT: A 1501 PHE cc_start: 0.6853 (t80) cc_final: 0.6528 (t80) REVERT: B 136 ARG cc_start: 0.8181 (mtp85) cc_final: 0.7865 (mtp180) REVERT: B 144 LYS cc_start: 0.8470 (mtmm) cc_final: 0.8192 (mtmm) REVERT: B 179 TYR cc_start: 0.8374 (m-80) cc_final: 0.7866 (m-80) REVERT: B 209 MET cc_start: 0.7497 (mmp) cc_final: 0.7110 (mmp) outliers start: 27 outliers final: 14 residues processed: 102 average time/residue: 0.1030 time to fit residues: 15.1710 Evaluate side-chains 103 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 128 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 49 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 121 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.159392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.124473 restraints weight = 16299.888| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.05 r_work: 0.3622 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10751 Z= 0.122 Angle : 0.661 12.730 14713 Z= 0.309 Chirality : 0.043 0.301 1620 Planarity : 0.004 0.049 1832 Dihedral : 7.939 89.333 1665 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.91 % Favored : 94.01 % Rotamer: Outliers : 2.38 % Allowed : 14.59 % 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: -1.02 (0.24), residues: 1285 helix: 0.59 (0.22), residues: 606 sheet: -1.46 (0.49), residues: 110 loop : -1.94 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1424 TYR 0.014 0.001 TYR A1099 PHE 0.025 0.001 PHE A1404 TRP 0.011 0.001 TRP A1421 HIS 0.004 0.001 HIS A1144 Details of bonding type rmsd covalent geometry : bond 0.00284 (10738) covalent geometry : angle 0.65187 (14678) SS BOND : bond 0.00351 ( 4) SS BOND : angle 1.42681 ( 8) hydrogen bonds : bond 0.04442 ( 430) hydrogen bonds : angle 4.34142 ( 1290) link_ALPHA1-3 : bond 0.00929 ( 1) link_ALPHA1-3 : angle 3.76653 ( 3) link_ALPHA1-6 : bond 0.00893 ( 1) link_ALPHA1-6 : angle 1.15874 ( 3) link_BETA1-4 : bond 0.00806 ( 2) link_BETA1-4 : angle 3.04124 ( 6) link_NAG-ASN : bond 0.00259 ( 5) link_NAG-ASN : angle 2.09608 ( 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 110 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.269 Fit side-chains REVERT: A 92 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7706 (tt) REVERT: A 265 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7161 (mp10) REVERT: A 300 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8114 (pp) REVERT: A 339 TYR cc_start: 0.9088 (OUTLIER) cc_final: 0.8477 (m-10) REVERT: A 414 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.8266 (t80) REVERT: A 1225 HIS cc_start: 0.8447 (OUTLIER) cc_final: 0.7602 (t-90) REVERT: A 1288 THR cc_start: 0.9005 (OUTLIER) cc_final: 0.8786 (t) REVERT: A 1402 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7598 (tt) REVERT: A 1418 TYR cc_start: 0.7948 (m-80) cc_final: 0.7713 (m-80) REVERT: A 1495 ARG cc_start: 0.7443 (mmm160) cc_final: 0.6087 (ptp90) REVERT: A 1501 PHE cc_start: 0.6810 (t80) cc_final: 0.6492 (t80) REVERT: B 136 ARG cc_start: 0.8071 (mtp85) cc_final: 0.7771 (mtp180) REVERT: B 144 LYS cc_start: 0.8485 (mtmm) cc_final: 0.8203 (mtmm) REVERT: B 209 MET cc_start: 0.7460 (mmp) cc_final: 0.7074 (mmp) outliers start: 25 outliers final: 17 residues processed: 104 average time/residue: 0.0914 time to fit residues: 13.8622 Evaluate side-chains 109 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 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 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 260 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 81 optimal weight: 0.0980 chunk 111 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.159201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.124256 restraints weight = 16502.442| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.06 r_work: 0.3617 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 10751 Z= 0.192 Angle : 0.961 59.199 14713 Z= 0.539 Chirality : 0.043 0.301 1620 Planarity : 0.005 0.049 1832 Dihedral : 7.950 89.303 1665 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.91 % Favored : 94.01 % Rotamer: Outliers : 2.29 % Allowed : 14.78 % Favored : 82.94 % Cbeta Deviations : 0.08 % 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: -1.01 (0.24), residues: 1285 helix: 0.59 (0.21), residues: 606 sheet: -1.45 (0.49), residues: 110 loop : -1.93 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1424 TYR 0.014 0.001 TYR A1099 PHE 0.024 0.001 PHE A1404 TRP 0.010 0.001 TRP A1421 HIS 0.005 0.001 HIS A1144 Details of bonding type rmsd covalent geometry : bond 0.00384 (10738) covalent geometry : angle 0.95577 (14678) SS BOND : bond 0.00365 ( 4) SS BOND : angle 1.39620 ( 8) hydrogen bonds : bond 0.04482 ( 430) hydrogen bonds : angle 4.33935 ( 1290) link_ALPHA1-3 : bond 0.00862 ( 1) link_ALPHA1-3 : angle 3.75988 ( 3) link_ALPHA1-6 : bond 0.00930 ( 1) link_ALPHA1-6 : angle 1.16860 ( 3) link_BETA1-4 : bond 0.00621 ( 2) link_BETA1-4 : angle 3.07842 ( 6) link_NAG-ASN : bond 0.00268 ( 5) link_NAG-ASN : angle 2.09165 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2591.10 seconds wall clock time: 45 minutes 5.18 seconds (2705.18 seconds total)