Starting phenix.real_space_refine on Tue Jul 29 02:26:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wxr_21962/07_2025/6wxr_21962.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wxr_21962/07_2025/6wxr_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_21962/07_2025/6wxr_21962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wxr_21962/07_2025/6wxr_21962.map" model { file = "/net/cci-nas-00/data/ceres_data/6wxr_21962/07_2025/6wxr_21962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wxr_21962/07_2025/6wxr_21962.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'ASN:plan1': 4, 'HIS:plan': 3, 'GLU:plan': 17, 'ARG:plan': 7} 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: {'GLN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG: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: 7.15, per 1000 atoms: 0.69 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: 3.13 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.40 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: 3.43 Time building geometry restraints manager: 3.62 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: 1.180 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: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 29.120 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.920 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.027 0.001 TRP A1421 HIS 0.014 0.001 HIS A1238 PHE 0.014 0.001 PHE B 222 TYR 0.014 0.001 TYR A1099 ARG 0.003 0.000 ARG A 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00688 ( 5) link_NAG-ASN : angle 3.26384 ( 15) 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_ALPHA1-3 : bond 0.00559 ( 1) link_ALPHA1-3 : angle 4.18883 ( 3) hydrogen bonds : bond 0.16112 ( 430) hydrogen bonds : angle 6.63273 ( 1290) SS BOND : bond 0.00422 ( 4) SS BOND : angle 1.76810 ( 8) covalent geometry : bond 0.01055 (10738) covalent geometry : angle 0.96274 (14678) *********************** 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 : 1.050 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: 0.6877 (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: 0.7693 (mtt) outliers start: 2 outliers final: 2 residues processed: 110 average time/residue: 0.2725 time to fit residues: 40.7440 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 : 1.073 ------------------------------------------------------------------------------- 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 108 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.158399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.122716 restraints weight = 16405.948| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.23 r_work: 0.3594 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1129 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= 0.143 Angle : 0.754 17.565 14713 Z= 0.338 Chirality : 0.044 0.286 1620 Planarity : 0.005 0.057 1832 Dihedral : 11.137 88.079 1668 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.69 % Favored : 93.23 % Rotamer: Outliers : 1.33 % Allowed : 8.48 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.22), residues: 1285 helix: -0.42 (0.21), residues: 591 sheet: -1.67 (0.44), residues: 116 loop : -2.59 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1421 HIS 0.004 0.001 HIS A1148 PHE 0.014 0.001 PHE A 253 TYR 0.014 0.001 TYR A1099 ARG 0.003 0.000 ARG B 174 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 5) link_NAG-ASN : angle 3.05389 ( 15) link_ALPHA1-6 : bond 0.00742 ( 1) link_ALPHA1-6 : angle 1.57171 ( 3) link_BETA1-4 : bond 0.01071 ( 2) link_BETA1-4 : angle 3.38623 ( 6) link_ALPHA1-3 : bond 0.00663 ( 1) link_ALPHA1-3 : angle 3.90181 ( 3) hydrogen bonds : bond 0.05129 ( 430) hydrogen bonds : angle 4.81520 ( 1290) SS BOND : bond 0.00359 ( 4) SS BOND : angle 1.32551 ( 8) covalent geometry : bond 0.00326 (10738) covalent geometry : angle 0.74192 (14678) *********************** 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 98 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: A 300 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8224 (pp) REVERT: A 1241 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.7453 (m-80) REVERT: A 1288 THR cc_start: 0.9110 (OUTLIER) cc_final: 0.8885 (t) REVERT: A 1374 HIS cc_start: 0.7053 (m-70) cc_final: 0.6820 (m-70) REVERT: A 1495 ARG cc_start: 0.7681 (mmm160) cc_final: 0.6312 (ptp90) REVERT: A 1501 PHE cc_start: 0.7109 (t80) cc_final: 0.6611 (t80) REVERT: B 136 ARG cc_start: 0.8000 (mtp85) cc_final: 0.7738 (mtp180) REVERT: B 197 MET cc_start: 0.7779 (mtt) cc_final: 0.7564 (mtt) outliers start: 14 outliers final: 5 residues processed: 93 average time/residue: 0.2411 time to fit residues: 31.7165 Evaluate side-chains 85 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 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 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 52 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 116 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1375 GLN B 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.159425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.124658 restraints weight = 16652.050| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.08 r_work: 0.3623 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10751 Z= 0.127 Angle : 0.666 12.378 14713 Z= 0.311 Chirality : 0.042 0.293 1620 Planarity : 0.005 0.055 1832 Dihedral : 10.603 89.842 1665 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.99 % Favored : 93.93 % Rotamer: Outliers : 2.00 % Allowed : 9.82 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.23), residues: 1285 helix: 0.06 (0.21), residues: 606 sheet: -1.52 (0.45), residues: 116 loop : -2.30 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1421 HIS 0.004 0.001 HIS A1144 PHE 0.021 0.001 PHE A1404 TYR 0.012 0.001 TYR A1099 ARG 0.003 0.000 ARG A1424 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 5) link_NAG-ASN : angle 2.72040 ( 15) link_ALPHA1-6 : bond 0.00826 ( 1) link_ALPHA1-6 : angle 1.35819 ( 3) link_BETA1-4 : bond 0.00981 ( 2) link_BETA1-4 : angle 3.39846 ( 6) link_ALPHA1-3 : bond 0.00810 ( 1) link_ALPHA1-3 : angle 4.10316 ( 3) hydrogen bonds : bond 0.04729 ( 430) hydrogen bonds : angle 4.55243 ( 1290) SS BOND : bond 0.00321 ( 4) SS BOND : angle 1.17585 ( 8) covalent geometry : bond 0.00299 (10738) covalent geometry : angle 0.65393 (14678) *********************** 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 107 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 1.322 Fit side-chains revert: symmetry clash REVERT: A 265 GLN cc_start: 0.7780 (mp10) cc_final: 0.7177 (mp10) REVERT: A 300 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8122 (pp) REVERT: A 1241 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.7177 (m-80) REVERT: A 1288 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8835 (t) REVERT: A 1495 ARG cc_start: 0.7617 (mmm160) cc_final: 0.6322 (ptp90) REVERT: A 1501 PHE cc_start: 0.7155 (t80) cc_final: 0.6711 (t80) REVERT: B 136 ARG cc_start: 0.7984 (mtp85) cc_final: 0.7713 (mtm180) REVERT: B 179 TYR cc_start: 0.8220 (m-10) cc_final: 0.7993 (m-80) REVERT: B 197 MET cc_start: 0.7824 (mtt) cc_final: 0.7505 (mtp) REVERT: B 216 PHE cc_start: 0.7962 (m-80) cc_final: 0.7759 (m-80) outliers start: 21 outliers final: 8 residues processed: 102 average time/residue: 0.2889 time to fit residues: 43.5652 Evaluate side-chains 92 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 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 171 ASN 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 46 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 121 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.156222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.121229 restraints weight = 16446.363| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.22 r_work: 0.3569 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10751 Z= 0.181 Angle : 0.700 12.145 14713 Z= 0.329 Chirality : 0.044 0.303 1620 Planarity : 0.005 0.055 1832 Dihedral : 10.469 82.359 1665 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.15 % Favored : 93.77 % Rotamer: Outliers : 2.29 % Allowed : 11.15 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.23), residues: 1285 helix: 0.13 (0.21), residues: 615 sheet: -1.54 (0.46), residues: 116 loop : -2.24 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1421 HIS 0.006 0.001 HIS A1144 PHE 0.015 0.001 PHE A 253 TYR 0.016 0.001 TYR B 170 ARG 0.004 0.000 ARG A 362 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 5) link_NAG-ASN : angle 2.63794 ( 15) link_ALPHA1-6 : bond 0.00858 ( 1) link_ALPHA1-6 : angle 1.56598 ( 3) link_BETA1-4 : bond 0.00964 ( 2) link_BETA1-4 : angle 3.53713 ( 6) link_ALPHA1-3 : bond 0.00797 ( 1) link_ALPHA1-3 : angle 3.91536 ( 3) hydrogen bonds : bond 0.05099 ( 430) hydrogen bonds : angle 4.53387 ( 1290) SS BOND : bond 0.00324 ( 4) SS BOND : angle 1.17651 ( 8) covalent geometry : bond 0.00442 (10738) covalent geometry : angle 0.68865 (14678) *********************** 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 108 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 1.182 Fit side-chains REVERT: A 265 GLN cc_start: 0.7830 (mp10) cc_final: 0.7264 (mp10) REVERT: A 300 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8198 (pp) REVERT: A 339 TYR cc_start: 0.9132 (OUTLIER) cc_final: 0.8623 (m-10) REVERT: A 1241 PHE cc_start: 0.7856 (OUTLIER) cc_final: 0.7324 (m-80) REVERT: A 1288 THR cc_start: 0.9075 (OUTLIER) cc_final: 0.8840 (t) REVERT: A 1452 ILE cc_start: 0.6879 (OUTLIER) cc_final: 0.6452 (mt) REVERT: A 1495 ARG cc_start: 0.7640 (mmm160) cc_final: 0.6346 (ptp90) REVERT: A 1501 PHE cc_start: 0.7089 (t80) cc_final: 0.6646 (t80) REVERT: B 136 ARG cc_start: 0.8047 (mtp85) cc_final: 0.7777 (mtm180) REVERT: B 197 MET cc_start: 0.7954 (mtt) cc_final: 0.7647 (mtp) outliers start: 24 outliers final: 10 residues processed: 104 average time/residue: 0.2394 time to fit residues: 36.0396 Evaluate side-chains 95 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 1.365 ------------------------------------------------------------------------------- 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 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 A residue 1452 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 113 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 83 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 64 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 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 = 0.155092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.121098 restraints weight = 16408.657| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.19 r_work: 0.3574 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10751 Z= 0.170 Angle : 0.693 12.348 14713 Z= 0.326 Chirality : 0.044 0.301 1620 Planarity : 0.005 0.054 1832 Dihedral : 10.184 86.388 1665 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.30 % Favored : 93.62 % Rotamer: Outliers : 2.48 % Allowed : 11.73 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.23), residues: 1285 helix: 0.23 (0.21), residues: 614 sheet: -1.49 (0.46), residues: 116 loop : -2.15 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1421 HIS 0.006 0.001 HIS A1225 PHE 0.022 0.001 PHE A1370 TYR 0.014 0.001 TYR A1099 ARG 0.004 0.000 ARG A1424 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 5) link_NAG-ASN : angle 2.50716 ( 15) link_ALPHA1-6 : bond 0.00811 ( 1) link_ALPHA1-6 : angle 1.50254 ( 3) link_BETA1-4 : bond 0.00894 ( 2) link_BETA1-4 : angle 3.62166 ( 6) link_ALPHA1-3 : bond 0.00749 ( 1) link_ALPHA1-3 : angle 3.93935 ( 3) hydrogen bonds : bond 0.05049 ( 430) hydrogen bonds : angle 4.49815 ( 1290) SS BOND : bond 0.00324 ( 4) SS BOND : angle 1.15264 ( 8) covalent geometry : bond 0.00415 (10738) covalent geometry : angle 0.68211 (14678) *********************** 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 112 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 1.149 Fit side-chains REVERT: A 92 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7791 (tt) REVERT: A 265 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7265 (mp10) REVERT: A 300 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8192 (pp) REVERT: A 339 TYR cc_start: 0.9127 (OUTLIER) cc_final: 0.8561 (m-10) REVERT: A 414 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8361 (t80) REVERT: A 1225 HIS cc_start: 0.8503 (OUTLIER) cc_final: 0.7878 (t-90) REVERT: A 1241 PHE cc_start: 0.7784 (OUTLIER) cc_final: 0.7174 (m-80) REVERT: A 1288 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8821 (t) REVERT: A 1401 ASP cc_start: 0.7582 (t0) cc_final: 0.7338 (t0) REVERT: A 1495 ARG cc_start: 0.7658 (mmm160) cc_final: 0.6354 (ptp90) REVERT: A 1501 PHE cc_start: 0.6947 (t80) cc_final: 0.6582 (t80) REVERT: B 136 ARG cc_start: 0.8121 (mtp85) cc_final: 0.7860 (mtm180) REVERT: B 144 LYS cc_start: 0.8395 (mttp) cc_final: 0.8189 (mtmm) REVERT: B 179 TYR cc_start: 0.8440 (m-10) cc_final: 0.8196 (m-80) REVERT: B 197 MET cc_start: 0.7977 (mtt) cc_final: 0.7666 (mtp) outliers start: 26 outliers final: 12 residues processed: 107 average time/residue: 0.2363 time to fit residues: 36.3334 Evaluate side-chains 102 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 1.137 ------------------------------------------------------------------------------- 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 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 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 10 optimal weight: 3.9990 chunk 101 optimal weight: 0.0870 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 110 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.156201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.121206 restraints weight = 16507.731| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.21 r_work: 0.3567 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10751 Z= 0.161 Angle : 0.685 12.525 14713 Z= 0.322 Chirality : 0.044 0.300 1620 Planarity : 0.005 0.055 1832 Dihedral : 9.876 89.983 1665 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.30 % Favored : 93.62 % Rotamer: Outliers : 2.76 % Allowed : 12.49 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.23), residues: 1285 helix: 0.32 (0.21), residues: 614 sheet: -1.53 (0.46), residues: 116 loop : -2.08 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1421 HIS 0.005 0.001 HIS A1225 PHE 0.020 0.001 PHE A1370 TYR 0.014 0.001 TYR A1099 ARG 0.005 0.000 ARG A 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 5) link_NAG-ASN : angle 2.38928 ( 15) link_ALPHA1-6 : bond 0.00858 ( 1) link_ALPHA1-6 : angle 1.44281 ( 3) link_BETA1-4 : bond 0.00848 ( 2) link_BETA1-4 : angle 3.70834 ( 6) link_ALPHA1-3 : bond 0.00824 ( 1) link_ALPHA1-3 : angle 3.90430 ( 3) hydrogen bonds : bond 0.04954 ( 430) hydrogen bonds : angle 4.44207 ( 1290) SS BOND : bond 0.00321 ( 4) SS BOND : angle 1.12633 ( 8) covalent geometry : bond 0.00389 (10738) covalent geometry : angle 0.67418 (14678) *********************** 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 113 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 1.163 Fit side-chains REVERT: A 92 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7786 (tt) REVERT: A 265 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7251 (mp10) REVERT: A 300 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8193 (pp) REVERT: A 339 TYR cc_start: 0.9122 (OUTLIER) cc_final: 0.8567 (m-10) REVERT: A 414 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.8397 (t80) REVERT: A 1225 HIS cc_start: 0.8512 (OUTLIER) cc_final: 0.7875 (t-90) REVERT: A 1241 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7143 (m-80) REVERT: A 1288 THR cc_start: 0.9055 (OUTLIER) cc_final: 0.8815 (t) REVERT: A 1401 ASP cc_start: 0.7534 (t0) cc_final: 0.7315 (t0) REVERT: A 1495 ARG cc_start: 0.7668 (mmm160) cc_final: 0.6356 (ptp90) REVERT: A 1501 PHE cc_start: 0.6911 (t80) cc_final: 0.6576 (t80) REVERT: B 136 ARG cc_start: 0.8151 (mtp85) cc_final: 0.7864 (mtp180) REVERT: B 144 LYS cc_start: 0.8307 (mttp) cc_final: 0.8096 (mtmm) outliers start: 29 outliers final: 11 residues processed: 107 average time/residue: 0.2345 time to fit residues: 36.4214 Evaluate side-chains 100 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 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 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 128 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 117 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 34 optimal weight: 0.0060 chunk 102 optimal weight: 0.1980 chunk 80 optimal weight: 2.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.4083 r_free = 0.4083 target = 0.161254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.125724 restraints weight = 16460.613| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.22 r_work: 0.3630 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10751 Z= 0.109 Angle : 0.632 12.486 14713 Z= 0.295 Chirality : 0.042 0.290 1620 Planarity : 0.004 0.053 1832 Dihedral : 9.133 87.373 1665 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.76 % Favored : 94.16 % Rotamer: Outliers : 2.38 % Allowed : 13.54 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.24), residues: 1285 helix: 0.72 (0.22), residues: 596 sheet: -1.49 (0.47), residues: 116 loop : -1.92 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1421 HIS 0.004 0.001 HIS A1238 PHE 0.017 0.001 PHE A1370 TYR 0.011 0.001 TYR A1099 ARG 0.005 0.000 ARG A1424 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 5) link_NAG-ASN : angle 2.07581 ( 15) link_ALPHA1-6 : bond 0.00723 ( 1) link_ALPHA1-6 : angle 1.19163 ( 3) link_BETA1-4 : bond 0.00703 ( 2) link_BETA1-4 : angle 3.71740 ( 6) link_ALPHA1-3 : bond 0.00776 ( 1) link_ALPHA1-3 : angle 4.14666 ( 3) hydrogen bonds : bond 0.04130 ( 430) hydrogen bonds : angle 4.27831 ( 1290) SS BOND : bond 0.00721 ( 4) SS BOND : angle 1.18552 ( 8) covalent geometry : bond 0.00247 (10738) covalent geometry : angle 0.62104 (14678) *********************** 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 122 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 1.115 Fit side-chains REVERT: A 265 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7239 (mp10) REVERT: A 300 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8101 (pp) REVERT: A 339 TYR cc_start: 0.9121 (OUTLIER) cc_final: 0.8421 (m-10) REVERT: A 414 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.8295 (t80) REVERT: A 1225 HIS cc_start: 0.8489 (OUTLIER) cc_final: 0.7886 (t-90) REVERT: A 1288 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8751 (t) REVERT: A 1402 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7502 (tt) REVERT: A 1418 TYR cc_start: 0.7953 (m-80) cc_final: 0.7720 (m-80) REVERT: A 1495 ARG cc_start: 0.7564 (mmm160) cc_final: 0.6273 (ptp90) REVERT: A 1501 PHE cc_start: 0.6788 (t80) cc_final: 0.6451 (t80) REVERT: B 136 ARG cc_start: 0.8086 (mtp85) cc_final: 0.7805 (mtp180) REVERT: B 144 LYS cc_start: 0.8278 (mttp) cc_final: 0.8058 (mtmm) outliers start: 25 outliers final: 13 residues processed: 117 average time/residue: 0.2241 time to fit residues: 38.0611 Evaluate side-chains 106 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 605 PHE 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 1535 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 81 optimal weight: 0.6980 chunk 49 optimal weight: 0.4980 chunk 38 optimal weight: 0.0770 chunk 41 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 73 optimal weight: 0.0370 chunk 45 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 HIS B 125 ASN B 171 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.162765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.127437 restraints weight = 16285.177| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.22 r_work: 0.3727 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10751 Z= 0.110 Angle : 0.630 12.352 14713 Z= 0.296 Chirality : 0.042 0.298 1620 Planarity : 0.004 0.047 1832 Dihedral : 8.560 88.087 1665 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.37 % Favored : 94.55 % Rotamer: Outliers : 2.29 % Allowed : 14.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.24), residues: 1285 helix: 0.91 (0.22), residues: 599 sheet: -1.48 (0.48), residues: 118 loop : -1.74 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1342 HIS 0.004 0.001 HIS A 346 PHE 0.012 0.001 PHE A 253 TYR 0.009 0.001 TYR A1099 ARG 0.004 0.000 ARG A1424 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 5) link_NAG-ASN : angle 2.00769 ( 15) link_ALPHA1-6 : bond 0.01022 ( 1) link_ALPHA1-6 : angle 1.23388 ( 3) link_BETA1-4 : bond 0.00751 ( 2) link_BETA1-4 : angle 3.61799 ( 6) link_ALPHA1-3 : bond 0.00582 ( 1) link_ALPHA1-3 : angle 4.19747 ( 3) hydrogen bonds : bond 0.03922 ( 430) hydrogen bonds : angle 4.20710 ( 1290) SS BOND : bond 0.00372 ( 4) SS BOND : angle 1.62668 ( 8) covalent geometry : bond 0.00246 (10738) covalent geometry : angle 0.61879 (14678) *********************** 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 112 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 1.183 Fit side-chains REVERT: A 92 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7671 (tt) REVERT: A 265 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7222 (mp10) REVERT: A 300 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8056 (pp) REVERT: A 339 TYR cc_start: 0.9083 (OUTLIER) cc_final: 0.8382 (m-10) REVERT: A 414 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8282 (t80) REVERT: A 1225 HIS cc_start: 0.8462 (OUTLIER) cc_final: 0.7868 (t-90) REVERT: A 1495 ARG cc_start: 0.7486 (mmm160) cc_final: 0.6086 (ptp90) REVERT: A 1501 PHE cc_start: 0.6747 (t80) cc_final: 0.6435 (t80) REVERT: B 136 ARG cc_start: 0.8070 (mtp85) cc_final: 0.7776 (mtp180) outliers start: 24 outliers final: 14 residues processed: 105 average time/residue: 0.2207 time to fit residues: 34.1377 Evaluate side-chains 107 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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 414 PHE 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 1345 ARG Chi-restraints excluded: chain A residue 1366 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 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 63 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.161664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.126011 restraints weight = 16487.921| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.23 r_work: 0.3708 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2233 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= 0.123 Angle : 0.638 12.194 14713 Z= 0.302 Chirality : 0.043 0.303 1620 Planarity : 0.004 0.052 1832 Dihedral : 8.262 89.486 1665 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.29 % Favored : 94.63 % Rotamer: Outliers : 2.38 % Allowed : 14.01 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.24), residues: 1285 helix: 0.90 (0.22), residues: 600 sheet: -1.45 (0.48), residues: 118 loop : -1.70 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 252 HIS 0.004 0.001 HIS A1144 PHE 0.017 0.001 PHE A1370 TYR 0.011 0.001 TYR B 173 ARG 0.003 0.000 ARG A1424 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 5) link_NAG-ASN : angle 1.98767 ( 15) link_ALPHA1-6 : bond 0.01062 ( 1) link_ALPHA1-6 : angle 1.27757 ( 3) link_BETA1-4 : bond 0.00737 ( 2) link_BETA1-4 : angle 3.47211 ( 6) link_ALPHA1-3 : bond 0.00890 ( 1) link_ALPHA1-3 : angle 4.00466 ( 3) hydrogen bonds : bond 0.04150 ( 430) hydrogen bonds : angle 4.19198 ( 1290) SS BOND : bond 0.00310 ( 4) SS BOND : angle 1.65078 ( 8) covalent geometry : bond 0.00289 (10738) covalent geometry : angle 0.62799 (14678) *********************** 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 110 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 1.099 Fit side-chains REVERT: A 92 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7701 (tt) REVERT: A 265 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7198 (mp10) REVERT: A 300 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8062 (pp) REVERT: A 339 TYR cc_start: 0.9065 (OUTLIER) cc_final: 0.8454 (m-10) REVERT: A 414 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.8285 (t80) REVERT: A 1225 HIS cc_start: 0.8444 (OUTLIER) cc_final: 0.7860 (t-90) REVERT: A 1495 ARG cc_start: 0.7482 (mmm160) cc_final: 0.6082 (ptp90) REVERT: A 1501 PHE cc_start: 0.6728 (t80) cc_final: 0.6418 (t80) REVERT: B 136 ARG cc_start: 0.8095 (mtp85) cc_final: 0.7788 (mtp180) REVERT: B 171 ASN cc_start: 0.8575 (OUTLIER) cc_final: 0.8290 (t0) outliers start: 25 outliers final: 15 residues processed: 103 average time/residue: 0.2315 time to fit residues: 34.4729 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 : 1.153 ------------------------------------------------------------------------------- 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 605 PHE 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 1366 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 Chi-restraints excluded: chain B residue 263 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 79 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.158377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.123272 restraints weight = 16436.789| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.23 r_work: 0.3599 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2183 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= 0.153 Angle : 0.670 12.208 14713 Z= 0.318 Chirality : 0.044 0.306 1620 Planarity : 0.005 0.048 1832 Dihedral : 7.920 87.869 1665 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.53 % Favored : 94.40 % Rotamer: Outliers : 2.38 % Allowed : 14.11 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.24), residues: 1285 helix: 0.79 (0.22), residues: 600 sheet: -1.40 (0.48), residues: 118 loop : -1.75 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1421 HIS 0.005 0.001 HIS A1225 PHE 0.014 0.001 PHE A 253 TYR 0.013 0.001 TYR A1099 ARG 0.003 0.000 ARG A1424 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 5) link_NAG-ASN : angle 2.06724 ( 15) link_ALPHA1-6 : bond 0.00883 ( 1) link_ALPHA1-6 : angle 1.31049 ( 3) link_BETA1-4 : bond 0.00823 ( 2) link_BETA1-4 : angle 3.13338 ( 6) link_ALPHA1-3 : bond 0.00957 ( 1) link_ALPHA1-3 : angle 3.71306 ( 3) hydrogen bonds : bond 0.04673 ( 430) hydrogen bonds : angle 4.29186 ( 1290) SS BOND : bond 0.00329 ( 4) SS BOND : angle 1.49323 ( 8) covalent geometry : bond 0.00374 (10738) covalent geometry : angle 0.66100 (14678) ********************** 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 109 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 1.074 Fit side-chains REVERT: A 92 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7754 (tt) REVERT: A 265 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7223 (mp10) REVERT: A 300 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8091 (pp) REVERT: A 339 TYR cc_start: 0.9143 (OUTLIER) cc_final: 0.8596 (m-10) REVERT: A 414 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.8344 (t80) REVERT: A 1225 HIS cc_start: 0.8514 (OUTLIER) cc_final: 0.7855 (t-90) REVERT: A 1495 ARG cc_start: 0.7454 (mmm160) cc_final: 0.6030 (ptp90) REVERT: A 1501 PHE cc_start: 0.6699 (t80) cc_final: 0.6420 (t80) REVERT: B 136 ARG cc_start: 0.8187 (mtp85) cc_final: 0.7886 (mtp180) REVERT: B 171 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8322 (t0) outliers start: 25 outliers final: 16 residues processed: 103 average time/residue: 0.2227 time to fit residues: 33.1364 Evaluate side-chains 106 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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 618 ARG 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 1366 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 85 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 91 optimal weight: 0.5980 chunk 105 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4073 r_free = 0.4073 target = 0.159401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.124483 restraints weight = 16238.895| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.22 r_work: 0.3620 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10751 Z= 0.128 Angle : 0.653 12.471 14713 Z= 0.310 Chirality : 0.044 0.302 1620 Planarity : 0.004 0.051 1832 Dihedral : 7.728 89.339 1665 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.76 % Favored : 94.16 % Rotamer: Outliers : 2.19 % Allowed : 14.30 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.24), residues: 1285 helix: 0.86 (0.22), residues: 598 sheet: -1.32 (0.48), residues: 118 loop : -1.72 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1421 HIS 0.004 0.001 HIS A1144 PHE 0.014 0.001 PHE A1370 TYR 0.024 0.001 TYR B 170 ARG 0.003 0.000 ARG A1424 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 5) link_NAG-ASN : angle 2.00549 ( 15) link_ALPHA1-6 : bond 0.00912 ( 1) link_ALPHA1-6 : angle 1.19321 ( 3) link_BETA1-4 : bond 0.00806 ( 2) link_BETA1-4 : angle 2.88722 ( 6) link_ALPHA1-3 : bond 0.00854 ( 1) link_ALPHA1-3 : angle 3.80745 ( 3) hydrogen bonds : bond 0.04407 ( 430) hydrogen bonds : angle 4.27050 ( 1290) SS BOND : bond 0.00317 ( 4) SS BOND : angle 1.43804 ( 8) covalent geometry : bond 0.00303 (10738) covalent geometry : angle 0.64465 (14678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5728.06 seconds wall clock time: 98 minutes 59.88 seconds (5939.88 seconds total)