Starting phenix.real_space_refine on Sat Mar 16 08:43:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt5_26111/03_2024/7tt5_26111.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt5_26111/03_2024/7tt5_26111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt5_26111/03_2024/7tt5_26111.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt5_26111/03_2024/7tt5_26111.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt5_26111/03_2024/7tt5_26111.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt5_26111/03_2024/7tt5_26111.pdb" } resolution = 4.3 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= 0.006 sd= 0.056 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: 5 Type Number sf(0) Gaussians S 27 5.16 5 C 4636 2.51 5 N 1237 2.21 5 O 1417 1.98 5 H 6938 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 1108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 1113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 1283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 614": "OD1" <-> "OD2" Residue "A PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 729": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 754": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 760": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 791": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "D PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14255 Number of models: 1 Model: "" Number of chains: 5 Chain: "P" Number of atoms: 2263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 2263 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 147} Chain breaks: 7 Chain: "A" Number of atoms: 7732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 7732 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 21, 'TRANS': 483} Chain breaks: 4 Chain: "E" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1381 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "D" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 2423 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 4, 'TRANS': 148} Chain breaks: 3 Chain: "C" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 456 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 4, 'TRANS': 27} Time building chain proxies: 6.45, per 1000 atoms: 0.45 Number of scatterers: 14255 At special positions: 0 Unit cell: (91.2747, 104.161, 143.892, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 O 1417 8.00 N 1237 7.00 C 4636 6.00 H 6938 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS P1299 " - pdb=" SG CYS A 425 " distance=2.04 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.41 Conformation dependent library (CDL) restraints added in 1.4 seconds 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1684 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 6 sheets defined 24.6% alpha, 35.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 303 through 316 Processing helix chain 'A' and resid 361 through 367 removed outlier: 4.002A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 393 removed outlier: 3.576A pdb=" N GLN A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'D' and resid 47 through 54 Processing helix chain 'D' and resid 55 through 57 No H-bonds generated for 'chain 'D' and resid 55 through 57' Processing helix chain 'D' and resid 75 through 82 Processing helix chain 'D' and resid 84 through 89 removed outlier: 3.929A pdb=" N GLN D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 116 through 121 removed outlier: 3.572A pdb=" N ASP D 121 " --> pdb=" O ALA D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 135 removed outlier: 4.407A pdb=" N ASP D 134 " --> pdb=" O ASP D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 152 Processing helix chain 'D' and resid 160 through 189 removed outlier: 3.738A pdb=" N LYS D 165 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR D 177 " --> pdb=" O ARG D 173 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 224 removed outlier: 3.646A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix removed outlier: 3.836A pdb=" N GLU D 219 " --> pdb=" O LEU D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 241 removed outlier: 3.530A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 44 Processing sheet with id=AA1, first strand: chain 'P' and resid 1039 through 1045 removed outlier: 3.574A pdb=" N TYR P1108 " --> pdb=" O GLY P1081 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY P1156 " --> pdb=" O TYR P1118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 1159 through 1162 removed outlier: 6.545A pdb=" N ALA P1165 " --> pdb=" O VAL P1161 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL P1208 " --> pdb=" O LEU P1227 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU P1227 " --> pdb=" O VAL P1208 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL P1210 " --> pdb=" O ALA P1225 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA P1225 " --> pdb=" O VAL P1210 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS P1212 " --> pdb=" O ALA P1223 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA P1223 " --> pdb=" O LYS P1212 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU P1276 " --> pdb=" O LEU P1264 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE P1274 " --> pdb=" O ALA P1266 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS A 425 " --> pdb=" O GLN A 445 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN A 445 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 524 " --> pdb=" O THR A 577 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 530 " --> pdb=" O THR A 571 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY A 636 " --> pdb=" O MET A 711 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET A 711 " --> pdb=" O GLY A 636 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 771 " --> pdb=" O PHE A 738 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE A 791 " --> pdb=" O MET A 768 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 770 " --> pdb=" O GLN A 789 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN A 803 " --> pdb=" O SER A 786 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 273 through 276 Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 355 removed outlier: 7.504A pdb=" N VAL A 414 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE A 352 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N TYR A 416 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE A 354 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL A 418 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLN A 411 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ARG A 404 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASP A 413 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N THR A 402 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A 415 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N THR A 400 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.605A pdb=" N ILE E 32 " --> pdb=" O GLN E 80 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.605A pdb=" N ILE E 32 " --> pdb=" O GLN E 80 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR E 90 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASN E 106 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR E 92 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE E 104 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR E 94 " --> pdb=" O THR E 102 " (cutoff:3.500A) 370 hydrogen bonds defined for protein. 1032 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: 5.27 Time building geometry restraints manager: 10.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 6938 1.04 - 1.23: 397 1.23 - 1.43: 2953 1.43 - 1.63: 4082 1.63 - 1.83: 50 Bond restraints: 14420 Sorted by residual: bond pdb=" CA PHE A 395 " pdb=" CB PHE A 395 " ideal model delta sigma weight residual 1.536 1.504 0.032 2.53e-02 1.56e+03 1.63e+00 bond pdb=" CA ALA D 193 " pdb=" C ALA D 193 " ideal model delta sigma weight residual 1.523 1.508 0.015 1.35e-02 5.49e+03 1.23e+00 bond pdb=" CG LEU A 365 " pdb=" CD2 LEU A 365 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.13e+00 bond pdb=" CB PHE A 395 " pdb=" CG PHE A 395 " ideal model delta sigma weight residual 1.502 1.478 0.024 2.30e-02 1.89e+03 1.06e+00 bond pdb=" CG PRO A 587 " pdb=" CD PRO A 587 " ideal model delta sigma weight residual 1.503 1.472 0.031 3.40e-02 8.65e+02 8.57e-01 ... (remaining 14415 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.14: 165 106.14 - 113.11: 16024 113.11 - 120.08: 4757 120.08 - 127.05: 4793 127.05 - 134.01: 78 Bond angle restraints: 25817 Sorted by residual: angle pdb=" N ASP P1270 " pdb=" CA ASP P1270 " pdb=" C ASP P1270 " ideal model delta sigma weight residual 110.80 117.07 -6.27 2.13e+00 2.20e-01 8.67e+00 angle pdb=" N GLN D 224 " pdb=" CA GLN D 224 " pdb=" C GLN D 224 " ideal model delta sigma weight residual 113.18 109.62 3.56 1.21e+00 6.83e-01 8.65e+00 angle pdb=" N TYR P1286 " pdb=" CA TYR P1286 " pdb=" C TYR P1286 " ideal model delta sigma weight residual 109.50 105.09 4.41 1.58e+00 4.01e-01 7.79e+00 angle pdb=" N ASP A 569 " pdb=" CA ASP A 569 " pdb=" C ASP A 569 " ideal model delta sigma weight residual 108.41 112.93 -4.52 1.63e+00 3.76e-01 7.70e+00 angle pdb=" N ASP A 410 " pdb=" CA ASP A 410 " pdb=" C ASP A 410 " ideal model delta sigma weight residual 111.87 115.72 -3.85 1.41e+00 5.03e-01 7.45e+00 ... (remaining 25812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 6499 17.55 - 35.11: 196 35.11 - 52.66: 129 52.66 - 70.21: 37 70.21 - 87.77: 8 Dihedral angle restraints: 6869 sinusoidal: 3615 harmonic: 3254 Sorted by residual: dihedral pdb=" CA CYS P1299 " pdb=" CB CYS P1299 " pdb=" SG CYS P1299 " pdb=" SG CYS A 425 " ideal model delta sinusoidal sigma weight residual -73.00 -20.09 -52.91 1 2.00e+01 2.50e-03 9.53e+00 dihedral pdb=" CB GLU E 84 " pdb=" CG GLU E 84 " pdb=" CD GLU E 84 " pdb=" OE1 GLU E 84 " ideal model delta sinusoidal sigma weight residual 0.00 -79.09 79.09 1 3.00e+01 1.11e-03 8.65e+00 dihedral pdb=" CB GLU A 272 " pdb=" CG GLU A 272 " pdb=" CD GLU A 272 " pdb=" OE1 GLU A 272 " ideal model delta sinusoidal sigma weight residual 0.00 -76.55 76.55 1 3.00e+01 1.11e-03 8.19e+00 ... (remaining 6866 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 599 0.027 - 0.053: 268 0.053 - 0.080: 93 0.080 - 0.107: 71 0.107 - 0.133: 34 Chirality restraints: 1065 Sorted by residual: chirality pdb=" CA PRO A 409 " pdb=" N PRO A 409 " pdb=" C PRO A 409 " pdb=" CB PRO A 409 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA VAL A 513 " pdb=" N VAL A 513 " pdb=" C VAL A 513 " pdb=" CB VAL A 513 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA VAL A 744 " pdb=" N VAL A 744 " pdb=" C VAL A 744 " pdb=" CB VAL A 744 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 1062 not shown) Planarity restraints: 2199 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 586 " -0.058 5.00e-02 4.00e+02 8.84e-02 1.25e+01 pdb=" N PRO A 587 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO A 587 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 587 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU P1168 " 0.057 5.00e-02 4.00e+02 8.68e-02 1.21e+01 pdb=" N PRO P1169 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO P1169 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO P1169 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 136 " 0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO D 137 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO D 137 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 137 " 0.032 5.00e-02 4.00e+02 ... (remaining 2196 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 388 2.14 - 2.76: 26265 2.76 - 3.37: 36226 3.37 - 3.99: 46968 3.99 - 4.60: 73322 Nonbonded interactions: 183169 Sorted by model distance: nonbonded pdb="HD22 ASN P1271 " pdb=" O CYS P1299 " model vdw 1.528 1.850 nonbonded pdb=" OD1 ASP D 136 " pdb=" H GLN D 138 " model vdw 1.571 1.850 nonbonded pdb=" H ILE A 352 " pdb=" OE2 GLU A 373 " model vdw 1.601 1.850 nonbonded pdb=" OD2 ASP A 703 " pdb=" HZ1 LYS A 798 " model vdw 1.611 1.850 nonbonded pdb=" OD1 ASP D 172 " pdb=" HG1 THR D 208 " model vdw 1.614 1.850 ... (remaining 183164 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue 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: 0.640 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: 0.210 Extract box with map and model: 3.520 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 44.970 Find NCS groups from input model: 0.260 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: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 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 : 0.004 0.035 7482 Z= 0.244 Angle : 0.694 6.271 10131 Z= 0.429 Chirality : 0.043 0.133 1065 Planarity : 0.005 0.088 1325 Dihedral : 10.021 87.766 2667 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.27), residues: 890 helix: -0.22 (0.33), residues: 193 sheet: 1.43 (0.26), residues: 347 loop : 1.06 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 546 HIS 0.002 0.001 HIS D 139 PHE 0.035 0.002 PHE A 395 TYR 0.024 0.002 TYR A 348 ARG 0.017 0.002 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1265 ASN cc_start: 0.9638 (m-40) cc_final: 0.9437 (p0) REVERT: P 1296 PHE cc_start: 0.9284 (t80) cc_final: 0.8766 (t80) REVERT: A 306 ASP cc_start: 0.9382 (m-30) cc_final: 0.8469 (m-30) REVERT: A 372 MET cc_start: 0.8203 (mmp) cc_final: 0.7708 (mmm) REVERT: A 386 LYS cc_start: 0.9361 (tttt) cc_final: 0.9114 (ttpt) REVERT: A 388 ARG cc_start: 0.8662 (tpp-160) cc_final: 0.8438 (tpp-160) REVERT: A 440 PHE cc_start: 0.8256 (m-80) cc_final: 0.7859 (m-10) REVERT: A 474 THR cc_start: 0.9117 (m) cc_final: 0.8865 (p) REVERT: A 491 TYR cc_start: 0.8490 (t80) cc_final: 0.8157 (t80) REVERT: A 535 SER cc_start: 0.7688 (t) cc_final: 0.7405 (t) REVERT: A 582 ASP cc_start: 0.8688 (p0) cc_final: 0.8207 (t70) REVERT: A 637 TYR cc_start: 0.8225 (t80) cc_final: 0.7884 (t80) REVERT: A 711 MET cc_start: 0.8728 (ppp) cc_final: 0.8099 (ppp) REVERT: A 741 MET cc_start: 0.8245 (pmm) cc_final: 0.7763 (pmm) REVERT: A 765 ASN cc_start: 0.9266 (m-40) cc_final: 0.8941 (m-40) REVERT: E 27 VAL cc_start: 0.9545 (t) cc_final: 0.9265 (m) REVERT: E 42 ASP cc_start: 0.9189 (m-30) cc_final: 0.8755 (m-30) REVERT: E 80 GLN cc_start: 0.8881 (tt0) cc_final: 0.8570 (tp-100) REVERT: E 84 GLU cc_start: 0.8532 (tp30) cc_final: 0.8256 (mm-30) REVERT: E 90 THR cc_start: 0.8901 (m) cc_final: 0.8375 (m) REVERT: D 84 ASP cc_start: 0.8424 (m-30) cc_final: 0.7101 (m-30) REVERT: D 131 ASP cc_start: 0.7846 (t0) cc_final: 0.7622 (t0) REVERT: D 136 ASP cc_start: 0.9341 (t0) cc_final: 0.8239 (t0) REVERT: D 213 ASP cc_start: 0.8557 (m-30) cc_final: 0.8156 (t70) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.4784 time to fit residues: 185.6778 Evaluate side-chains 209 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 ASN D 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 7482 Z= 0.242 Angle : 0.579 15.340 10131 Z= 0.328 Chirality : 0.043 0.176 1065 Planarity : 0.005 0.059 1325 Dihedral : 4.447 50.990 1018 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.28), residues: 890 helix: 1.54 (0.38), residues: 199 sheet: 1.09 (0.26), residues: 356 loop : 1.03 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 546 HIS 0.003 0.001 HIS A 533 PHE 0.016 0.002 PHE A 395 TYR 0.026 0.001 TYR A 550 ARG 0.006 0.001 ARG P1269 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.8566 (pmm) cc_final: 0.8310 (pmm) REVERT: A 307 ASP cc_start: 0.9275 (m-30) cc_final: 0.9050 (m-30) REVERT: A 386 LYS cc_start: 0.9338 (tttt) cc_final: 0.9010 (ttpt) REVERT: A 408 SER cc_start: 0.8715 (t) cc_final: 0.8468 (t) REVERT: A 474 THR cc_start: 0.9089 (m) cc_final: 0.8806 (p) REVERT: A 535 SER cc_start: 0.8603 (t) cc_final: 0.8268 (p) REVERT: A 582 ASP cc_start: 0.8744 (p0) cc_final: 0.8254 (t70) REVERT: A 609 TYR cc_start: 0.8492 (p90) cc_final: 0.8264 (p90) REVERT: A 635 TRP cc_start: 0.8426 (m100) cc_final: 0.8088 (m-10) REVERT: A 637 TYR cc_start: 0.8134 (t80) cc_final: 0.7841 (t80) REVERT: A 711 MET cc_start: 0.8695 (ppp) cc_final: 0.8073 (ppp) REVERT: A 741 MET cc_start: 0.8000 (pmm) cc_final: 0.7597 (pmm) REVERT: E 80 GLN cc_start: 0.8994 (tt0) cc_final: 0.8596 (tp-100) REVERT: E 105 ASP cc_start: 0.7751 (m-30) cc_final: 0.7271 (m-30) REVERT: D 87 LEU cc_start: 0.9428 (mt) cc_final: 0.9045 (mt) REVERT: D 204 ASP cc_start: 0.8367 (t70) cc_final: 0.7975 (t0) REVERT: D 213 ASP cc_start: 0.8552 (m-30) cc_final: 0.8157 (t70) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.4159 time to fit residues: 128.9314 Evaluate side-chains 198 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7482 Z= 0.193 Angle : 0.517 10.076 10131 Z= 0.290 Chirality : 0.042 0.161 1065 Planarity : 0.004 0.046 1325 Dihedral : 4.542 61.887 1018 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.13 % Allowed : 0.66 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.28), residues: 890 helix: 1.78 (0.38), residues: 199 sheet: 0.75 (0.26), residues: 357 loop : 0.95 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 576 HIS 0.002 0.001 HIS P1062 PHE 0.014 0.001 PHE A 718 TYR 0.016 0.001 TYR A 550 ARG 0.004 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 224 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1300 PHE cc_start: 0.7729 (m-80) cc_final: 0.7500 (m-10) REVERT: A 304 MET cc_start: 0.8579 (pmm) cc_final: 0.8298 (pmm) REVERT: A 307 ASP cc_start: 0.9212 (m-30) cc_final: 0.8986 (m-30) REVERT: A 352 ILE cc_start: 0.9098 (mt) cc_final: 0.8442 (mt) REVERT: A 386 LYS cc_start: 0.9348 (tttt) cc_final: 0.9035 (ttpt) REVERT: A 408 SER cc_start: 0.8859 (t) cc_final: 0.8629 (t) REVERT: A 474 THR cc_start: 0.9102 (m) cc_final: 0.8821 (p) REVERT: A 614 ASP cc_start: 0.8636 (t70) cc_final: 0.8271 (t0) REVERT: A 635 TRP cc_start: 0.8450 (m100) cc_final: 0.8112 (m-10) REVERT: A 644 LYS cc_start: 0.8514 (mttt) cc_final: 0.8192 (mtpt) REVERT: A 645 GLU cc_start: 0.7965 (tp30) cc_final: 0.6905 (tt0) REVERT: A 711 MET cc_start: 0.8765 (ppp) cc_final: 0.8137 (ppp) REVERT: A 741 MET cc_start: 0.8016 (pmm) cc_final: 0.7612 (pmm) REVERT: E 105 ASP cc_start: 0.7731 (m-30) cc_final: 0.7293 (m-30) REVERT: D 84 ASP cc_start: 0.7342 (t0) cc_final: 0.6969 (t0) REVERT: D 199 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7865 (tm-30) REVERT: D 213 ASP cc_start: 0.8527 (m-30) cc_final: 0.8119 (t70) outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 0.4312 time to fit residues: 126.5463 Evaluate side-chains 200 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN D 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7482 Z= 0.233 Angle : 0.508 7.565 10131 Z= 0.285 Chirality : 0.041 0.152 1065 Planarity : 0.004 0.042 1325 Dihedral : 4.622 63.238 1018 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.28), residues: 890 helix: 1.43 (0.37), residues: 199 sheet: 0.47 (0.26), residues: 353 loop : 0.50 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 576 HIS 0.002 0.001 HIS A 533 PHE 0.014 0.001 PHE A 395 TYR 0.013 0.001 TYR D 205 ARG 0.004 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1260 MET cc_start: 0.8900 (mtm) cc_final: 0.8662 (mpp) REVERT: A 304 MET cc_start: 0.8588 (pmm) cc_final: 0.8297 (pmm) REVERT: A 307 ASP cc_start: 0.9185 (m-30) cc_final: 0.8969 (m-30) REVERT: A 386 LYS cc_start: 0.9369 (tttt) cc_final: 0.9060 (ttpt) REVERT: A 408 SER cc_start: 0.9073 (t) cc_final: 0.8832 (t) REVERT: A 445 GLN cc_start: 0.8850 (pt0) cc_final: 0.8295 (pp30) REVERT: A 474 THR cc_start: 0.9167 (m) cc_final: 0.8875 (p) REVERT: A 614 ASP cc_start: 0.8743 (t70) cc_final: 0.8460 (t0) REVERT: A 635 TRP cc_start: 0.8486 (m100) cc_final: 0.8220 (m-10) REVERT: A 637 TYR cc_start: 0.8100 (t80) cc_final: 0.7724 (t80) REVERT: A 711 MET cc_start: 0.8883 (ppp) cc_final: 0.8221 (ppp) REVERT: E 65 SER cc_start: 0.9124 (p) cc_final: 0.8851 (t) REVERT: E 88 GLN cc_start: 0.7681 (pp30) cc_final: 0.7423 (pp30) REVERT: E 105 ASP cc_start: 0.7623 (m-30) cc_final: 0.7211 (m-30) REVERT: D 84 ASP cc_start: 0.7580 (t0) cc_final: 0.7129 (t0) REVERT: D 199 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8026 (tm-30) REVERT: D 213 ASP cc_start: 0.8507 (m-30) cc_final: 0.8114 (t70) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.4520 time to fit residues: 128.3795 Evaluate side-chains 188 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 50.0000 chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 74 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 44 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN D 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.5376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7482 Z= 0.274 Angle : 0.525 6.698 10131 Z= 0.295 Chirality : 0.042 0.159 1065 Planarity : 0.004 0.047 1325 Dihedral : 4.712 64.617 1018 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.27), residues: 890 helix: 1.08 (0.37), residues: 199 sheet: 0.33 (0.26), residues: 353 loop : 0.13 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 576 HIS 0.002 0.001 HIS A 555 PHE 0.032 0.002 PHE E 74 TYR 0.022 0.001 TYR D 205 ARG 0.004 0.000 ARG D 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ASP cc_start: 0.9157 (m-30) cc_final: 0.8909 (m-30) REVERT: A 323 GLN cc_start: 0.8791 (pt0) cc_final: 0.8557 (pm20) REVERT: A 386 LYS cc_start: 0.9393 (tttt) cc_final: 0.9107 (ttpt) REVERT: A 445 GLN cc_start: 0.8934 (pt0) cc_final: 0.8396 (pp30) REVERT: A 535 SER cc_start: 0.7997 (t) cc_final: 0.7789 (m) REVERT: A 614 ASP cc_start: 0.8776 (t70) cc_final: 0.8515 (t0) REVERT: A 635 TRP cc_start: 0.8526 (m100) cc_final: 0.8133 (m-10) REVERT: A 637 TYR cc_start: 0.8146 (t80) cc_final: 0.7671 (t80) REVERT: A 711 MET cc_start: 0.8940 (ppp) cc_final: 0.8310 (ppp) REVERT: E 65 SER cc_start: 0.9040 (p) cc_final: 0.8730 (t) REVERT: E 88 GLN cc_start: 0.7755 (pp30) cc_final: 0.7514 (pp30) REVERT: E 104 ILE cc_start: 0.8749 (mt) cc_final: 0.8427 (mt) REVERT: E 105 ASP cc_start: 0.7428 (m-30) cc_final: 0.6708 (m-30) REVERT: D 84 ASP cc_start: 0.7807 (t0) cc_final: 0.7386 (t0) REVERT: D 136 ASP cc_start: 0.8761 (t0) cc_final: 0.8543 (t0) REVERT: D 199 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8047 (tm-30) REVERT: D 213 ASP cc_start: 0.8534 (m-30) cc_final: 0.8139 (t70) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.4364 time to fit residues: 122.1770 Evaluate side-chains 188 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 83 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN D 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.5693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7482 Z= 0.173 Angle : 0.476 6.127 10131 Z= 0.263 Chirality : 0.041 0.143 1065 Planarity : 0.004 0.059 1325 Dihedral : 4.550 62.858 1018 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.27), residues: 890 helix: 1.27 (0.37), residues: 199 sheet: 0.27 (0.25), residues: 353 loop : 0.14 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 191 HIS 0.002 0.000 HIS D 139 PHE 0.020 0.001 PHE E 74 TYR 0.022 0.001 TYR A 550 ARG 0.012 0.001 ARG P1269 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ASP cc_start: 0.9146 (m-30) cc_final: 0.8883 (m-30) REVERT: A 323 GLN cc_start: 0.8788 (pt0) cc_final: 0.8537 (pm20) REVERT: A 386 LYS cc_start: 0.9360 (tttt) cc_final: 0.9031 (ttpt) REVERT: A 445 GLN cc_start: 0.8910 (pt0) cc_final: 0.8358 (pp30) REVERT: A 582 ASP cc_start: 0.9058 (p0) cc_final: 0.8419 (t0) REVERT: A 614 ASP cc_start: 0.8738 (t70) cc_final: 0.8514 (t0) REVERT: A 637 TYR cc_start: 0.8110 (t80) cc_final: 0.7793 (t80) REVERT: A 711 MET cc_start: 0.8973 (ppp) cc_final: 0.8294 (ppp) REVERT: A 765 ASN cc_start: 0.9237 (m110) cc_final: 0.8856 (m-40) REVERT: E 65 SER cc_start: 0.8968 (p) cc_final: 0.8679 (t) REVERT: E 88 GLN cc_start: 0.7743 (pp30) cc_final: 0.7494 (pp30) REVERT: E 105 ASP cc_start: 0.7554 (m-30) cc_final: 0.6553 (m-30) REVERT: D 84 ASP cc_start: 0.7838 (t0) cc_final: 0.7398 (t0) REVERT: D 136 ASP cc_start: 0.8786 (t0) cc_final: 0.8569 (t0) REVERT: D 199 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8025 (tm-30) REVERT: D 213 ASP cc_start: 0.8509 (m-30) cc_final: 0.8117 (t70) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.4126 time to fit residues: 114.2081 Evaluate side-chains 187 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 48 optimal weight: 0.3980 chunk 86 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN D 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.5842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7482 Z= 0.165 Angle : 0.468 5.936 10131 Z= 0.258 Chirality : 0.041 0.144 1065 Planarity : 0.004 0.058 1325 Dihedral : 4.473 60.833 1018 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.27), residues: 890 helix: 1.45 (0.37), residues: 199 sheet: 0.24 (0.25), residues: 353 loop : 0.17 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 191 HIS 0.003 0.001 HIS D 139 PHE 0.018 0.001 PHE E 74 TYR 0.017 0.001 TYR A 550 ARG 0.011 0.000 ARG P1269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1274 PHE cc_start: 0.9202 (t80) cc_final: 0.8983 (t80) REVERT: A 307 ASP cc_start: 0.9134 (m-30) cc_final: 0.8853 (m-30) REVERT: A 323 GLN cc_start: 0.8765 (pt0) cc_final: 0.8555 (pm20) REVERT: A 386 LYS cc_start: 0.9357 (tttt) cc_final: 0.9016 (ttpt) REVERT: A 445 GLN cc_start: 0.8945 (pt0) cc_final: 0.8382 (pp30) REVERT: A 582 ASP cc_start: 0.9116 (p0) cc_final: 0.8365 (t0) REVERT: A 614 ASP cc_start: 0.8712 (t70) cc_final: 0.8504 (t0) REVERT: A 635 TRP cc_start: 0.8398 (m-10) cc_final: 0.7987 (m-10) REVERT: A 637 TYR cc_start: 0.8113 (t80) cc_final: 0.7839 (t80) REVERT: A 711 MET cc_start: 0.8960 (ppp) cc_final: 0.8369 (ppp) REVERT: A 765 ASN cc_start: 0.9228 (m110) cc_final: 0.8840 (m-40) REVERT: E 65 SER cc_start: 0.8908 (p) cc_final: 0.8634 (t) REVERT: E 80 GLN cc_start: 0.8952 (tt0) cc_final: 0.8597 (tt0) REVERT: E 105 ASP cc_start: 0.7674 (m-30) cc_final: 0.6674 (m-30) REVERT: D 84 ASP cc_start: 0.7849 (t0) cc_final: 0.7408 (t0) REVERT: D 136 ASP cc_start: 0.8393 (t0) cc_final: 0.8191 (p0) REVERT: D 213 ASP cc_start: 0.8528 (m-30) cc_final: 0.8123 (t70) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.4280 time to fit residues: 116.7253 Evaluate side-chains 175 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 0.0770 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 20.0000 chunk 68 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 chunk 75 optimal weight: 2.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN D 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.5960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7482 Z= 0.125 Angle : 0.455 4.882 10131 Z= 0.248 Chirality : 0.041 0.137 1065 Planarity : 0.004 0.070 1325 Dihedral : 4.273 57.686 1018 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.28), residues: 890 helix: 1.72 (0.38), residues: 198 sheet: 0.28 (0.26), residues: 346 loop : 0.27 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 191 HIS 0.001 0.000 HIS E 83 PHE 0.019 0.001 PHE E 74 TYR 0.023 0.001 TYR D 205 ARG 0.011 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1258 MET cc_start: 0.6257 (tmm) cc_final: 0.5736 (tmm) REVERT: P 1260 MET cc_start: 0.8658 (mtm) cc_final: 0.8050 (mtm) REVERT: P 1274 PHE cc_start: 0.9195 (t80) cc_final: 0.8947 (t80) REVERT: A 307 ASP cc_start: 0.9121 (m-30) cc_final: 0.8839 (m-30) REVERT: A 323 GLN cc_start: 0.8749 (pt0) cc_final: 0.8531 (pm20) REVERT: A 386 LYS cc_start: 0.9381 (tttt) cc_final: 0.9046 (ttpt) REVERT: A 445 GLN cc_start: 0.8923 (pt0) cc_final: 0.8362 (pp30) REVERT: A 582 ASP cc_start: 0.9142 (p0) cc_final: 0.8224 (t0) REVERT: A 635 TRP cc_start: 0.8365 (m-10) cc_final: 0.7948 (m-10) REVERT: A 711 MET cc_start: 0.8969 (ppp) cc_final: 0.8331 (ppp) REVERT: A 765 ASN cc_start: 0.9247 (m110) cc_final: 0.8786 (m-40) REVERT: E 65 SER cc_start: 0.8674 (p) cc_final: 0.8403 (t) REVERT: E 80 GLN cc_start: 0.8978 (tt0) cc_final: 0.8581 (tt0) REVERT: E 88 GLN cc_start: 0.7818 (pp30) cc_final: 0.7508 (pp30) REVERT: E 105 ASP cc_start: 0.7657 (m-30) cc_final: 0.6684 (m-30) REVERT: D 84 ASP cc_start: 0.7852 (t0) cc_final: 0.7402 (t0) REVERT: D 213 ASP cc_start: 0.8516 (m-30) cc_final: 0.8098 (t70) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.4125 time to fit residues: 114.2661 Evaluate side-chains 179 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.6098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7482 Z= 0.149 Angle : 0.460 7.237 10131 Z= 0.249 Chirality : 0.041 0.136 1065 Planarity : 0.004 0.059 1325 Dihedral : 4.203 55.569 1018 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.28), residues: 890 helix: 1.77 (0.37), residues: 199 sheet: 0.20 (0.26), residues: 346 loop : 0.16 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 191 HIS 0.001 0.000 HIS A 555 PHE 0.017 0.001 PHE E 74 TYR 0.014 0.001 TYR A 550 ARG 0.009 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1258 MET cc_start: 0.6119 (tmm) cc_final: 0.5600 (tmm) REVERT: P 1260 MET cc_start: 0.8674 (mtm) cc_final: 0.8123 (mtm) REVERT: P 1274 PHE cc_start: 0.9198 (t80) cc_final: 0.8950 (t80) REVERT: A 307 ASP cc_start: 0.9123 (m-30) cc_final: 0.8830 (m-30) REVERT: A 386 LYS cc_start: 0.9396 (tttt) cc_final: 0.9064 (ttpt) REVERT: A 445 GLN cc_start: 0.8942 (pt0) cc_final: 0.8306 (pp30) REVERT: A 582 ASP cc_start: 0.9166 (p0) cc_final: 0.8201 (t0) REVERT: A 635 TRP cc_start: 0.8362 (m-10) cc_final: 0.7991 (m-10) REVERT: A 711 MET cc_start: 0.8947 (ppp) cc_final: 0.8373 (ppp) REVERT: A 765 ASN cc_start: 0.9260 (m110) cc_final: 0.8819 (m-40) REVERT: E 53 GLN cc_start: 0.9522 (mp10) cc_final: 0.9281 (pm20) REVERT: E 65 SER cc_start: 0.8686 (p) cc_final: 0.8417 (t) REVERT: E 80 GLN cc_start: 0.8962 (tt0) cc_final: 0.8600 (tt0) REVERT: E 88 GLN cc_start: 0.7853 (pp30) cc_final: 0.7481 (pp30) REVERT: E 105 ASP cc_start: 0.7680 (m-30) cc_final: 0.6763 (m-30) REVERT: D 84 ASP cc_start: 0.7869 (t0) cc_final: 0.7404 (t0) REVERT: D 149 LYS cc_start: 0.8876 (mmpt) cc_final: 0.8515 (tppt) REVERT: D 213 ASP cc_start: 0.8512 (m-30) cc_final: 0.8114 (t70) REVERT: D 227 MET cc_start: 0.9069 (mmm) cc_final: 0.8663 (mmp) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.4270 time to fit residues: 115.7679 Evaluate side-chains 181 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 89 optimal weight: 0.3980 chunk 82 optimal weight: 0.3980 chunk 71 optimal weight: 0.1980 chunk 7 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN A 651 ASN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.6224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7482 Z= 0.126 Angle : 0.443 5.092 10131 Z= 0.239 Chirality : 0.041 0.135 1065 Planarity : 0.004 0.069 1325 Dihedral : 4.151 53.879 1018 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.28), residues: 890 helix: 1.86 (0.37), residues: 199 sheet: 0.20 (0.26), residues: 346 loop : 0.20 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 191 HIS 0.001 0.000 HIS E 83 PHE 0.017 0.001 PHE E 74 TYR 0.014 0.001 TYR A 550 ARG 0.013 0.000 ARG A 321 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1258 MET cc_start: 0.6014 (tmm) cc_final: 0.5484 (tmm) REVERT: P 1260 MET cc_start: 0.8644 (mtm) cc_final: 0.8073 (mtm) REVERT: P 1274 PHE cc_start: 0.9195 (t80) cc_final: 0.8917 (t80) REVERT: A 307 ASP cc_start: 0.9108 (m-30) cc_final: 0.8813 (m-30) REVERT: A 386 LYS cc_start: 0.9352 (tttt) cc_final: 0.9096 (ttpt) REVERT: A 445 GLN cc_start: 0.8953 (pt0) cc_final: 0.8327 (pp30) REVERT: A 635 TRP cc_start: 0.8340 (m-10) cc_final: 0.8007 (m-10) REVERT: A 711 MET cc_start: 0.8945 (ppp) cc_final: 0.8402 (ppp) REVERT: A 765 ASN cc_start: 0.9247 (m110) cc_final: 0.8812 (m-40) REVERT: E 53 GLN cc_start: 0.9520 (mp10) cc_final: 0.9274 (pm20) REVERT: E 65 SER cc_start: 0.8626 (p) cc_final: 0.8393 (t) REVERT: E 88 GLN cc_start: 0.7864 (pp30) cc_final: 0.7590 (pp30) REVERT: E 105 ASP cc_start: 0.7708 (m-30) cc_final: 0.6792 (m-30) REVERT: D 84 ASP cc_start: 0.7827 (t0) cc_final: 0.7496 (t0) REVERT: D 149 LYS cc_start: 0.8865 (mmpt) cc_final: 0.8498 (tppt) REVERT: D 204 ASP cc_start: 0.8800 (t0) cc_final: 0.8322 (t0) REVERT: D 213 ASP cc_start: 0.8443 (m-30) cc_final: 0.8002 (t70) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.4272 time to fit residues: 115.2400 Evaluate side-chains 183 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 30.0000 chunk 19 optimal weight: 0.6980 chunk 71 optimal weight: 0.0970 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 4 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.140177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.093007 restraints weight = 42383.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.095090 restraints weight = 19464.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.095827 restraints weight = 13305.745| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.6328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7482 Z= 0.157 Angle : 0.459 8.067 10131 Z= 0.247 Chirality : 0.040 0.144 1065 Planarity : 0.003 0.040 1325 Dihedral : 4.115 53.331 1018 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.28), residues: 890 helix: 1.82 (0.37), residues: 199 sheet: 0.14 (0.25), residues: 353 loop : 0.13 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 191 HIS 0.001 0.000 HIS E 83 PHE 0.017 0.001 PHE E 74 TYR 0.012 0.001 TYR D 184 ARG 0.006 0.000 ARG A 321 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3961.17 seconds wall clock time: 70 minutes 23.77 seconds (4223.77 seconds total)