Starting phenix.real_space_refine on Wed Jan 14 08:39:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xzj_33529/01_2026/7xzj_33529.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xzj_33529/01_2026/7xzj_33529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xzj_33529/01_2026/7xzj_33529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xzj_33529/01_2026/7xzj_33529.map" model { file = "/net/cci-nas-00/data/ceres_data/7xzj_33529/01_2026/7xzj_33529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xzj_33529/01_2026/7xzj_33529.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 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 P 6 5.49 5 S 40 5.16 5 C 8740 2.51 5 N 2492 2.21 5 O 2622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13900 Number of models: 1 Model: "" Number of chains: 9 Chain: "3" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 182 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 29} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 6, 'HIS:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "4" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1635 Classifications: {'peptide': 262} Incomplete info: {'backbone_only': 7, 'truncation_to_alanine': 97} Link IDs: {'PTRANS': 12, 'TRANS': 249} Unresolved chain links: 1 Chain breaks: 3 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 402 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 321 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'PHE:plan': 5, 'GLU:plan': 5, 'TRP:plan': 2, 'ARG:plan': 15, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 201 Chain: "7" Number of atoms: 4770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 4770 Classifications: {'peptide': 643} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 72} Link IDs: {'PTRANS': 31, 'TRANS': 611} Chain breaks: 1 Unresolved non-hydrogen bonds: 288 Unresolved non-hydrogen angles: 355 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLU:plan': 18, 'ARG:plan': 8, 'ASN:plan1': 3, 'PHE:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 159 Chain: "9" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2909 Classifications: {'peptide': 386} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 26} Link IDs: {'PTRANS': 21, 'TRANS': 364} Chain breaks: 3 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 12, 'ASP:plan': 5, 'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 86 Chain: "A" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3291 Classifications: {'peptide': 423} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 69} Link IDs: {'PTRANS': 7, 'TRANS': 415} Chain breaks: 5 Unresolved non-hydrogen bonds: 315 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 266 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 3, 'GLU:plan': 8, 'TYR:plan': 3, 'ARG:plan': 10, 'PHE:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 163 Chain: "E" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 325 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain breaks: 2 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "G" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 597 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 68} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 4, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "X" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 155 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.00, per 1000 atoms: 0.22 Number of scatterers: 13900 At special positions: 0 Unit cell: (98.55, 168.75, 135.675, 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 40 16.00 P 6 15.00 O 2622 8.00 N 2492 7.00 C 8740 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 483.5 milliseconds 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3484 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 12 sheets defined 34.3% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain '3' and resid 260 through 286 Processing helix chain '4' and resid 14 through 18 Processing helix chain '4' and resid 20 through 31 Processing helix chain '4' and resid 222 through 237 Processing helix chain '4' and resid 237 through 242 removed outlier: 4.202A pdb=" N ASN 4 241 " --> pdb=" O ARG 4 237 " (cutoff:3.500A) Processing helix chain '4' and resid 243 through 248 removed outlier: 4.073A pdb=" N TRP 4 247 " --> pdb=" O PRO 4 243 " (cutoff:3.500A) Processing helix chain '4' and resid 251 through 260 Processing helix chain '7' and resid 179 through 187 Processing helix chain '7' and resid 196 through 211 removed outlier: 3.582A pdb=" N LEU 7 200 " --> pdb=" O GLU 7 196 " (cutoff:3.500A) Processing helix chain '7' and resid 258 through 270 removed outlier: 3.643A pdb=" N VAL 7 262 " --> pdb=" O PRO 7 258 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU 7 263 " --> pdb=" O ALA 7 259 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG 7 264 " --> pdb=" O SER 7 260 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE 7 265 " --> pdb=" O GLU 7 261 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N CYS 7 266 " --> pdb=" O VAL 7 262 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN 7 267 " --> pdb=" O GLU 7 263 " (cutoff:3.500A) Processing helix chain '7' and resid 279 through 297 removed outlier: 4.012A pdb=" N ASP 7 283 " --> pdb=" O ILE 7 279 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE 7 289 " --> pdb=" O VAL 7 285 " (cutoff:3.500A) Processing helix chain '7' and resid 350 through 362 Processing helix chain '7' and resid 370 through 383 removed outlier: 3.555A pdb=" N GLY 7 374 " --> pdb=" O HIS 7 370 " (cutoff:3.500A) Processing helix chain '7' and resid 685 through 689 Processing helix chain '7' and resid 751 through 756 Processing helix chain '9' and resid 532 through 541 removed outlier: 3.698A pdb=" N PHE 9 536 " --> pdb=" O PRO 9 532 " (cutoff:3.500A) Processing helix chain '9' and resid 566 through 586 removed outlier: 3.985A pdb=" N ALA 9 586 " --> pdb=" O GLU 9 582 " (cutoff:3.500A) Processing helix chain '9' and resid 588 through 625 removed outlier: 3.562A pdb=" N VAL 9 618 " --> pdb=" O GLU 9 614 " (cutoff:3.500A) Processing helix chain '9' and resid 646 through 651 removed outlier: 3.562A pdb=" N ALA 9 651 " --> pdb=" O HIS 9 648 " (cutoff:3.500A) Processing helix chain '9' and resid 904 through 910 removed outlier: 3.980A pdb=" N TRP 9 908 " --> pdb=" O TYR 9 904 " (cutoff:3.500A) Processing helix chain '9' and resid 911 through 927 removed outlier: 3.615A pdb=" N VAL 9 915 " --> pdb=" O LEU 9 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 611 Processing helix chain 'A' and resid 616 through 633 Processing helix chain 'A' and resid 641 through 648 removed outlier: 3.559A pdb=" N ILE A 647 " --> pdb=" O LYS A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 667 Processing helix chain 'A' and resid 1046 through 1063 Processing helix chain 'A' and resid 1065 through 1077 Processing helix chain 'A' and resid 1077 through 1088 Processing helix chain 'A' and resid 1231 through 1244 removed outlier: 3.699A pdb=" N VAL A1241 " --> pdb=" O THR A1237 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS A1244 " --> pdb=" O ARG A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1250 removed outlier: 4.174A pdb=" N LYS A1250 " --> pdb=" O LYS A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1256 Processing helix chain 'A' and resid 1272 through 1277 Processing helix chain 'A' and resid 1397 through 1412 Processing helix chain 'A' and resid 1430 through 1437 Processing helix chain 'A' and resid 1438 through 1449 Processing helix chain 'A' and resid 1455 through 1481 Processing helix chain 'A' and resid 1481 through 1494 removed outlier: 3.556A pdb=" N ARG A1485 " --> pdb=" O SER A1481 " (cutoff:3.500A) Processing helix chain 'A' and resid 1690 through 1694 Processing helix chain 'A' and resid 1698 through 1719 removed outlier: 3.750A pdb=" N LYS A1708 " --> pdb=" O GLN A1704 " (cutoff:3.500A) Processing helix chain 'A' and resid 1720 through 1726 Processing helix chain 'A' and resid 1955 through 1971 Processing helix chain 'A' and resid 1973 through 1975 No H-bonds generated for 'chain 'A' and resid 1973 through 1975' Processing helix chain 'A' and resid 1976 through 1990 removed outlier: 3.575A pdb=" N GLN A1982 " --> pdb=" O THR A1978 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 560 Processing helix chain 'G' and resid 325 through 345 Proline residue: G 331 - end of helix removed outlier: 3.611A pdb=" N PHE G 340 " --> pdb=" O ALA G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 373 removed outlier: 3.501A pdb=" N ALA G 373 " --> pdb=" O GLN G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 374 through 376 No H-bonds generated for 'chain 'G' and resid 374 through 376' Processing helix chain 'G' and resid 383 through 391 removed outlier: 4.052A pdb=" N TRP G 388 " --> pdb=" O LYS G 384 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG G 389 " --> pdb=" O ASP G 385 " (cutoff:3.500A) Processing helix chain 'X' and resid 3 through 15 Processing helix chain 'X' and resid 15 through 21 removed outlier: 4.147A pdb=" N ALA X 19 " --> pdb=" O ALA X 15 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '4' and resid 137 through 145 removed outlier: 3.570A pdb=" N SER 4 162 " --> pdb=" O ASP 4 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '4' and resid 187 through 189 removed outlier: 3.606A pdb=" N LEU 4 187 " --> pdb=" O ASN 4 182 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '4' and resid 204 through 206 Processing sheet with id=AA4, first strand: chain '4' and resid 275 through 280 removed outlier: 4.236A pdb=" N VAL 4 320 " --> pdb=" O ALA 4 331 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '7' and resid 163 through 169 removed outlier: 6.133A pdb=" N GLN 7 232 " --> pdb=" O CYS 7 163 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU 7 165 " --> pdb=" O GLN 7 232 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '7' and resid 248 through 249 removed outlier: 7.628A pdb=" N ALA 7 248 " --> pdb=" O LEU 7 314 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N ALA 7 316 " --> pdb=" O ALA 7 248 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ARG 7 315 " --> pdb=" O PHE 7 306 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N PHE 7 306 " --> pdb=" O ARG 7 315 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASN 7 317 " --> pdb=" O GLY 7 304 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '7' and resid 343 through 345 removed outlier: 5.651A pdb=" N ILE 7 404 " --> pdb=" O ILE 7 323 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASN 7 325 " --> pdb=" O ILE 7 404 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL 7 406 " --> pdb=" O ASN 7 325 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU 7 412 " --> pdb=" O VAL 7 331 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '7' and resid 418 through 426 removed outlier: 3.521A pdb=" N MET 7 418 " --> pdb=" O SER 9 900 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET 9 844 " --> pdb=" O VAL 9 834 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N HIS 9 733 " --> pdb=" O HIS 9 724 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS 9 713 " --> pdb=" O GLU 9 706 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS 9 707 " --> pdb=" O ASN 9 678 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ASN 9 678 " --> pdb=" O LYS 9 707 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLY 9 679 " --> pdb=" O SER 9 665 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER 9 665 " --> pdb=" O GLY 9 679 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '7' and resid 446 through 450 removed outlier: 19.654A pdb=" N LEU 7 476 " --> pdb=" O ARG 7 501 " (cutoff:3.500A) removed outlier: 15.446A pdb=" N ARG 7 501 " --> pdb=" O LEU 7 476 " (cutoff:3.500A) removed outlier: 11.040A pdb=" N PHE 7 478 " --> pdb=" O ASN 7 499 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASN 7 499 " --> pdb=" O PHE 7 478 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL 7 480 " --> pdb=" O LEU 7 497 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN 7 537 " --> pdb=" O THR 7 533 " (cutoff:3.500A) removed outlier: 11.701A pdb=" N GLN 7 605 " --> pdb=" O GLU 7 649 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU 7 649 " --> pdb=" O GLN 7 605 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR 7 731 " --> pdb=" O LYS 7 770 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '7' and resid 691 through 692 Processing sheet with id=AB2, first strand: chain 'A' and resid 1280 through 1283 Processing sheet with id=AB3, first strand: chain 'A' and resid 1375 through 1376 773 hydrogen bonds defined for protein. 2199 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: 2.00 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2928 1.33 - 1.45: 3241 1.45 - 1.57: 7945 1.57 - 1.69: 6 1.69 - 1.81: 62 Bond restraints: 14182 Sorted by residual: bond pdb=" N LEU 7 270 " pdb=" CA LEU 7 270 " ideal model delta sigma weight residual 1.460 1.497 -0.037 7.10e-03 1.98e+04 2.67e+01 bond pdb=" N ILE 4 107 " pdb=" CA ILE 4 107 " ideal model delta sigma weight residual 1.456 1.495 -0.039 8.70e-03 1.32e+04 1.99e+01 bond pdb=" N ASN 7 751 " pdb=" CA ASN 7 751 " ideal model delta sigma weight residual 1.458 1.490 -0.032 7.40e-03 1.83e+04 1.90e+01 bond pdb=" N ILE A1063 " pdb=" CA ILE A1063 " ideal model delta sigma weight residual 1.458 1.496 -0.038 9.00e-03 1.23e+04 1.81e+01 bond pdb=" N ILE 9 663 " pdb=" CA ILE 9 663 " ideal model delta sigma weight residual 1.457 1.493 -0.036 9.00e-03 1.23e+04 1.57e+01 ... (remaining 14177 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 14951 1.55 - 3.09: 3780 3.09 - 4.64: 481 4.64 - 6.18: 47 6.18 - 7.73: 11 Bond angle restraints: 19270 Sorted by residual: angle pdb=" N ILE A1385 " pdb=" CA ILE A1385 " pdb=" C ILE A1385 " ideal model delta sigma weight residual 111.90 105.13 6.77 8.10e-01 1.52e+00 6.99e+01 angle pdb=" C MET 7 276 " pdb=" CA MET 7 276 " pdb=" CB MET 7 276 " ideal model delta sigma weight residual 116.54 109.63 6.91 1.15e+00 7.56e-01 3.61e+01 angle pdb=" CA GLY 7 730 " pdb=" C GLY 7 730 " pdb=" O GLY 7 730 " ideal model delta sigma weight residual 122.37 118.10 4.27 7.30e-01 1.88e+00 3.42e+01 angle pdb=" N PRO 9 786 " pdb=" CA PRO 9 786 " pdb=" C PRO 9 786 " ideal model delta sigma weight residual 114.68 109.48 5.20 1.04e+00 9.25e-01 2.50e+01 angle pdb=" CA ASN 7 751 " pdb=" C ASN 7 751 " pdb=" N PRO 7 752 " ideal model delta sigma weight residual 118.09 122.14 -4.05 8.20e-01 1.49e+00 2.44e+01 ... (remaining 19265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.72: 7784 14.72 - 29.43: 456 29.43 - 44.15: 150 44.15 - 58.87: 24 58.87 - 73.58: 9 Dihedral angle restraints: 8423 sinusoidal: 3003 harmonic: 5420 Sorted by residual: dihedral pdb=" C HIS 4 198 " pdb=" N HIS 4 198 " pdb=" CA HIS 4 198 " pdb=" CB HIS 4 198 " ideal model delta harmonic sigma weight residual -122.60 -132.91 10.31 0 2.50e+00 1.60e-01 1.70e+01 dihedral pdb=" C ASP 7 202 " pdb=" N ASP 7 202 " pdb=" CA ASP 7 202 " pdb=" CB ASP 7 202 " ideal model delta harmonic sigma weight residual -122.60 -132.55 9.95 0 2.50e+00 1.60e-01 1.59e+01 dihedral pdb=" C ASP 9 903 " pdb=" N ASP 9 903 " pdb=" CA ASP 9 903 " pdb=" CB ASP 9 903 " ideal model delta harmonic sigma weight residual -122.60 -132.25 9.65 0 2.50e+00 1.60e-01 1.49e+01 ... (remaining 8420 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1207 0.070 - 0.139: 652 0.139 - 0.209: 233 0.209 - 0.278: 36 0.278 - 0.348: 3 Chirality restraints: 2131 Sorted by residual: chirality pdb=" CA ASP 9 903 " pdb=" N ASP 9 903 " pdb=" C ASP 9 903 " pdb=" CB ASP 9 903 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" C1 IHP A2001 " pdb=" C2 IHP A2001 " pdb=" C6 IHP A2001 " pdb=" O11 IHP A2001 " both_signs ideal model delta sigma weight residual False 2.32 2.61 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA ASP 7 202 " pdb=" N ASP 7 202 " pdb=" C ASP 7 202 " pdb=" CB ASP 7 202 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 2128 not shown) Planarity restraints: 2534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN 7 597 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.49e+00 pdb=" C ASN 7 597 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN 7 597 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL 7 598 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP 7 373 " 0.009 2.00e-02 2.50e+03 1.93e-02 3.72e+00 pdb=" C ASP 7 373 " -0.033 2.00e-02 2.50e+03 pdb=" O ASP 7 373 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY 7 374 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER 4 16 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C SER 4 16 " 0.033 2.00e-02 2.50e+03 pdb=" O SER 4 16 " -0.012 2.00e-02 2.50e+03 pdb=" N PHE 4 17 " -0.011 2.00e-02 2.50e+03 ... (remaining 2531 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3496 2.82 - 3.34: 12791 3.34 - 3.86: 21929 3.86 - 4.38: 24645 4.38 - 4.90: 41690 Nonbonded interactions: 104551 Sorted by model distance: nonbonded pdb=" O HIS A1451 " pdb=" OG1 THR A1452 " model vdw 2.298 3.040 nonbonded pdb=" O ARG A1427 " pdb=" OG SER A1428 " model vdw 2.389 3.040 nonbonded pdb=" OG SER 9 725 " pdb=" O PRO 9 731 " model vdw 2.447 3.040 nonbonded pdb=" O ASP 9 769 " pdb=" OG1 THR 9 800 " model vdw 2.461 3.040 nonbonded pdb=" N GLN A1695 " pdb=" OE1 GLN A1695 " model vdw 2.489 3.120 ... (remaining 104546 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: 0.010 Normalize map: mean=0, sd=1: 23.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.530 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 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 0.076 14182 Z= 0.825 Angle : 1.307 7.727 19270 Z= 1.012 Chirality : 0.089 0.348 2131 Planarity : 0.004 0.041 2534 Dihedral : 11.254 73.585 4939 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.40 % Allowed : 7.80 % Favored : 91.81 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.20), residues: 1844 helix: 2.23 (0.22), residues: 572 sheet: 0.94 (0.23), residues: 491 loop : -1.26 (0.20), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 389 TYR 0.013 0.001 TYR 7 696 PHE 0.012 0.001 PHE 9 899 TRP 0.008 0.001 TRP 9 550 HIS 0.007 0.001 HIS 4 198 Details of bonding type rmsd covalent geometry : bond 0.01082 (14182) covalent geometry : angle 1.30686 (19270) hydrogen bonds : bond 0.16714 ( 773) hydrogen bonds : angle 6.84267 ( 2199) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 225 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 7 275 TYR cc_start: 0.7793 (m-80) cc_final: 0.7244 (m-10) REVERT: A 1721 TYR cc_start: 0.6800 (t80) cc_final: 0.6018 (t80) REVERT: G 357 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7912 (mt-10) outliers start: 5 outliers final: 3 residues processed: 227 average time/residue: 0.5455 time to fit residues: 136.3275 Evaluate side-chains 112 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 278 ASP Chi-restraints excluded: chain 7 residue 283 ASP Chi-restraints excluded: chain 7 residue 596 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 198 GLN 7 287 ASN 7 294 GLN 7 317 ASN 7 325 ASN 7 402 ASN 7 405 ASN 7 430 ASN 7 452 ASN 7 471 ASN 7 581 ASN 9 573 ASN 9 733 HIS 9 736 GLN A 666 ASN A1066 GLN ** A1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1381 ASN A1406 ASN A1462 ASN ** A1726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1730 GLN G 352 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.085807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.071068 restraints weight = 54231.604| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 3.71 r_work: 0.3474 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14182 Z= 0.158 Angle : 0.615 9.166 19270 Z= 0.326 Chirality : 0.042 0.181 2131 Planarity : 0.004 0.049 2534 Dihedral : 4.630 54.737 2077 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.34 % Allowed : 13.76 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.19), residues: 1844 helix: 2.39 (0.21), residues: 581 sheet: 0.72 (0.22), residues: 518 loop : -1.25 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 355 TYR 0.028 0.002 TYR A1072 PHE 0.021 0.002 PHE 7 478 TRP 0.009 0.001 TRP 9 550 HIS 0.013 0.001 HIS 4 198 Details of bonding type rmsd covalent geometry : bond 0.00341 (14182) covalent geometry : angle 0.61521 (19270) hydrogen bonds : bond 0.05063 ( 773) hydrogen bonds : angle 5.13143 ( 2199) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 103 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 184 GLU cc_start: 0.8347 (mp0) cc_final: 0.7934 (mp0) REVERT: 7 282 MET cc_start: 0.8202 (tmm) cc_final: 0.7997 (tmm) REVERT: 7 306 PHE cc_start: 0.7566 (m-80) cc_final: 0.7052 (m-10) REVERT: 9 540 MET cc_start: 0.8211 (mmp) cc_final: 0.7898 (mmt) REVERT: 9 801 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8295 (mm) REVERT: G 337 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8299 (mt-10) REVERT: G 357 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8458 (mt-10) REVERT: X 12 PHE cc_start: 0.6237 (m-10) cc_final: 0.5861 (m-10) outliers start: 42 outliers final: 14 residues processed: 134 average time/residue: 0.4864 time to fit residues: 72.9655 Evaluate side-chains 111 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 272 VAL Chi-restraints excluded: chain 4 residue 188 LEU Chi-restraints excluded: chain 7 residue 179 THR Chi-restraints excluded: chain 7 residue 239 THR Chi-restraints excluded: chain 7 residue 283 ASP Chi-restraints excluded: chain 7 residue 314 LEU Chi-restraints excluded: chain 7 residue 645 THR Chi-restraints excluded: chain 7 residue 719 VAL Chi-restraints excluded: chain 9 residue 609 TYR Chi-restraints excluded: chain 9 residue 773 CYS Chi-restraints excluded: chain 9 residue 801 LEU Chi-restraints excluded: chain A residue 1686 THR Chi-restraints excluded: chain A residue 1959 HIS Chi-restraints excluded: chain E residue 414 THR Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain G residue 370 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 41 optimal weight: 0.0010 chunk 110 optimal weight: 2.9990 chunk 17 optimal weight: 20.0000 chunk 158 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 136 optimal weight: 0.7980 chunk 121 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 164 optimal weight: 0.0980 chunk 87 optimal weight: 1.9990 chunk 132 optimal weight: 0.0020 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 241 HIS 7 590 GLN 7 613 GLN 9 733 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.087171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.072562 restraints weight = 53817.158| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 3.71 r_work: 0.3514 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14182 Z= 0.107 Angle : 0.548 12.012 19270 Z= 0.279 Chirality : 0.040 0.199 2131 Planarity : 0.004 0.043 2534 Dihedral : 4.317 70.344 2073 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.18 % Allowed : 15.12 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.19), residues: 1844 helix: 2.54 (0.21), residues: 581 sheet: 0.81 (0.22), residues: 517 loop : -1.15 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 355 TYR 0.023 0.001 TYR A1984 PHE 0.022 0.001 PHE 7 478 TRP 0.009 0.001 TRP G 364 HIS 0.009 0.001 HIS 4 198 Details of bonding type rmsd covalent geometry : bond 0.00213 (14182) covalent geometry : angle 0.54773 (19270) hydrogen bonds : bond 0.03824 ( 773) hydrogen bonds : angle 4.51988 ( 2199) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 110 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 184 GLU cc_start: 0.8290 (mp0) cc_final: 0.7889 (mp0) REVERT: 7 185 ASP cc_start: 0.9141 (m-30) cc_final: 0.8719 (m-30) REVERT: 7 282 MET cc_start: 0.7916 (tmm) cc_final: 0.7581 (tmm) REVERT: 7 338 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.8296 (p0) REVERT: 9 801 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8232 (mm) REVERT: G 357 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8418 (mt-10) REVERT: G 359 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7396 (mm-30) REVERT: X 6 PHE cc_start: 0.8055 (t80) cc_final: 0.7849 (t80) outliers start: 40 outliers final: 13 residues processed: 138 average time/residue: 0.4560 time to fit residues: 70.9866 Evaluate side-chains 115 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 188 LEU Chi-restraints excluded: chain 7 residue 179 THR Chi-restraints excluded: chain 7 residue 241 HIS Chi-restraints excluded: chain 7 residue 338 ASP Chi-restraints excluded: chain 7 residue 645 THR Chi-restraints excluded: chain 7 residue 719 VAL Chi-restraints excluded: chain 9 residue 609 TYR Chi-restraints excluded: chain 9 residue 801 LEU Chi-restraints excluded: chain A residue 1075 HIS Chi-restraints excluded: chain A residue 1228 THR Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1686 THR Chi-restraints excluded: chain A residue 1959 HIS Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 370 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 120 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 chunk 7 optimal weight: 0.0040 chunk 136 optimal weight: 0.5980 chunk 118 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 chunk 158 optimal weight: 0.0670 chunk 26 optimal weight: 9.9990 overall best weight: 0.4530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 241 HIS 7 325 ASN 9 573 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.086869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.072251 restraints weight = 53672.942| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 3.69 r_work: 0.3510 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14182 Z= 0.104 Angle : 0.544 10.092 19270 Z= 0.276 Chirality : 0.040 0.205 2131 Planarity : 0.004 0.043 2534 Dihedral : 3.926 24.022 2071 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.78 % Allowed : 16.71 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.20), residues: 1844 helix: 2.60 (0.21), residues: 575 sheet: 0.85 (0.22), residues: 516 loop : -1.15 (0.21), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 354 TYR 0.021 0.001 TYR 4 256 PHE 0.023 0.001 PHE 7 478 TRP 0.007 0.001 TRP G 364 HIS 0.008 0.001 HIS 4 198 Details of bonding type rmsd covalent geometry : bond 0.00219 (14182) covalent geometry : angle 0.54383 (19270) hydrogen bonds : bond 0.03583 ( 773) hydrogen bonds : angle 4.33802 ( 2199) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: 4 184 GLU cc_start: 0.8304 (mp0) cc_final: 0.7896 (mp0) REVERT: 4 259 LEU cc_start: 0.9380 (tm) cc_final: 0.9179 (tt) REVERT: 4 308 THR cc_start: 0.8135 (t) cc_final: 0.7737 (p) REVERT: 7 185 ASP cc_start: 0.9144 (m-30) cc_final: 0.8747 (m-30) REVERT: 7 283 ASP cc_start: 0.9266 (t0) cc_final: 0.9018 (OUTLIER) REVERT: 7 338 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.8361 (p0) REVERT: 7 414 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7464 (mt0) REVERT: 9 801 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8258 (mm) REVERT: G 357 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8368 (mt-10) REVERT: G 358 ARG cc_start: 0.7349 (ptp-170) cc_final: 0.7080 (ptp-170) REVERT: G 359 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7301 (mm-30) REVERT: X 6 PHE cc_start: 0.8094 (t80) cc_final: 0.7887 (t80) outliers start: 35 outliers final: 18 residues processed: 128 average time/residue: 0.4808 time to fit residues: 69.1752 Evaluate side-chains 121 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 188 LEU Chi-restraints excluded: chain 7 residue 179 THR Chi-restraints excluded: chain 7 residue 209 ILE Chi-restraints excluded: chain 7 residue 241 HIS Chi-restraints excluded: chain 7 residue 338 ASP Chi-restraints excluded: chain 7 residue 414 GLN Chi-restraints excluded: chain 7 residue 557 VAL Chi-restraints excluded: chain 7 residue 645 THR Chi-restraints excluded: chain 7 residue 719 VAL Chi-restraints excluded: chain 9 residue 609 TYR Chi-restraints excluded: chain 9 residue 801 LEU Chi-restraints excluded: chain A residue 1075 HIS Chi-restraints excluded: chain A residue 1228 THR Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1490 LEU Chi-restraints excluded: chain A residue 1959 HIS Chi-restraints excluded: chain E residue 531 TRP Chi-restraints excluded: chain G residue 330 LEU Chi-restraints excluded: chain X residue 14 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 154 optimal weight: 0.4980 chunk 83 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 203 GLN ** 4 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 427 GLN A1976 GLN G 352 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.083559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.068727 restraints weight = 55181.004| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 3.67 r_work: 0.3428 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14182 Z= 0.186 Angle : 0.596 9.380 19270 Z= 0.312 Chirality : 0.042 0.254 2131 Planarity : 0.004 0.043 2534 Dihedral : 4.212 26.243 2071 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.02 % Allowed : 16.87 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.20), residues: 1844 helix: 2.40 (0.22), residues: 574 sheet: 0.74 (0.22), residues: 511 loop : -1.28 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 354 TYR 0.023 0.002 TYR 4 256 PHE 0.022 0.002 PHE 7 478 TRP 0.010 0.001 TRP 9 872 HIS 0.038 0.002 HIS 7 241 Details of bonding type rmsd covalent geometry : bond 0.00406 (14182) covalent geometry : angle 0.59636 (19270) hydrogen bonds : bond 0.04393 ( 773) hydrogen bonds : angle 4.49664 ( 2199) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 90 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: 4 184 GLU cc_start: 0.8306 (mp0) cc_final: 0.7886 (mp0) REVERT: 4 198 HIS cc_start: 0.7840 (OUTLIER) cc_final: 0.7624 (p-80) REVERT: 7 414 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7649 (mt0) REVERT: 7 544 MET cc_start: 0.8462 (ptp) cc_final: 0.8221 (mtt) REVERT: 9 801 LEU cc_start: 0.8739 (tt) cc_final: 0.8276 (mm) REVERT: G 337 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8047 (mt-10) outliers start: 38 outliers final: 22 residues processed: 122 average time/residue: 0.4751 time to fit residues: 65.2082 Evaluate side-chains 114 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 272 VAL Chi-restraints excluded: chain 4 residue 188 LEU Chi-restraints excluded: chain 4 residue 198 HIS Chi-restraints excluded: chain 7 residue 179 THR Chi-restraints excluded: chain 7 residue 209 ILE Chi-restraints excluded: chain 7 residue 278 ASP Chi-restraints excluded: chain 7 residue 283 ASP Chi-restraints excluded: chain 7 residue 314 LEU Chi-restraints excluded: chain 7 residue 414 GLN Chi-restraints excluded: chain 7 residue 614 VAL Chi-restraints excluded: chain 7 residue 645 THR Chi-restraints excluded: chain 7 residue 719 VAL Chi-restraints excluded: chain 9 residue 609 TYR Chi-restraints excluded: chain 9 residue 704 CYS Chi-restraints excluded: chain 9 residue 773 CYS Chi-restraints excluded: chain 9 residue 817 VAL Chi-restraints excluded: chain A residue 1075 HIS Chi-restraints excluded: chain A residue 1228 THR Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1686 THR Chi-restraints excluded: chain A residue 1959 HIS Chi-restraints excluded: chain E residue 414 THR Chi-restraints excluded: chain E residue 531 TRP Chi-restraints excluded: chain G residue 330 LEU Chi-restraints excluded: chain G residue 337 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 142 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 168 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 140 optimal weight: 0.6980 chunk 166 optimal weight: 0.0670 chunk 115 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 148 optimal weight: 0.0970 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 450 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.085130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.070402 restraints weight = 54113.702| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 3.67 r_work: 0.3468 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14182 Z= 0.108 Angle : 0.552 9.314 19270 Z= 0.283 Chirality : 0.040 0.262 2131 Planarity : 0.004 0.043 2534 Dihedral : 3.991 24.082 2071 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.31 % Allowed : 17.74 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.20), residues: 1844 helix: 2.49 (0.22), residues: 575 sheet: 0.72 (0.22), residues: 513 loop : -1.20 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 354 TYR 0.022 0.001 TYR 4 256 PHE 0.016 0.001 PHE 7 478 TRP 0.009 0.001 TRP G 364 HIS 0.008 0.001 HIS 4 198 Details of bonding type rmsd covalent geometry : bond 0.00233 (14182) covalent geometry : angle 0.55214 (19270) hydrogen bonds : bond 0.03649 ( 773) hydrogen bonds : angle 4.25524 ( 2199) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: 4 184 GLU cc_start: 0.8291 (mp0) cc_final: 0.7881 (mp0) REVERT: 7 544 MET cc_start: 0.8452 (ptp) cc_final: 0.8235 (mtt) REVERT: 7 648 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8042 (pp) REVERT: 9 801 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8261 (mm) REVERT: G 357 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8228 (mt-10) REVERT: G 359 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7195 (mm-30) outliers start: 29 outliers final: 17 residues processed: 118 average time/residue: 0.4777 time to fit residues: 63.2550 Evaluate side-chains 112 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 188 LEU Chi-restraints excluded: chain 7 residue 209 ILE Chi-restraints excluded: chain 7 residue 283 ASP Chi-restraints excluded: chain 7 residue 557 VAL Chi-restraints excluded: chain 7 residue 645 THR Chi-restraints excluded: chain 7 residue 648 LEU Chi-restraints excluded: chain 7 residue 719 VAL Chi-restraints excluded: chain 9 residue 609 TYR Chi-restraints excluded: chain 9 residue 704 CYS Chi-restraints excluded: chain 9 residue 801 LEU Chi-restraints excluded: chain 9 residue 817 VAL Chi-restraints excluded: chain A residue 1075 HIS Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1686 THR Chi-restraints excluded: chain A residue 1959 HIS Chi-restraints excluded: chain E residue 414 THR Chi-restraints excluded: chain E residue 531 TRP Chi-restraints excluded: chain G residue 330 LEU Chi-restraints excluded: chain G residue 370 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 128 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 149 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.081138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.067057 restraints weight = 56039.157| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 3.93 r_work: 0.3362 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14182 Z= 0.242 Angle : 0.661 8.598 19270 Z= 0.350 Chirality : 0.042 0.162 2131 Planarity : 0.005 0.043 2534 Dihedral : 4.495 28.613 2071 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.45 % Favored : 95.50 % Rotamer: Outliers : 3.02 % Allowed : 17.74 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.19), residues: 1844 helix: 2.02 (0.21), residues: 580 sheet: 0.64 (0.22), residues: 524 loop : -1.50 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 9 779 TYR 0.027 0.002 TYR 7 733 PHE 0.022 0.002 PHE A 626 TRP 0.011 0.002 TRP 9 872 HIS 0.011 0.002 HIS 7 367 Details of bonding type rmsd covalent geometry : bond 0.00529 (14182) covalent geometry : angle 0.66114 (19270) hydrogen bonds : bond 0.04883 ( 773) hydrogen bonds : angle 4.67593 ( 2199) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 87 time to evaluate : 0.584 Fit side-chains REVERT: 4 184 GLU cc_start: 0.8321 (mp0) cc_final: 0.7892 (mp0) REVERT: 7 648 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8116 (pp) REVERT: G 337 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8142 (mt-10) REVERT: G 357 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8313 (mt-10) REVERT: G 358 ARG cc_start: 0.7798 (ptp-170) cc_final: 0.7542 (ptp-170) REVERT: G 359 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7403 (mm-30) REVERT: G 360 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7855 (tm-30) outliers start: 38 outliers final: 20 residues processed: 119 average time/residue: 0.4804 time to fit residues: 64.2213 Evaluate side-chains 106 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 209 ILE Chi-restraints excluded: chain 7 residue 283 ASP Chi-restraints excluded: chain 7 residue 314 LEU Chi-restraints excluded: chain 7 residue 448 VAL Chi-restraints excluded: chain 7 residue 614 VAL Chi-restraints excluded: chain 7 residue 645 THR Chi-restraints excluded: chain 7 residue 648 LEU Chi-restraints excluded: chain 7 residue 670 THR Chi-restraints excluded: chain 7 residue 719 VAL Chi-restraints excluded: chain 9 residue 609 TYR Chi-restraints excluded: chain 9 residue 704 CYS Chi-restraints excluded: chain 9 residue 817 VAL Chi-restraints excluded: chain A residue 1075 HIS Chi-restraints excluded: chain A residue 1228 THR Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1490 LEU Chi-restraints excluded: chain A residue 1686 THR Chi-restraints excluded: chain A residue 1959 HIS Chi-restraints excluded: chain E residue 414 THR Chi-restraints excluded: chain E residue 531 TRP Chi-restraints excluded: chain G residue 330 LEU Chi-restraints excluded: chain G residue 337 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 80 optimal weight: 0.7980 chunk 165 optimal weight: 0.0970 chunk 74 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.082020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.067972 restraints weight = 55535.088| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 3.99 r_work: 0.3385 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14182 Z= 0.160 Angle : 0.598 9.072 19270 Z= 0.310 Chirality : 0.041 0.155 2131 Planarity : 0.004 0.043 2534 Dihedral : 4.303 27.320 2071 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.96 % Favored : 95.99 % Rotamer: Outliers : 2.39 % Allowed : 18.54 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.19), residues: 1844 helix: 2.17 (0.22), residues: 580 sheet: 0.61 (0.22), residues: 528 loop : -1.48 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 354 TYR 0.016 0.001 TYR 7 733 PHE 0.019 0.001 PHE 7 478 TRP 0.009 0.001 TRP 9 872 HIS 0.010 0.001 HIS 4 198 Details of bonding type rmsd covalent geometry : bond 0.00352 (14182) covalent geometry : angle 0.59784 (19270) hydrogen bonds : bond 0.04186 ( 773) hydrogen bonds : angle 4.47120 ( 2199) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 0.473 Fit side-chains REVERT: 4 184 GLU cc_start: 0.8341 (mp0) cc_final: 0.7915 (mp0) REVERT: 7 282 MET cc_start: 0.8860 (ttp) cc_final: 0.8567 (ttp) REVERT: 7 414 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7879 (mt0) REVERT: 7 648 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8089 (pp) REVERT: 9 540 MET cc_start: 0.8150 (tpt) cc_final: 0.7891 (mmt) REVERT: G 337 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8080 (mt-10) REVERT: G 357 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8240 (mt-10) REVERT: G 358 ARG cc_start: 0.7747 (ptp-170) cc_final: 0.7537 (ptp-170) REVERT: G 359 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7353 (mm-30) REVERT: G 360 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7758 (tm-30) outliers start: 30 outliers final: 23 residues processed: 114 average time/residue: 0.4729 time to fit residues: 60.6732 Evaluate side-chains 109 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 188 LEU Chi-restraints excluded: chain 7 residue 209 ILE Chi-restraints excluded: chain 7 residue 314 LEU Chi-restraints excluded: chain 7 residue 414 GLN Chi-restraints excluded: chain 7 residue 446 VAL Chi-restraints excluded: chain 7 residue 448 VAL Chi-restraints excluded: chain 7 residue 614 VAL Chi-restraints excluded: chain 7 residue 645 THR Chi-restraints excluded: chain 7 residue 648 LEU Chi-restraints excluded: chain 7 residue 719 VAL Chi-restraints excluded: chain 9 residue 609 TYR Chi-restraints excluded: chain 9 residue 704 CYS Chi-restraints excluded: chain 9 residue 773 CYS Chi-restraints excluded: chain 9 residue 817 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 1075 HIS Chi-restraints excluded: chain A residue 1228 THR Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1490 LEU Chi-restraints excluded: chain A residue 1686 THR Chi-restraints excluded: chain A residue 1959 HIS Chi-restraints excluded: chain E residue 414 THR Chi-restraints excluded: chain E residue 531 TRP Chi-restraints excluded: chain G residue 330 LEU Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain X residue 14 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 140 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 17 optimal weight: 0.1980 chunk 58 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 183 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 198 HIS ** 4 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.083257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.069214 restraints weight = 55337.731| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 3.96 r_work: 0.3420 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14182 Z= 0.117 Angle : 0.577 10.288 19270 Z= 0.296 Chirality : 0.040 0.164 2131 Planarity : 0.004 0.043 2534 Dihedral : 4.053 25.047 2071 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.74 % Favored : 96.20 % Rotamer: Outliers : 2.31 % Allowed : 18.85 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.20), residues: 1844 helix: 2.38 (0.22), residues: 574 sheet: 0.72 (0.22), residues: 527 loop : -1.38 (0.21), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 354 TYR 0.016 0.001 TYR 7 214 PHE 0.019 0.001 PHE 7 478 TRP 0.010 0.001 TRP G 364 HIS 0.010 0.001 HIS 4 198 Details of bonding type rmsd covalent geometry : bond 0.00259 (14182) covalent geometry : angle 0.57702 (19270) hydrogen bonds : bond 0.03620 ( 773) hydrogen bonds : angle 4.25842 ( 2199) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.631 Fit side-chains REVERT: 4 184 GLU cc_start: 0.8313 (mp0) cc_final: 0.7914 (mp0) REVERT: 7 282 MET cc_start: 0.8817 (ttp) cc_final: 0.8535 (ttp) REVERT: 7 414 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.7759 (mt0) REVERT: 7 648 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8067 (pp) REVERT: 9 540 MET cc_start: 0.8120 (tpt) cc_final: 0.7861 (mmt) REVERT: 9 767 LYS cc_start: 0.8967 (mtpt) cc_final: 0.8749 (mppt) REVERT: 9 801 LEU cc_start: 0.8710 (tt) cc_final: 0.8076 (mp) REVERT: G 337 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8023 (mt-10) REVERT: G 357 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8271 (mt-10) REVERT: G 359 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7369 (mm-30) outliers start: 29 outliers final: 19 residues processed: 111 average time/residue: 0.4762 time to fit residues: 59.4793 Evaluate side-chains 104 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 314 LEU Chi-restraints excluded: chain 7 residue 414 GLN Chi-restraints excluded: chain 7 residue 448 VAL Chi-restraints excluded: chain 7 residue 645 THR Chi-restraints excluded: chain 7 residue 648 LEU Chi-restraints excluded: chain 7 residue 670 THR Chi-restraints excluded: chain 7 residue 719 VAL Chi-restraints excluded: chain 9 residue 609 TYR Chi-restraints excluded: chain 9 residue 704 CYS Chi-restraints excluded: chain 9 residue 743 VAL Chi-restraints excluded: chain 9 residue 817 VAL Chi-restraints excluded: chain A residue 1075 HIS Chi-restraints excluded: chain A residue 1228 THR Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1490 LEU Chi-restraints excluded: chain A residue 1686 THR Chi-restraints excluded: chain A residue 1959 HIS Chi-restraints excluded: chain E residue 414 THR Chi-restraints excluded: chain E residue 531 TRP Chi-restraints excluded: chain G residue 330 LEU Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain X residue 14 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 161 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 184 optimal weight: 0.5980 chunk 28 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 138 optimal weight: 0.4980 chunk 167 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 198 HIS ** 4 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.083356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.069381 restraints weight = 54839.627| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 3.97 r_work: 0.3420 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14182 Z= 0.116 Angle : 0.576 10.559 19270 Z= 0.295 Chirality : 0.040 0.205 2131 Planarity : 0.004 0.043 2534 Dihedral : 3.974 24.048 2071 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.80 % Favored : 96.15 % Rotamer: Outliers : 1.99 % Allowed : 19.01 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.20), residues: 1844 helix: 2.38 (0.22), residues: 574 sheet: 0.72 (0.22), residues: 529 loop : -1.32 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 7 162 TYR 0.020 0.001 TYR 7 302 PHE 0.019 0.001 PHE 7 478 TRP 0.010 0.001 TRP 4 247 HIS 0.018 0.001 HIS 4 198 Details of bonding type rmsd covalent geometry : bond 0.00254 (14182) covalent geometry : angle 0.57642 (19270) hydrogen bonds : bond 0.03544 ( 773) hydrogen bonds : angle 4.19676 ( 2199) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.564 Fit side-chains REVERT: 4 184 GLU cc_start: 0.8359 (mp0) cc_final: 0.7910 (mp0) REVERT: 7 282 MET cc_start: 0.8779 (ttp) cc_final: 0.8503 (ttp) REVERT: 7 414 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7713 (mt0) REVERT: 7 648 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8044 (pp) REVERT: 9 540 MET cc_start: 0.8113 (tpt) cc_final: 0.7884 (mmt) REVERT: 9 767 LYS cc_start: 0.8962 (mtpt) cc_final: 0.8746 (mppt) REVERT: 9 801 LEU cc_start: 0.8712 (tt) cc_final: 0.8100 (mp) REVERT: G 337 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7973 (mt-10) REVERT: G 357 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8300 (mt-10) REVERT: G 359 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7342 (mm-30) outliers start: 25 outliers final: 17 residues processed: 105 average time/residue: 0.4860 time to fit residues: 57.5060 Evaluate side-chains 101 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 314 LEU Chi-restraints excluded: chain 7 residue 414 GLN Chi-restraints excluded: chain 7 residue 448 VAL Chi-restraints excluded: chain 7 residue 645 THR Chi-restraints excluded: chain 7 residue 648 LEU Chi-restraints excluded: chain 7 residue 670 THR Chi-restraints excluded: chain 7 residue 719 VAL Chi-restraints excluded: chain 9 residue 609 TYR Chi-restraints excluded: chain 9 residue 704 CYS Chi-restraints excluded: chain 9 residue 743 VAL Chi-restraints excluded: chain 9 residue 817 VAL Chi-restraints excluded: chain A residue 1075 HIS Chi-restraints excluded: chain A residue 1228 THR Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1490 LEU Chi-restraints excluded: chain A residue 1686 THR Chi-restraints excluded: chain A residue 1959 HIS Chi-restraints excluded: chain E residue 414 THR Chi-restraints excluded: chain E residue 531 TRP Chi-restraints excluded: chain G residue 337 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 25 optimal weight: 0.4980 chunk 149 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 93 optimal weight: 0.0980 chunk 26 optimal weight: 8.9990 chunk 95 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.083708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.069785 restraints weight = 54617.589| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 3.83 r_work: 0.3437 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14182 Z= 0.110 Angle : 0.571 10.565 19270 Z= 0.292 Chirality : 0.040 0.158 2131 Planarity : 0.004 0.043 2534 Dihedral : 3.858 22.501 2071 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.69 % Favored : 96.26 % Rotamer: Outliers : 1.67 % Allowed : 19.81 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.20), residues: 1844 helix: 2.38 (0.22), residues: 580 sheet: 0.74 (0.22), residues: 529 loop : -1.33 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 7 162 TYR 0.014 0.001 TYR A1072 PHE 0.018 0.001 PHE 7 478 TRP 0.011 0.001 TRP G 364 HIS 0.007 0.001 HIS 4 198 Details of bonding type rmsd covalent geometry : bond 0.00244 (14182) covalent geometry : angle 0.57116 (19270) hydrogen bonds : bond 0.03367 ( 773) hydrogen bonds : angle 4.11665 ( 2199) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4279.06 seconds wall clock time: 73 minutes 50.04 seconds (4430.04 seconds total)