Starting phenix.real_space_refine (version: dev) on Tue Dec 13 03:43:18 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyr_28693/12_2022/8eyr_28693.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyr_28693/12_2022/8eyr_28693.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyr_28693/12_2022/8eyr_28693.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyr_28693/12_2022/8eyr_28693.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyr_28693/12_2022/8eyr_28693.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyr_28693/12_2022/8eyr_28693.pdb" } resolution = 4.0 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 ------------------------------------------------------------------------------- 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= 0.001 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 250": "OD1" <-> "OD2" Residue "A GLU 687": "OE1" <-> "OE2" Residue "A PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 20": "OD1" <-> "OD2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 20": "OD1" <-> "OD2" Residue "D PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D ASP 53": "OD1" <-> "OD2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 13635 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 794, 6382 Classifications: {'peptide': 794} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 749} Chain breaks: 7 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 6387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 6387 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 750} Chain breaks: 7 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 433 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 433 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 7.79, per 1000 atoms: 0.57 Number of scatterers: 13635 At special positions: 0 Unit cell: (126.99, 122.01, 166, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 106 16.00 O 2537 8.00 N 2367 7.00 C 8625 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 22 " distance=2.03 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 181 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 218 " distance=2.03 Simple disulfide: pdb=" SG CYS B 221 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 252 " - pdb=" SG CYS B 273 " distance=2.04 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 324 " distance=2.03 Simple disulfide: pdb=" SG CYS B 781 " - pdb=" SG CYS B 790 " distance=2.03 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 22 " distance=2.03 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 175 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 181 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 200 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 218 " distance=2.03 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 252 " - pdb=" SG CYS A 273 " distance=2.04 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 324 " distance=2.03 Simple disulfide: pdb=" SG CYS A 781 " - pdb=" SG CYS A 790 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 48 " distance=2.02 Simple disulfide: pdb=" SG CYS C 18 " - pdb=" SG CYS C 61 " distance=2.03 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 52 " distance=2.03 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 48 " distance=2.03 Simple disulfide: pdb=" SG CYS D 18 " - pdb=" SG CYS D 61 " distance=2.03 Simple disulfide: pdb=" SG CYS D 47 " - pdb=" SG CYS D 52 " distance=2.03 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: 5.71 Conformation dependent library (CDL) restraints added in 2.0 seconds 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3202 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 32 sheets defined 15.2% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'B' and resid 12 through 20 Processing helix chain 'B' and resid 133 through 137 removed outlier: 3.915A pdb=" N ASN B 136 " --> pdb=" O ALA B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 149 Processing helix chain 'B' and resid 248 through 254 removed outlier: 3.519A pdb=" N CYS B 252 " --> pdb=" O ASP B 248 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASN B 254 " --> pdb=" O ASP B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 320 Processing helix chain 'B' and resid 341 through 350 Processing helix chain 'B' and resid 426 through 438 Processing helix chain 'B' and resid 439 through 443 removed outlier: 3.627A pdb=" N GLN B 443 " --> pdb=" O LYS B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 631 Processing helix chain 'B' and resid 680 through 706 Processing helix chain 'B' and resid 856 through 863 Processing helix chain 'A' and resid 12 through 20 Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 314 through 320 removed outlier: 3.974A pdb=" N MET A 320 " --> pdb=" O THR A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 350 removed outlier: 3.871A pdb=" N ASN A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 438 Processing helix chain 'A' and resid 439 through 443 removed outlier: 3.689A pdb=" N GLN A 443 " --> pdb=" O LYS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 631 Processing helix chain 'A' and resid 680 through 706 removed outlier: 3.673A pdb=" N PHE A 706 " --> pdb=" O HIS A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 863 Processing helix chain 'C' and resid 7 through 19 removed outlier: 3.908A pdb=" N VAL C 11 " --> pdb=" O GLY C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 22 No H-bonds generated for 'chain 'C' and resid 20 through 22' Processing helix chain 'C' and resid 43 through 48 Processing helix chain 'C' and resid 53 through 58 Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'D' and resid 7 through 19 Processing helix chain 'D' and resid 43 through 48 Processing helix chain 'D' and resid 53 through 58 Processing helix chain 'D' and resid 59 through 61 No H-bonds generated for 'chain 'D' and resid 59 through 61' Processing sheet with id=AA1, first strand: chain 'B' and resid 2 through 3 removed outlier: 3.617A pdb=" N ILE B 25 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 51 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 7 through 10 removed outlier: 6.479A pdb=" N ILE B 7 " --> pdb=" O HIS B 30 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N LEU B 32 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ILE B 9 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE B 34 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 60 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU B 55 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N PHE B 90 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU B 57 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ALA B 110 " --> pdb=" O TYR B 85 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU B 87 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL B 140 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 115 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN B 142 " --> pdb=" O LYS B 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 164 through 166 Processing sheet with id=AA4, first strand: chain 'B' and resid 239 through 241 Processing sheet with id=AA5, first strand: chain 'B' and resid 267 through 269 Processing sheet with id=AA6, first strand: chain 'B' and resid 281 through 284 removed outlier: 5.901A pdb=" N TYR B 290 " --> pdb=" O ASN B 284 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 310 through 312 removed outlier: 3.873A pdb=" N LEU B 332 " --> pdb=" O LYS B 310 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 326 through 327 removed outlier: 9.131A pdb=" N LEU B 327 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 10.590A pdb=" N VAL B 354 " --> pdb=" O LEU B 380 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N GLU B 382 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N THR B 356 " --> pdb=" O GLU B 382 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 462 through 464 removed outlier: 5.466A pdb=" N ASP B 462 " --> pdb=" O LYS B 569 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA B 568 " --> pdb=" O ALA B 554 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL B 552 " --> pdb=" O SER B 570 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE B 494 " --> pdb=" O VAL B 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 462 through 464 removed outlier: 5.466A pdb=" N ASP B 462 " --> pdb=" O LYS B 569 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA B 568 " --> pdb=" O ALA B 554 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL B 552 " --> pdb=" O SER B 570 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 466 through 471 Processing sheet with id=AB3, first strand: chain 'B' and resid 589 through 594 removed outlier: 3.782A pdb=" N ASN B 593 " --> pdb=" O GLN B 597 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLN B 597 " --> pdb=" O ASN B 593 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 752 through 756 Processing sheet with id=AB5, first strand: chain 'B' and resid 814 through 816 Processing sheet with id=AB6, first strand: chain 'B' and resid 841 through 844 Processing sheet with id=AB7, first strand: chain 'B' and resid 881 through 884 removed outlier: 6.173A pdb=" N SER B 884 " --> pdb=" O ASN B 888 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ASN B 888 " --> pdb=" O SER B 884 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2 through 3 removed outlier: 3.607A pdb=" N ILE A 51 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 6 through 10 removed outlier: 6.491A pdb=" N ILE A 7 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU A 32 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE A 9 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE A 34 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A 60 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N PHE A 90 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 57 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ALA A 110 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU A 87 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 112 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 140 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A 115 " --> pdb=" O VAL A 140 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN A 142 " --> pdb=" O LYS A 115 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 239 through 241 Processing sheet with id=AC2, first strand: chain 'A' and resid 267 through 269 Processing sheet with id=AC3, first strand: chain 'A' and resid 281 through 284 removed outlier: 5.817A pdb=" N TYR A 290 " --> pdb=" O ASN A 284 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 309 through 312 removed outlier: 3.800A pdb=" N LEU A 332 " --> pdb=" O LYS A 310 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL A 359 " --> pdb=" O TYR A 392 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N LEU A 394 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE A 361 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 326 through 327 Processing sheet with id=AC6, first strand: chain 'A' and resid 462 through 464 removed outlier: 5.588A pdb=" N ASP A 462 " --> pdb=" O LYS A 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'A' and resid 466 through 471 Processing sheet with id=AC8, first strand: chain 'A' and resid 522 through 525 removed outlier: 3.743A pdb=" N PHE A 494 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 589 through 594 removed outlier: 6.833A pdb=" N GLN A 597 " --> pdb=" O ASN A 593 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 752 through 756 removed outlier: 7.121A pdb=" N CYS A 781 " --> pdb=" O SER A 613 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 776 through 777 Processing sheet with id=AD3, first strand: chain 'A' and resid 814 through 816 Processing sheet with id=AD4, first strand: chain 'A' and resid 841 through 844 removed outlier: 3.891A pdb=" N ILE A 842 " --> pdb=" O GLU A 853 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 881 through 884 removed outlier: 5.688A pdb=" N ALA A 882 " --> pdb=" O GLY A 889 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY A 889 " --> pdb=" O ALA A 882 " (cutoff:3.500A) 308 hydrogen bonds defined for protein. 795 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: 5.00 Time building geometry restraints manager: 6.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4487 1.34 - 1.46: 3219 1.46 - 1.58: 6113 1.58 - 1.70: 2 1.70 - 1.82: 132 Bond restraints: 13953 Sorted by residual: bond pdb=" CB PRO B 894 " pdb=" CG PRO B 894 " ideal model delta sigma weight residual 1.492 1.666 -0.174 5.00e-02 4.00e+02 1.20e+01 bond pdb=" CB PRO A 894 " pdb=" CG PRO A 894 " ideal model delta sigma weight residual 1.492 1.606 -0.114 5.00e-02 4.00e+02 5.17e+00 bond pdb=" N PRO B 894 " pdb=" CA PRO B 894 " ideal model delta sigma weight residual 1.469 1.444 0.025 1.28e-02 6.10e+03 3.79e+00 bond pdb=" CG GLU B 386 " pdb=" CD GLU B 386 " ideal model delta sigma weight residual 1.516 1.474 0.042 2.50e-02 1.60e+03 2.79e+00 bond pdb=" CB ARG D 55 " pdb=" CG ARG D 55 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.94e+00 ... (remaining 13948 not shown) Histogram of bond angle deviations from ideal: 96.33 - 103.87: 219 103.87 - 111.40: 5779 111.40 - 118.93: 5183 118.93 - 126.47: 7515 126.47 - 134.00: 227 Bond angle restraints: 18923 Sorted by residual: angle pdb=" CA PRO B 894 " pdb=" N PRO B 894 " pdb=" CD PRO B 894 " ideal model delta sigma weight residual 112.00 98.56 13.44 1.40e+00 5.10e-01 9.21e+01 angle pdb=" C HIS A 564 " pdb=" CA HIS A 564 " pdb=" CB HIS A 564 " ideal model delta sigma weight residual 115.79 109.61 6.18 1.19e+00 7.06e-01 2.70e+01 angle pdb=" CA PRO A 894 " pdb=" N PRO A 894 " pdb=" CD PRO A 894 " ideal model delta sigma weight residual 112.00 105.51 6.49 1.40e+00 5.10e-01 2.15e+01 angle pdb=" N PRO B 894 " pdb=" CD PRO B 894 " pdb=" CG PRO B 894 " ideal model delta sigma weight residual 103.20 96.33 6.87 1.50e+00 4.44e-01 2.10e+01 angle pdb=" CA ARG D 55 " pdb=" CB ARG D 55 " pdb=" CG ARG D 55 " ideal model delta sigma weight residual 114.10 123.04 -8.94 2.00e+00 2.50e-01 2.00e+01 ... (remaining 18918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 7027 16.84 - 33.68: 1019 33.68 - 50.52: 314 50.52 - 67.36: 64 67.36 - 84.20: 25 Dihedral angle restraints: 8449 sinusoidal: 3470 harmonic: 4979 Sorted by residual: dihedral pdb=" CB CYS D 18 " pdb=" SG CYS D 18 " pdb=" SG CYS D 61 " pdb=" CB CYS D 61 " ideal model delta sinusoidal sigma weight residual 93.00 175.61 -82.61 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" CB CYS C 18 " pdb=" SG CYS C 18 " pdb=" SG CYS C 61 " pdb=" CB CYS C 61 " ideal model delta sinusoidal sigma weight residual 93.00 173.15 -80.15 1 1.00e+01 1.00e-02 7.96e+01 dihedral pdb=" CB CYS B 162 " pdb=" SG CYS B 162 " pdb=" SG CYS B 181 " pdb=" CB CYS B 181 " ideal model delta sinusoidal sigma weight residual 93.00 16.25 76.75 1 1.00e+01 1.00e-02 7.40e+01 ... (remaining 8446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1299 0.038 - 0.075: 507 0.075 - 0.113: 190 0.113 - 0.151: 40 0.151 - 0.188: 5 Chirality restraints: 2041 Sorted by residual: chirality pdb=" CG LEU A 32 " pdb=" CB LEU A 32 " pdb=" CD1 LEU A 32 " pdb=" CD2 LEU A 32 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" CB ILE A 448 " pdb=" CA ILE A 448 " pdb=" CG1 ILE A 448 " pdb=" CG2 ILE A 448 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CA VAL A 899 " pdb=" N VAL A 899 " pdb=" C VAL A 899 " pdb=" CB VAL A 899 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.41e-01 ... (remaining 2038 not shown) Planarity restraints: 2459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 893 " 0.098 5.00e-02 4.00e+02 1.38e-01 3.05e+01 pdb=" N PRO B 894 " -0.238 5.00e-02 4.00e+02 pdb=" CA PRO B 894 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO B 894 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 893 " -0.068 5.00e-02 4.00e+02 9.94e-02 1.58e+01 pdb=" N PRO A 894 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO A 894 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 894 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 403 " 0.000 2.00e-02 2.50e+03 1.39e-02 4.85e+00 pdb=" CG TRP A 403 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 403 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 403 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 403 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 403 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 403 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 403 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 403 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 403 " -0.003 2.00e-02 2.50e+03 ... (remaining 2456 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 407 2.66 - 3.22: 14008 3.22 - 3.78: 22603 3.78 - 4.34: 29630 4.34 - 4.90: 46281 Nonbonded interactions: 112929 Sorted by model distance: nonbonded pdb=" OD1 ASP A 313 " pdb=" OG SER A 317 " model vdw 2.099 2.440 nonbonded pdb=" OD1 ASP B 313 " pdb=" OG SER B 317 " model vdw 2.101 2.440 nonbonded pdb=" OE2 GLU B 690 " pdb=" OH TYR A 138 " model vdw 2.151 2.440 nonbonded pdb=" O ARG B 77 " pdb=" OG1 THR B 107 " model vdw 2.153 2.440 nonbonded pdb=" OG SER A 461 " pdb=" O ARG A 566 " model vdw 2.194 2.440 ... (remaining 112924 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 294 or resid 301 through 901)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 106 5.16 5 C 8625 2.51 5 N 2367 2.21 5 O 2537 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.430 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: 10.150 Check model and map are aligned: 0.230 Convert atoms to be neutral: 0.130 Process input model: 38.880 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 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 : 0.005 0.174 13953 Z= 0.358 Angle : 0.755 13.437 18923 Z= 0.398 Chirality : 0.046 0.188 2041 Planarity : 0.006 0.138 2459 Dihedral : 17.459 84.202 5151 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 23.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.47 % Favored : 88.35 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.20), residues: 1665 helix: -1.38 (0.36), residues: 190 sheet: -1.70 (0.29), residues: 333 loop : -1.91 (0.18), residues: 1142 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 2.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 93 average time/residue: 0.2534 time to fit residues: 36.6100 Evaluate side-chains 85 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 2.714 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1312 time to fit residues: 3.1806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.8980 chunk 127 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 152 optimal weight: 50.0000 overall best weight: 3.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 13953 Z= 0.395 Angle : 0.684 9.260 18923 Z= 0.349 Chirality : 0.046 0.161 2041 Planarity : 0.005 0.067 2459 Dihedral : 5.589 36.712 1887 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 25.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.77 % Favored : 88.05 % Rotamer Outliers : 6.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.20), residues: 1665 helix: -1.02 (0.37), residues: 195 sheet: -1.75 (0.29), residues: 341 loop : -1.84 (0.18), residues: 1129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 87 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 54 residues processed: 172 average time/residue: 0.2477 time to fit residues: 64.8808 Evaluate side-chains 135 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 81 time to evaluate : 1.811 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.1242 time to fit residues: 14.9803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 152 optimal weight: 40.0000 chunk 165 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 151 optimal weight: 30.0000 chunk 52 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 13953 Z= 0.202 Angle : 0.622 9.361 18923 Z= 0.311 Chirality : 0.045 0.173 2041 Planarity : 0.005 0.054 2459 Dihedral : 5.188 37.271 1887 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.79 % Favored : 90.03 % Rotamer Outliers : 2.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.21), residues: 1665 helix: -0.84 (0.38), residues: 195 sheet: -1.61 (0.29), residues: 337 loop : -1.74 (0.19), residues: 1133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 100 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 15 residues processed: 136 average time/residue: 0.2266 time to fit residues: 47.9491 Evaluate side-chains 106 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 1.699 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1236 time to fit residues: 5.6565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 10.0000 chunk 114 optimal weight: 0.7980 chunk 79 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 72 optimal weight: 40.0000 chunk 102 optimal weight: 3.9990 chunk 153 optimal weight: 40.0000 chunk 162 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 145 optimal weight: 8.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN A 453 ASN ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 13953 Z= 0.174 Angle : 0.599 10.619 18923 Z= 0.301 Chirality : 0.045 0.284 2041 Planarity : 0.004 0.054 2459 Dihedral : 5.117 44.009 1887 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.21 % Favored : 89.61 % Rotamer Outliers : 3.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.20), residues: 1665 helix: -0.76 (0.38), residues: 195 sheet: -1.45 (0.30), residues: 328 loop : -1.73 (0.18), residues: 1142 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 98 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 14 residues processed: 140 average time/residue: 0.2409 time to fit residues: 51.4113 Evaluate side-chains 111 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 1.702 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1670 time to fit residues: 6.0806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 40.0000 chunk 92 optimal weight: 0.9980 chunk 2 optimal weight: 0.0970 chunk 120 optimal weight: 0.0670 chunk 67 optimal weight: 20.0000 chunk 138 optimal weight: 20.0000 chunk 112 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 145 optimal weight: 40.0000 chunk 40 optimal weight: 3.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 ASN ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.053 13953 Z= 0.160 Angle : 0.605 11.921 18923 Z= 0.295 Chirality : 0.045 0.193 2041 Planarity : 0.004 0.052 2459 Dihedral : 4.918 37.136 1887 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.07 % Favored : 90.75 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.20), residues: 1665 helix: -0.63 (0.38), residues: 195 sheet: -1.33 (0.30), residues: 320 loop : -1.74 (0.18), residues: 1150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 104 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 14 residues processed: 135 average time/residue: 0.2147 time to fit residues: 46.8475 Evaluate side-chains 112 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 1.673 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1315 time to fit residues: 5.6672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 8.9990 chunk 146 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 162 optimal weight: 0.6980 chunk 134 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 ASN ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 HIS ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 13953 Z= 0.289 Angle : 0.632 10.089 18923 Z= 0.318 Chirality : 0.046 0.167 2041 Planarity : 0.004 0.052 2459 Dihedral : 5.153 37.279 1887 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.91 % Favored : 89.91 % Rotamer Outliers : 2.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.21), residues: 1665 helix: -0.80 (0.38), residues: 189 sheet: -1.35 (0.30), residues: 321 loop : -1.72 (0.18), residues: 1155 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 95 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 13 residues processed: 128 average time/residue: 0.2340 time to fit residues: 47.8845 Evaluate side-chains 106 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 1.712 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1486 time to fit residues: 5.7451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 92 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 161 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 ASN ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 13953 Z= 0.266 Angle : 0.627 10.079 18923 Z= 0.313 Chirality : 0.046 0.210 2041 Planarity : 0.004 0.051 2459 Dihedral : 5.141 37.616 1887 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 20.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.03 % Favored : 89.79 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.20), residues: 1665 helix: -0.88 (0.37), residues: 202 sheet: -1.36 (0.30), residues: 321 loop : -1.73 (0.18), residues: 1142 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 93 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 117 average time/residue: 0.2240 time to fit residues: 41.4008 Evaluate side-chains 101 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 1.691 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1203 time to fit residues: 5.1307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 48 optimal weight: 0.0370 chunk 31 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 ASN ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 13953 Z= 0.159 Angle : 0.613 11.033 18923 Z= 0.300 Chirality : 0.045 0.183 2041 Planarity : 0.004 0.051 2459 Dihedral : 4.899 37.141 1887 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.13 % Favored : 90.69 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.20), residues: 1665 helix: -0.64 (0.37), residues: 197 sheet: -1.28 (0.30), residues: 321 loop : -1.71 (0.18), residues: 1147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 114 average time/residue: 0.2129 time to fit residues: 38.9764 Evaluate side-chains 101 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 1.715 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1302 time to fit residues: 4.0642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 20.0000 chunk 141 optimal weight: 4.9990 chunk 150 optimal weight: 20.0000 chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 118 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 136 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 159 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 13953 Z= 0.313 Angle : 0.667 10.043 18923 Z= 0.330 Chirality : 0.047 0.216 2041 Planarity : 0.004 0.051 2459 Dihedral : 5.202 37.754 1887 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.09 % Favored : 89.73 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.21), residues: 1665 helix: -0.92 (0.36), residues: 202 sheet: -1.35 (0.30), residues: 330 loop : -1.72 (0.19), residues: 1133 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 94 average time/residue: 0.2342 time to fit residues: 35.2378 Evaluate side-chains 88 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 1.741 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1210 time to fit residues: 3.3425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.0870 chunk 75 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 chunk 133 optimal weight: 10.0000 chunk 13 optimal weight: 0.1980 chunk 102 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 overall best weight: 1.0564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 ASN ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 13953 Z= 0.190 Angle : 0.639 9.940 18923 Z= 0.312 Chirality : 0.046 0.222 2041 Planarity : 0.004 0.051 2459 Dihedral : 4.990 37.496 1887 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.13 % Favored : 90.69 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.20), residues: 1665 helix: -0.78 (0.37), residues: 202 sheet: -1.28 (0.30), residues: 322 loop : -1.69 (0.18), residues: 1141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 99 average time/residue: 0.2294 time to fit residues: 36.1962 Evaluate side-chains 96 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 1.673 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1207 time to fit residues: 2.7121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.2980 chunk 122 optimal weight: 0.5980 chunk 19 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 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 = 0.3975 r_free = 0.3975 target = 0.101502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.069475 restraints weight = 45401.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.067427 restraints weight = 36619.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.067726 restraints weight = 32587.826| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 13953 Z= 0.165 Angle : 0.622 10.599 18923 Z= 0.301 Chirality : 0.045 0.192 2041 Planarity : 0.004 0.051 2459 Dihedral : 4.835 37.548 1887 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.19 % Favored : 90.63 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.20), residues: 1665 helix: -0.49 (0.38), residues: 191 sheet: -1.20 (0.30), residues: 322 loop : -1.66 (0.18), residues: 1152 =============================================================================== Job complete usr+sys time: 2273.56 seconds wall clock time: 42 minutes 52.37 seconds (2572.37 seconds total)