Starting phenix.real_space_refine (version: dev) on Sun Feb 19 13:38:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pr5_20457/02_2023/6pr5_20457.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pr5_20457/02_2023/6pr5_20457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pr5_20457/02_2023/6pr5_20457.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pr5_20457/02_2023/6pr5_20457.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pr5_20457/02_2023/6pr5_20457.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pr5_20457/02_2023/6pr5_20457.pdb" } resolution = 3.3 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= 0.004 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 Process input model Symmetric amino acids flipped Residue "A TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A GLU 138": "OE1" <-> "OE2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A ASP 315": "OD1" <-> "OD2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 358": "OD1" <-> "OD2" Residue "A ASP 360": "OD1" <-> "OD2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A ASP 440": "OD1" <-> "OD2" Residue "A ARG 445": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ASP 460": "OD1" <-> "OD2" Residue "E TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 100": "NH1" <-> "NH2" Residue "E ASP 109": "OD1" <-> "OD2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 132": "NH1" <-> "NH2" Residue "E GLU 193": "OE1" <-> "OE2" Residue "E ASP 198": "OD1" <-> "OD2" Residue "E GLU 200": "OE1" <-> "OE2" Residue "E ARG 276": "NH1" <-> "NH2" Residue "E GLU 304": "OE1" <-> "OE2" Residue "E ARG 342": "NH1" <-> "NH2" Residue "E PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 376": "OE1" <-> "OE2" Residue "E ARG 388": "NH1" <-> "NH2" Residue "E TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 431": "OE1" <-> "OE2" Residue "E ARG 437": "NH1" <-> "NH2" Residue "E ASP 440": "OD1" <-> "OD2" Residue "E PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 445": "NH1" <-> "NH2" Residue "E ARG 454": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 10194 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3823 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 462} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 3823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3823 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 462} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 324 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "C" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "D" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 616 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "F" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 181 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "G" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "H" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 755 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1720 SG CYS A 240 28.075 20.995 56.182 1.00 66.94 S ATOM 1746 SG CYS A 243 26.675 18.929 53.984 1.00 66.43 S ATOM 5543 SG CYS E 240 66.736 74.745 53.312 1.00 75.78 S ATOM 5569 SG CYS E 243 68.439 75.903 50.736 1.00 75.72 S Time building chain proxies: 6.42, per 1000 atoms: 0.63 Number of scatterers: 10194 At special positions: 0 Unit cell: (97.65, 101.85, 120.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 36 16.00 P 124 15.00 Mg 4 11.99 O 2182 8.00 N 1773 7.00 C 6073 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 - 3.50 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: 5.56 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 603 " pdb="ZN ZN A 603 " - pdb=" NE2 HIS A 408 " pdb="ZN ZN A 603 " - pdb=" NE2 HIS A 413 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 243 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 240 " pdb=" ZN E 603 " pdb="ZN ZN E 603 " - pdb=" NE2 HIS E 408 " pdb="ZN ZN E 603 " - pdb=" NE2 HIS E 413 " pdb="ZN ZN E 603 " - pdb=" SG CYS E 243 " pdb="ZN ZN E 603 " - pdb=" SG CYS E 240 " Number of angles added : 4 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1836 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 7 sheets defined 53.3% alpha, 15.0% beta 60 base pairs and 96 stacking pairs defined. Time for finding SS restraints: 3.91 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 39 through 53 removed outlier: 3.535A pdb=" N GLU A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 69 Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 89 through 102 Processing helix chain 'A' and resid 186 through 203 Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.802A pdb=" N ILE A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 268 Processing helix chain 'A' and resid 271 through 289 removed outlier: 3.737A pdb=" N ARG A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG A 289 " --> pdb=" O HIS A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 322 Processing helix chain 'A' and resid 337 through 345 Processing helix chain 'A' and resid 347 through 356 removed outlier: 3.536A pdb=" N THR A 351 " --> pdb=" O PHE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 374 removed outlier: 3.572A pdb=" N ILE A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 398 Processing helix chain 'A' and resid 404 through 412 Processing helix chain 'A' and resid 413 through 421 removed outlier: 3.764A pdb=" N ASN A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 446 removed outlier: 3.583A pdb=" N ASN A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 443 " --> pdb=" O LYS A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 469 Processing helix chain 'A' and resid 470 through 476 removed outlier: 3.749A pdb=" N THR A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'E' and resid 25 through 36 Processing helix chain 'E' and resid 39 through 52 Processing helix chain 'E' and resid 61 through 69 Processing helix chain 'E' and resid 89 through 102 Processing helix chain 'E' and resid 186 through 203 Processing helix chain 'E' and resid 224 through 232 Processing helix chain 'E' and resid 246 through 251 removed outlier: 3.796A pdb=" N SER E 251 " --> pdb=" O THR E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 258 Processing helix chain 'E' and resid 264 through 268 Processing helix chain 'E' and resid 271 through 289 removed outlier: 3.675A pdb=" N ARG E 276 " --> pdb=" O THR E 272 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE E 277 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG E 289 " --> pdb=" O HIS E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 322 Processing helix chain 'E' and resid 337 through 347 removed outlier: 4.653A pdb=" N PHE E 347 " --> pdb=" O ARG E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 356 Processing helix chain 'E' and resid 358 through 374 Processing helix chain 'E' and resid 379 through 398 Processing helix chain 'E' and resid 404 through 412 Processing helix chain 'E' and resid 413 through 421 Processing helix chain 'E' and resid 431 through 448 removed outlier: 3.808A pdb=" N LYS E 439 " --> pdb=" O GLU E 435 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG E 443 " --> pdb=" O LYS E 439 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS E 447 " --> pdb=" O ARG E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 469 Processing helix chain 'E' and resid 470 through 476 removed outlier: 3.665A pdb=" N THR E 476 " --> pdb=" O LEU E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 491 through 495 Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.340A pdb=" N VAL A 178 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR A 149 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE A 180 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE A 147 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TRP A 164 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ALA A 158 " --> pdb=" O THR A 162 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N THR A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.340A pdb=" N VAL A 178 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR A 149 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE A 180 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE A 147 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N PHE A 147 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ALA A 127 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N THR A 149 " --> pdb=" O ASP A 125 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASP A 125 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU A 151 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLY A 123 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LYS A 121 " --> pdb=" O PRO A 153 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 116 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LYS A 217 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU A 118 " --> pdb=" O LYS A 217 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N MET A 219 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER A 120 " --> pdb=" O MET A 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 377 through 378 removed outlier: 4.128A pdb=" N ILE A 377 " --> pdb=" O GLN A 497 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 79 through 82 removed outlier: 3.723A pdb=" N SER E 85 " --> pdb=" O THR E 82 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL E 178 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR E 149 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE E 180 " --> pdb=" O PHE E 147 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE E 147 " --> pdb=" O PHE E 180 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TRP E 164 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA E 158 " --> pdb=" O THR E 162 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N THR E 162 " --> pdb=" O ALA E 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 79 through 82 removed outlier: 3.723A pdb=" N SER E 85 " --> pdb=" O THR E 82 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL E 178 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR E 149 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE E 180 " --> pdb=" O PHE E 147 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE E 147 " --> pdb=" O PHE E 180 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE E 119 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LEU E 156 " --> pdb=" O ILE E 117 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE E 117 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU E 116 " --> pdb=" O SER E 215 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LYS E 217 " --> pdb=" O LEU E 116 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU E 118 " --> pdb=" O LYS E 217 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N MET E 219 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N SER E 120 " --> pdb=" O MET E 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 328 through 329 Processing sheet with id=AA7, first strand: chain 'E' and resid 377 through 378 removed outlier: 4.145A pdb=" N ILE E 377 " --> pdb=" O GLN E 497 " (cutoff:3.500A) 388 hydrogen bonds defined for protein. 1113 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 149 hydrogen bonds 298 hydrogen bond angles 0 basepair planarities 60 basepair parallelities 96 stacking parallelities Total time for adding SS restraints: 4.46 Time building geometry restraints manager: 5.64 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: 2124 1.33 - 1.45: 2836 1.45 - 1.57: 5380 1.57 - 1.69: 242 1.69 - 1.81: 56 Bond restraints: 10638 Sorted by residual: bond pdb=" C TYR A 73 " pdb=" N PRO A 74 " ideal model delta sigma weight residual 1.329 1.367 -0.038 1.18e-02 7.18e+03 1.05e+01 bond pdb=" N GLN A 330 " pdb=" CA GLN A 330 " ideal model delta sigma weight residual 1.459 1.420 0.039 1.23e-02 6.61e+03 1.00e+01 bond pdb=" N CYS A 72 " pdb=" CA CYS A 72 " ideal model delta sigma weight residual 1.457 1.424 0.032 1.32e-02 5.74e+03 6.00e+00 bond pdb=" CB VAL A 152 " pdb=" CG1 VAL A 152 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.67e+00 bond pdb=" CB VAL E 152 " pdb=" CG1 VAL E 152 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.62e+00 ... (remaining 10633 not shown) Histogram of bond angle deviations from ideal: 98.28 - 105.44: 656 105.44 - 112.59: 5902 112.59 - 119.75: 3525 119.75 - 126.90: 4415 126.90 - 134.06: 394 Bond angle restraints: 14892 Sorted by residual: angle pdb=" O3' DT F 2 " pdb=" C3' DT F 2 " pdb=" C2' DT F 2 " ideal model delta sigma weight residual 111.50 102.43 9.07 1.50e+00 4.44e-01 3.66e+01 angle pdb=" C ASP E 379 " pdb=" N VAL E 380 " pdb=" CA VAL E 380 " ideal model delta sigma weight residual 120.24 123.50 -3.26 6.30e-01 2.52e+00 2.68e+01 angle pdb=" O3' DG H 31 " pdb=" C3' DG H 31 " pdb=" C2' DG H 31 " ideal model delta sigma weight residual 111.50 104.64 6.86 1.50e+00 4.44e-01 2.09e+01 angle pdb=" O3' DG B 12 " pdb=" C3' DG B 12 " pdb=" C2' DG B 12 " ideal model delta sigma weight residual 111.50 105.18 6.32 1.50e+00 4.44e-01 1.77e+01 angle pdb=" N GLU E 138 " pdb=" CA GLU E 138 " pdb=" C GLU E 138 " ideal model delta sigma weight residual 110.80 119.50 -8.70 2.13e+00 2.20e-01 1.67e+01 ... (remaining 14887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.04: 5331 32.04 - 64.08: 648 64.08 - 96.12: 24 96.12 - 128.15: 1 128.15 - 160.19: 2 Dihedral angle restraints: 6006 sinusoidal: 3178 harmonic: 2828 Sorted by residual: dihedral pdb=" CA GLY E 427 " pdb=" C GLY E 427 " pdb=" N SER E 428 " pdb=" CA SER E 428 " ideal model delta harmonic sigma weight residual 180.00 155.55 24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA GLY A 427 " pdb=" C GLY A 427 " pdb=" N SER A 428 " pdb=" CA SER A 428 " ideal model delta harmonic sigma weight residual 180.00 156.17 23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA GLU A 138 " pdb=" C GLU A 138 " pdb=" N SER A 139 " pdb=" CA SER A 139 " ideal model delta harmonic sigma weight residual 180.00 -156.34 -23.66 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 6003 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1369 0.058 - 0.117: 285 0.117 - 0.175: 31 0.175 - 0.233: 3 0.233 - 0.291: 2 Chirality restraints: 1690 Sorted by residual: chirality pdb=" CA GLU E 138 " pdb=" N GLU E 138 " pdb=" C GLU E 138 " pdb=" CB GLU E 138 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CB THR E 334 " pdb=" CA THR E 334 " pdb=" OG1 THR E 334 " pdb=" CG2 THR E 334 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA CYS A 72 " pdb=" N CYS A 72 " pdb=" C CYS A 72 " pdb=" CB CYS A 72 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1687 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT F 2 " -0.008 2.00e-02 2.50e+03 1.57e-02 6.19e+00 pdb=" N1 DT F 2 " -0.011 2.00e-02 2.50e+03 pdb=" C2 DT F 2 " -0.020 2.00e-02 2.50e+03 pdb=" O2 DT F 2 " 0.024 2.00e-02 2.50e+03 pdb=" N3 DT F 2 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT F 2 " -0.021 2.00e-02 2.50e+03 pdb=" O4 DT F 2 " 0.010 2.00e-02 2.50e+03 pdb=" C5 DT F 2 " -0.002 2.00e-02 2.50e+03 pdb=" C7 DT F 2 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DT F 2 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA D 11 " -0.027 2.00e-02 2.50e+03 1.44e-02 5.73e+00 pdb=" N9 DA D 11 " 0.039 2.00e-02 2.50e+03 pdb=" C8 DA D 11 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DA D 11 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA D 11 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA D 11 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA D 11 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DA D 11 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA D 11 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA D 11 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DA D 11 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT B 16 " -0.001 2.00e-02 2.50e+03 1.49e-02 5.55e+00 pdb=" N1 DT B 16 " -0.012 2.00e-02 2.50e+03 pdb=" C2 DT B 16 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DT B 16 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DT B 16 " 0.012 2.00e-02 2.50e+03 pdb=" C4 DT B 16 " -0.000 2.00e-02 2.50e+03 pdb=" O4 DT B 16 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DT B 16 " -0.034 2.00e-02 2.50e+03 pdb=" C7 DT B 16 " 0.010 2.00e-02 2.50e+03 pdb=" C6 DT B 16 " 0.026 2.00e-02 2.50e+03 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 95 2.55 - 3.14: 8049 3.14 - 3.73: 17032 3.73 - 4.31: 23758 4.31 - 4.90: 37759 Nonbonded interactions: 86693 Sorted by model distance: nonbonded pdb=" O3' DC F 9 " pdb="MG MG E 601 " model vdw 1.963 2.170 nonbonded pdb=" OD1 ASP E 125 " pdb="MG MG E 601 " model vdw 2.123 2.170 nonbonded pdb=" OD2 ASP E 125 " pdb="MG MG E 602 " model vdw 2.133 2.170 nonbonded pdb=" OD2 ASP E 224 " pdb="MG MG E 601 " model vdw 2.138 2.170 nonbonded pdb=" OE1 GLU E 435 " pdb="MG MG E 602 " model vdw 2.149 2.170 ... (remaining 86688 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' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'G' } 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 124 5.49 5 Mg 4 5.21 5 S 36 5.16 5 C 6073 2.51 5 N 1773 2.21 5 O 2182 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 4.560 Check model and map are aligned: 0.140 Process input model: 37.190 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.090 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 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 : 0.008 0.054 10638 Z= 0.491 Angle : 0.776 10.532 14892 Z= 0.447 Chirality : 0.047 0.291 1690 Planarity : 0.004 0.039 1452 Dihedral : 22.820 160.193 4170 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.36 % Favored : 98.33 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.21), residues: 956 helix: -1.83 (0.19), residues: 506 sheet: -1.05 (0.60), residues: 64 loop : -2.71 (0.23), residues: 386 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 116 average time/residue: 0.2750 time to fit residues: 44.0834 Evaluate side-chains 77 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 1.288 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1117 time to fit residues: 2.3487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.0060 chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 HIS A 216 HIS A 339 ASN A 486 GLN E 71 GLN E 91 GLN E 130 GLN E 136 ASN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 HIS E 322 ASN E 330 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 10638 Z= 0.178 Angle : 0.576 9.571 14892 Z= 0.322 Chirality : 0.038 0.183 1690 Planarity : 0.004 0.038 1452 Dihedral : 26.135 159.634 2262 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.72 % Favored : 97.18 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.25), residues: 956 helix: 0.17 (0.23), residues: 498 sheet: -0.90 (0.59), residues: 64 loop : -2.14 (0.27), residues: 394 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 1.121 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 109 average time/residue: 0.2501 time to fit residues: 39.4603 Evaluate side-chains 82 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 1.101 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0959 time to fit residues: 2.7218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 64 optimal weight: 0.0050 chunk 26 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 94 optimal weight: 0.3980 chunk 32 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN ** A 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 GLN ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 10638 Z= 0.158 Angle : 0.539 8.298 14892 Z= 0.304 Chirality : 0.036 0.185 1690 Planarity : 0.003 0.035 1452 Dihedral : 26.062 164.005 2262 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.93 % Favored : 96.97 % Rotamer Outliers : 2.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.27), residues: 956 helix: 1.15 (0.24), residues: 500 sheet: -0.69 (0.57), residues: 64 loop : -1.87 (0.28), residues: 392 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 1.165 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 14 residues processed: 106 average time/residue: 0.2149 time to fit residues: 33.8334 Evaluate side-chains 93 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 1.025 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1237 time to fit residues: 4.2877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.076 10638 Z= 0.329 Angle : 0.621 10.837 14892 Z= 0.340 Chirality : 0.041 0.210 1690 Planarity : 0.004 0.044 1452 Dihedral : 26.338 165.640 2262 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.71 % Favored : 95.19 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.27), residues: 956 helix: 1.17 (0.24), residues: 500 sheet: -0.69 (0.58), residues: 64 loop : -1.80 (0.29), residues: 392 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 1.060 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 85 average time/residue: 0.2096 time to fit residues: 27.0101 Evaluate side-chains 75 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 1.003 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0927 time to fit residues: 2.7982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 75 optimal weight: 0.0010 chunk 41 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 GLN ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 10638 Z= 0.172 Angle : 0.537 7.693 14892 Z= 0.302 Chirality : 0.037 0.212 1690 Planarity : 0.003 0.036 1452 Dihedral : 26.132 164.964 2262 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.18 % Favored : 95.71 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.27), residues: 956 helix: 1.44 (0.24), residues: 514 sheet: -0.46 (0.59), residues: 64 loop : -1.73 (0.29), residues: 378 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 1.012 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 90 average time/residue: 0.2063 time to fit residues: 28.1467 Evaluate side-chains 79 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 1.103 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1420 time to fit residues: 3.4599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 10638 Z= 0.242 Angle : 0.573 9.394 14892 Z= 0.316 Chirality : 0.038 0.216 1690 Planarity : 0.004 0.035 1452 Dihedral : 26.180 166.328 2262 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.71 % Favored : 95.19 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.27), residues: 956 helix: 1.57 (0.24), residues: 502 sheet: -0.38 (0.59), residues: 64 loop : -1.70 (0.30), residues: 390 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 1.039 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 86 average time/residue: 0.2002 time to fit residues: 26.2718 Evaluate side-chains 79 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 1.031 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0956 time to fit residues: 3.0610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 0.0980 chunk 101 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 62 optimal weight: 0.0050 overall best weight: 1.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 10638 Z= 0.252 Angle : 0.577 9.230 14892 Z= 0.318 Chirality : 0.038 0.231 1690 Planarity : 0.004 0.036 1452 Dihedral : 26.203 166.373 2262 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.28), residues: 956 helix: 1.56 (0.24), residues: 504 sheet: -0.35 (0.59), residues: 64 loop : -1.67 (0.30), residues: 388 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 1.143 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 85 average time/residue: 0.2012 time to fit residues: 25.8154 Evaluate side-chains 77 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.981 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0951 time to fit residues: 2.3277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 10638 Z= 0.164 Angle : 0.538 9.253 14892 Z= 0.301 Chirality : 0.037 0.239 1690 Planarity : 0.003 0.038 1452 Dihedral : 25.985 166.669 2262 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.28), residues: 956 helix: 1.87 (0.24), residues: 502 sheet: -0.31 (0.60), residues: 64 loop : -1.62 (0.30), residues: 390 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 1.110 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 91 average time/residue: 0.2067 time to fit residues: 28.6191 Evaluate side-chains 79 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 1.127 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1518 time to fit residues: 1.6062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 4.9990 chunk 94 optimal weight: 0.0370 chunk 96 optimal weight: 10.0000 chunk 56 optimal weight: 0.3980 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 61 optimal weight: 0.0370 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 10638 Z= 0.155 Angle : 0.533 9.159 14892 Z= 0.297 Chirality : 0.036 0.245 1690 Planarity : 0.003 0.037 1452 Dihedral : 25.882 168.407 2262 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.28), residues: 956 helix: 1.96 (0.24), residues: 502 sheet: 0.13 (0.62), residues: 64 loop : -1.59 (0.30), residues: 390 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 1.140 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 94 average time/residue: 0.2175 time to fit residues: 30.5002 Evaluate side-chains 80 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 1.020 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0926 time to fit residues: 1.6118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 83 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 10638 Z= 0.264 Angle : 0.594 9.723 14892 Z= 0.325 Chirality : 0.039 0.243 1690 Planarity : 0.004 0.035 1452 Dihedral : 26.093 167.990 2262 Min Nonbonded Distance : 1.653 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.28), residues: 956 helix: 1.67 (0.23), residues: 516 sheet: 0.25 (0.62), residues: 64 loop : -1.50 (0.31), residues: 376 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 1.016 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 78 average time/residue: 0.2222 time to fit residues: 25.6877 Evaluate side-chains 71 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 1.087 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0873 time to fit residues: 1.6152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.139789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.112568 restraints weight = 15922.640| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.97 r_work: 0.3368 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 10638 Z= 0.227 Angle : 0.573 7.913 14892 Z= 0.317 Chirality : 0.038 0.244 1690 Planarity : 0.004 0.032 1452 Dihedral : 26.081 167.005 2262 Min Nonbonded Distance : 1.511 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.28), residues: 956 helix: 1.65 (0.23), residues: 514 sheet: 0.27 (0.62), residues: 64 loop : -1.48 (0.31), residues: 378 =============================================================================== Job complete usr+sys time: 1861.46 seconds wall clock time: 35 minutes 10.98 seconds (2110.98 seconds total)