Starting phenix.real_space_refine on Fri Mar 15 00:26:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pr5_20457/03_2024/6pr5_20457.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pr5_20457/03_2024/6pr5_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_20457/03_2024/6pr5_20457.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pr5_20457/03_2024/6pr5_20457.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pr5_20457/03_2024/6pr5_20457.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pr5_20457/03_2024/6pr5_20457.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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 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. 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.88, per 1000 atoms: 0.58 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: 5.00 Conformation dependent library (CDL) restraints added in 1.4 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: 4.27 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: 4.10 Time building geometry restraints manager: 5.23 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: 5430 32.04 - 64.08: 673 64.08 - 96.12: 24 96.12 - 128.15: 1 128.15 - 160.19: 2 Dihedral angle restraints: 6130 sinusoidal: 3302 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 6127 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 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: 0.670 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: 4.180 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 36.340 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 : 22.941 160.193 4294 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 % Allowed : 10.47 % Favored : 88.82 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 41 HIS 0.006 0.001 HIS A 483 PHE 0.015 0.002 PHE A 292 TYR 0.012 0.002 TYR E 394 ARG 0.007 0.001 ARG A 477 *********************** 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 : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ASP cc_start: 0.8418 (p0) cc_final: 0.8170 (p0) REVERT: A 212 HIS cc_start: 0.7805 (m90) cc_final: 0.7395 (m170) REVERT: E 173 MET cc_start: 0.7295 (mtp) cc_final: 0.6998 (mtp) REVERT: E 184 LYS cc_start: 0.8311 (tttt) cc_final: 0.7833 (tppt) REVERT: E 295 TRP cc_start: 0.8549 (t60) cc_final: 0.8314 (t-100) REVERT: E 423 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8102 (tt) outliers start: 6 outliers final: 4 residues processed: 116 average time/residue: 0.2502 time to fit residues: 40.0482 Evaluate side-chains 80 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 423 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1489 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= 0.190 Angle : 0.574 9.687 14892 Z= 0.321 Chirality : 0.038 0.183 1690 Planarity : 0.004 0.038 1452 Dihedral : 25.933 159.745 2392 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.93 % Favored : 96.97 % Rotamer: Outliers : 2.35 % Allowed : 13.88 % Favored : 83.76 % 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: 0.16 (0.23), residues: 500 sheet: -0.91 (0.59), residues: 64 loop : -2.13 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 41 HIS 0.002 0.001 HIS A 408 PHE 0.012 0.002 PHE A 180 TYR 0.016 0.001 TYR E 241 ARG 0.002 0.000 ARG A 176 *********************** 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 120 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 1.126 Fit side-chains revert: symmetry clash REVERT: A 129 ASN cc_start: 0.6752 (OUTLIER) cc_final: 0.6449 (m-40) REVERT: E 173 MET cc_start: 0.7202 (mtp) cc_final: 0.6878 (mtp) REVERT: E 184 LYS cc_start: 0.8164 (tttt) cc_final: 0.7644 (tppt) REVERT: E 307 HIS cc_start: 0.7918 (m90) cc_final: 0.7684 (m90) outliers start: 20 outliers final: 13 residues processed: 113 average time/residue: 0.2248 time to fit residues: 36.6860 Evaluate side-chains 87 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 79 optimal weight: 0.0030 chunk 64 optimal weight: 3.9990 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: 0.5980 chunk 32 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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 141 GLN A 336 ASN ** A 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 GLN E 330 GLN ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1989 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= 0.169 Angle : 0.543 8.222 14892 Z= 0.306 Chirality : 0.037 0.190 1690 Planarity : 0.004 0.035 1452 Dihedral : 25.831 163.705 2390 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.24 % Favored : 96.65 % Rotamer: Outliers : 2.94 % Allowed : 16.59 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.27), residues: 956 helix: 1.07 (0.24), residues: 500 sheet: -0.79 (0.57), residues: 64 loop : -1.89 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 41 HIS 0.002 0.001 HIS A 447 PHE 0.014 0.001 PHE A 292 TYR 0.010 0.001 TYR E 241 ARG 0.002 0.000 ARG E 437 *********************** 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 113 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 88 time to evaluate : 0.999 Fit side-chains REVERT: A 315 ASP cc_start: 0.7504 (m-30) cc_final: 0.7230 (m-30) REVERT: E 173 MET cc_start: 0.7140 (mtp) cc_final: 0.6836 (mtp) REVERT: E 184 LYS cc_start: 0.8149 (tttt) cc_final: 0.7607 (tppt) outliers start: 25 outliers final: 18 residues processed: 107 average time/residue: 0.1760 time to fit residues: 28.7280 Evaluate side-chains 91 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 499 GLN ** E 330 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10638 Z= 0.194 Angle : 0.550 8.394 14892 Z= 0.307 Chirality : 0.037 0.205 1690 Planarity : 0.004 0.037 1452 Dihedral : 25.822 164.362 2390 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.87 % Favored : 96.03 % Rotamer: Outliers : 2.82 % Allowed : 18.59 % Favored : 78.59 % 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: 0.03 (0.27), residues: 956 helix: 1.41 (0.24), residues: 500 sheet: -0.52 (0.57), residues: 64 loop : -1.79 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 41 HIS 0.003 0.001 HIS E 408 PHE 0.011 0.001 PHE A 180 TYR 0.014 0.001 TYR E 73 ARG 0.003 0.000 ARG E 106 *********************** 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 98 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 74 time to evaluate : 1.044 Fit side-chains REVERT: E 173 MET cc_start: 0.7204 (mtp) cc_final: 0.6888 (mtp) REVERT: E 184 LYS cc_start: 0.8165 (tttt) cc_final: 0.7611 (tppt) outliers start: 24 outliers final: 21 residues processed: 94 average time/residue: 0.1862 time to fit residues: 26.7817 Evaluate side-chains 93 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 72 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 487 THR 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: 0.7980 chunk 1 optimal weight: 0.6980 chunk 75 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 499 GLN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7930 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10638 Z= 0.209 Angle : 0.551 8.663 14892 Z= 0.307 Chirality : 0.037 0.204 1690 Planarity : 0.003 0.036 1452 Dihedral : 25.829 164.838 2390 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.97 % Favored : 95.92 % Rotamer: Outliers : 2.94 % Allowed : 19.65 % Favored : 77.41 % 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: 0.15 (0.27), residues: 956 helix: 1.53 (0.24), residues: 500 sheet: -0.48 (0.58), residues: 64 loop : -1.76 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 41 HIS 0.003 0.001 HIS E 408 PHE 0.014 0.001 PHE A 292 TYR 0.011 0.001 TYR E 73 ARG 0.003 0.000 ARG E 106 *********************** 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 97 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 72 time to evaluate : 0.926 Fit side-chains REVERT: E 173 MET cc_start: 0.7187 (mtp) cc_final: 0.6883 (mtp) REVERT: E 184 LYS cc_start: 0.8179 (tttt) cc_final: 0.7646 (tppt) outliers start: 25 outliers final: 21 residues processed: 94 average time/residue: 0.1952 time to fit residues: 27.8697 Evaluate side-chains 90 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 69 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 59 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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** ** 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: 0.7934 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10638 Z= 0.216 Angle : 0.555 8.951 14892 Z= 0.309 Chirality : 0.038 0.236 1690 Planarity : 0.004 0.036 1452 Dihedral : 25.840 165.105 2390 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.39 % Favored : 95.50 % Rotamer: Outliers : 3.18 % Allowed : 19.88 % Favored : 76.94 % 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: 0.22 (0.27), residues: 956 helix: 1.58 (0.24), residues: 500 sheet: -0.42 (0.59), residues: 64 loop : -1.73 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 41 HIS 0.003 0.001 HIS E 408 PHE 0.014 0.001 PHE A 292 TYR 0.014 0.001 TYR E 241 ARG 0.003 0.000 ARG E 106 *********************** 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 101 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 74 time to evaluate : 1.039 Fit side-chains REVERT: E 173 MET cc_start: 0.7188 (mtp) cc_final: 0.6887 (mtp) REVERT: E 184 LYS cc_start: 0.8176 (tttt) cc_final: 0.7645 (tppt) outliers start: 27 outliers final: 24 residues processed: 98 average time/residue: 0.1859 time to fit residues: 27.8845 Evaluate side-chains 96 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 72 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 487 THR 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: 2.9990 chunk 74 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 62 optimal weight: 0.0980 overall best weight: 0.5382 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10638 Z= 0.154 Angle : 0.521 9.080 14892 Z= 0.293 Chirality : 0.036 0.227 1690 Planarity : 0.003 0.037 1452 Dihedral : 25.628 165.004 2390 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.59 % Allowed : 21.29 % Favored : 76.12 % 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: 0.50 (0.28), residues: 956 helix: 1.86 (0.24), residues: 502 sheet: -0.40 (0.57), residues: 64 loop : -1.67 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 41 HIS 0.003 0.000 HIS E 408 PHE 0.014 0.001 PHE A 292 TYR 0.017 0.001 TYR E 241 ARG 0.002 0.000 ARG E 437 *********************** 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 116 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: E 173 MET cc_start: 0.7154 (mtp) cc_final: 0.6881 (mtp) REVERT: E 184 LYS cc_start: 0.8146 (tttt) cc_final: 0.7603 (tppt) outliers start: 22 outliers final: 22 residues processed: 110 average time/residue: 0.1894 time to fit residues: 31.5614 Evaluate side-chains 102 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 80 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 30 optimal weight: 0.0970 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10638 Z= 0.275 Angle : 0.587 9.330 14892 Z= 0.323 Chirality : 0.039 0.235 1690 Planarity : 0.004 0.035 1452 Dihedral : 25.841 166.521 2390 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.18 % Allowed : 21.53 % Favored : 75.29 % 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: 0.40 (0.27), residues: 956 helix: 1.65 (0.24), residues: 514 sheet: -0.42 (0.58), residues: 64 loop : -1.63 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 41 HIS 0.004 0.001 HIS E 408 PHE 0.011 0.001 PHE A 180 TYR 0.018 0.001 TYR E 241 ARG 0.005 0.000 ARG A 52 *********************** 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 99 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 72 time to evaluate : 0.975 Fit side-chains REVERT: E 173 MET cc_start: 0.7257 (mtp) cc_final: 0.6958 (mtp) REVERT: E 184 LYS cc_start: 0.8187 (tttt) cc_final: 0.7658 (tppt) REVERT: E 403 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7618 (mtp) outliers start: 27 outliers final: 25 residues processed: 95 average time/residue: 0.1910 time to fit residues: 27.5314 Evaluate side-chains 94 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 68 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 403 MET Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 41 optimal weight: 0.0870 chunk 74 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 61 optimal weight: 0.0970 overall best weight: 0.5356 ------------------------------------------------------------------------------- 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** ** E 330 GLN ** 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: 0.7860 moved from start: 0.2844 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= 0.159 Angle : 0.532 9.119 14892 Z= 0.296 Chirality : 0.036 0.230 1690 Planarity : 0.003 0.037 1452 Dihedral : 25.591 165.791 2390 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.94 % Allowed : 21.65 % Favored : 75.41 % 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: 0.65 (0.28), residues: 956 helix: 1.85 (0.24), residues: 516 sheet: -0.38 (0.57), residues: 64 loop : -1.50 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 41 HIS 0.002 0.000 HIS E 408 PHE 0.012 0.001 PHE A 292 TYR 0.014 0.001 TYR E 241 ARG 0.005 0.000 ARG A 52 *********************** 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 110 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 85 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 212 HIS cc_start: 0.7877 (m90) cc_final: 0.7476 (m170) REVERT: E 173 MET cc_start: 0.7185 (mtp) cc_final: 0.6921 (mtp) REVERT: E 184 LYS cc_start: 0.8253 (tttt) cc_final: 0.7703 (tppt) REVERT: E 197 MET cc_start: 0.7276 (tpp) cc_final: 0.7072 (mpp) REVERT: E 403 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7443 (mtp) outliers start: 25 outliers final: 22 residues processed: 105 average time/residue: 0.1797 time to fit residues: 29.0068 Evaluate side-chains 103 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 80 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 403 MET Chi-restraints excluded: chain E residue 487 THR 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: 2.9990 chunk 47 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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** ** E 330 GLN ** 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: 0.7953 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10638 Z= 0.270 Angle : 0.589 9.575 14892 Z= 0.324 Chirality : 0.039 0.256 1690 Planarity : 0.004 0.031 1452 Dihedral : 25.856 167.245 2389 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.06 % Allowed : 22.12 % Favored : 74.82 % 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: 0.47 (0.27), residues: 956 helix: 1.64 (0.24), residues: 516 sheet: -0.38 (0.57), residues: 64 loop : -1.49 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 41 HIS 0.004 0.001 HIS E 447 PHE 0.011 0.001 PHE A 180 TYR 0.015 0.001 TYR E 241 ARG 0.005 0.000 ARG A 52 ********************** 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 94 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 68 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: E 173 MET cc_start: 0.7260 (mtp) cc_final: 0.6965 (mtp) REVERT: E 184 LYS cc_start: 0.8175 (tttt) cc_final: 0.7700 (tppt) REVERT: E 403 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7518 (mtp) outliers start: 26 outliers final: 25 residues processed: 91 average time/residue: 0.1945 time to fit residues: 27.4005 Evaluate side-chains 92 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 66 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 403 MET Chi-restraints excluded: chain E residue 487 THR 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: 7.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.0040 chunk 73 optimal weight: 0.7980 overall best weight: 1.1196 ------------------------------------------------------------------------------- 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** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.140402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.114041 restraints weight = 15738.744| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.94 r_work: 0.3408 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10638 Z= 0.197 Angle : 0.558 9.304 14892 Z= 0.309 Chirality : 0.037 0.244 1690 Planarity : 0.003 0.033 1452 Dihedral : 25.776 166.445 2389 Min Nonbonded Distance : 1.669 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.06 % Allowed : 22.00 % Favored : 74.94 % 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: 0.58 (0.28), residues: 956 helix: 1.73 (0.24), residues: 516 sheet: -0.36 (0.57), residues: 64 loop : -1.44 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 41 HIS 0.002 0.001 HIS E 408 PHE 0.013 0.001 PHE A 292 TYR 0.014 0.001 TYR E 241 ARG 0.005 0.000 ARG A 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1916.14 seconds wall clock time: 35 minutes 29.29 seconds (2129.29 seconds total)