Starting phenix.real_space_refine on Thu Mar 14 22:14:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6u_33648/03_2024/7y6u_33648.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6u_33648/03_2024/7y6u_33648.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6u_33648/03_2024/7y6u_33648.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6u_33648/03_2024/7y6u_33648.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6u_33648/03_2024/7y6u_33648.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6u_33648/03_2024/7y6u_33648.pdb" } resolution = 3.2 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= 0.039 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: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 6266 2.51 5 N 1583 2.21 5 O 2025 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 679": "OD1" <-> "OD2" Residue "A PHE 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1245": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9915 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 9398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1224, 9398 Classifications: {'peptide': 1224} Link IDs: {'PTRANS': 47, 'TRANS': 1176} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.95, per 1000 atoms: 0.60 Number of scatterers: 9915 At special positions: 0 Unit cell: (119.78, 99.64, 167.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 2025 8.00 N 1583 7.00 C 6266 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 234 " distance=2.02 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 373 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 473 " distance=2.03 Simple disulfide: pdb=" SG CYS A 543 " - pdb=" SG CYS A 589 " distance=2.03 Simple disulfide: pdb=" SG CYS A 572 " - pdb=" SG CYS A 599 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 700 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 808 " - pdb=" SG CYS A 830 " distance=2.03 Simple disulfide: pdb=" SG CYS A 920 " - pdb=" SG CYS A 931 " distance=2.03 Simple disulfide: pdb=" SG CYS A1122 " - pdb=" SG CYS A1133 " distance=2.03 Simple disulfide: pdb=" SG CYS A1173 " - pdb=" SG CYS A1226 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " BETA1-6 " NAG B 1 " - " FUC B 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG D 1 " - " FUC D 2 " " NAG G 1 " - " FUC G 2 " " NAG L 1 " - " FUC L 4 " NAG-ASN " NAG A1501 " - " ASN A 118 " " NAG A1502 " - " ASN A 514 " " NAG A1503 " - " ASN A 556 " " NAG A1504 " - " ASN A 667 " " NAG A1505 " - " ASN A 743 " " NAG A1506 " - " ASN A 787 " " NAG A1507 " - " ASN A1009 " " NAG B 1 " - " ASN A 216 " " NAG C 1 " - " ASN A 264 " " NAG D 1 " - " ASN A 300 " " NAG E 1 " - " ASN A 324 " " NAG F 1 " - " ASN A 344 " " NAG G 1 " - " ASN A 351 " " NAG H 1 " - " ASN A 425 " " NAG I 1 " - " ASN A 688 " " NAG J 1 " - " ASN A 781 " " NAG K 1 " - " ASN A 873 " " NAG L 1 " - " ASN A1232 " Time building additional restraints: 4.74 Conformation dependent library (CDL) restraints added in 1.7 seconds 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 19 sheets defined 22.1% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 32 through 38 removed outlier: 3.591A pdb=" N PHE A 36 " --> pdb=" O PHE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.857A pdb=" N TYR A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA A 238 " --> pdb=" O CYS A 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 238' Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 466 through 475 Processing helix chain 'A' and resid 807 through 814 Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.720A pdb=" N GLN A 821 " --> pdb=" O SER A 817 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 822 " --> pdb=" O ARG A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 827 No H-bonds generated for 'chain 'A' and resid 825 through 827' Processing helix chain 'A' and resid 828 through 852 removed outlier: 4.059A pdb=" N ILE A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU A 834 " --> pdb=" O CYS A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 861 removed outlier: 3.533A pdb=" N LEU A 861 " --> pdb=" O GLU A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 904 removed outlier: 3.522A pdb=" N LYS A 904 " --> pdb=" O LEU A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 914 Processing helix chain 'A' and resid 928 through 935 Processing helix chain 'A' and resid 946 through 961 Processing helix chain 'A' and resid 967 through 971 removed outlier: 3.504A pdb=" N ALA A 970 " --> pdb=" O THR A 967 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 971 " --> pdb=" O ALA A 968 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 967 through 971' Processing helix chain 'A' and resid 973 through 986 removed outlier: 3.575A pdb=" N LEU A 985 " --> pdb=" O ARG A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1016 removed outlier: 3.619A pdb=" N GLN A 996 " --> pdb=" O LEU A 992 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU A 999 " --> pdb=" O ASN A 995 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A1016 " --> pdb=" O SER A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1055 removed outlier: 3.823A pdb=" N GLN A1045 " --> pdb=" O VAL A1041 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY A1046 " --> pdb=" O VAL A1042 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN A1055 " --> pdb=" O GLN A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1058 No H-bonds generated for 'chain 'A' and resid 1056 through 1058' Processing helix chain 'A' and resid 1066 through 1074 Processing helix chain 'A' and resid 1075 through 1123 removed outlier: 3.544A pdb=" N VAL A1081 " --> pdb=" O PRO A1077 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A1086 " --> pdb=" O GLN A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1193 through 1197 removed outlier: 4.127A pdb=" N HIS A1197 " --> pdb=" O LEU A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1218 No H-bonds generated for 'chain 'A' and resid 1216 through 1218' Processing helix chain 'A' and resid 1237 through 1242 Processing helix chain 'A' and resid 1247 through 1253 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 75 removed outlier: 3.643A pdb=" N ALA A 74 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 192 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A 92 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE A 125 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASN A 147 " --> pdb=" O GLN A 127 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 75 removed outlier: 3.643A pdb=" N ALA A 74 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 192 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A 92 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 181 through 184 Processing sheet with id=AA5, first strand: chain 'A' and resid 270 through 288 removed outlier: 5.123A pdb=" N LYS A 272 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL A 453 " --> pdb=" O LYS A 272 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL A 274 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ILE A 451 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ASN A 276 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA A 449 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL A 447 " --> pdb=" O PRO A 278 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N SER A 443 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU A 284 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE A 441 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ALA A 286 " --> pdb=" O TRP A 439 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TRP A 439 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL A 406 " --> pdb=" O TYR A 413 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 270 through 288 removed outlier: 5.123A pdb=" N LYS A 272 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL A 453 " --> pdb=" O LYS A 272 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL A 274 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ILE A 451 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ASN A 276 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA A 449 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL A 447 " --> pdb=" O PRO A 278 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N SER A 443 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU A 284 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE A 441 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ALA A 286 " --> pdb=" O TRP A 439 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TRP A 439 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG A 460 " --> pdb=" O GLU A 452 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLN A 454 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ILE A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 294 through 298 removed outlier: 4.929A pdb=" N ILE A 335 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN A 344 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR A 371 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A 389 " --> pdb=" O CYS A 373 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N PHE A 375 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N PHE A 387 " --> pdb=" O PHE A 375 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL A 377 " --> pdb=" O TYR A 385 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N TYR A 385 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 483 through 488 removed outlier: 3.619A pdb=" N GLY A 715 " --> pdb=" O ALA A 707 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL A 709 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE A 713 " --> pdb=" O VAL A 709 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 499 through 502 removed outlier: 5.532A pdb=" N LEU A 684 " --> pdb=" O VAL A 697 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 510 through 513 removed outlier: 6.749A pdb=" N TYR A 619 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL A 590 " --> pdb=" O TYR A 619 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLN A 621 " --> pdb=" O PHE A 588 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE A 588 " --> pdb=" O GLN A 621 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR A 623 " --> pdb=" O SER A 586 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY A 625 " --> pdb=" O SER A 584 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N SER A 584 " --> pdb=" O GLY A 625 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 510 through 513 Processing sheet with id=AB3, first strand: chain 'A' and resid 528 through 535 removed outlier: 4.660A pdb=" N LEU A 529 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLY A 522 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL A 517 " --> pdb=" O ASN A 556 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N THR A 558 " --> pdb=" O VAL A 517 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA A 519 " --> pdb=" O THR A 558 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 565 through 568 Processing sheet with id=AB5, first strand: chain 'A' and resid 749 through 751 Processing sheet with id=AB6, first strand: chain 'A' and resid 780 through 786 removed outlier: 3.917A pdb=" N GLY A 780 " --> pdb=" O ALA A1168 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE A1167 " --> pdb=" O THR A1191 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A1191 " --> pdb=" O ILE A1167 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 789 through 798 removed outlier: 7.266A pdb=" N GLY A1150 " --> pdb=" O ALA A1146 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ALA A1146 " --> pdb=" O GLY A1150 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU A1152 " --> pdb=" O VAL A1144 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N VAL A1144 " --> pdb=" O LEU A1152 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU A1154 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER A1142 " --> pdb=" O LEU A1154 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N THR A1156 " --> pdb=" O ILE A1140 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 804 through 806 Processing sheet with id=AB9, first strand: chain 'A' and resid 881 through 882 Processing sheet with id=AC1, first strand: chain 'A' and resid 1220 through 1223 removed outlier: 3.745A pdb=" N ALA A1179 " --> pdb=" O ILE A1223 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 1002 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.69 Time building geometry restraints manager: 5.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3123 1.34 - 1.46: 2378 1.46 - 1.58: 4574 1.58 - 1.69: 1 1.69 - 1.81: 51 Bond restraints: 10127 Sorted by residual: bond pdb=" C1 BMA K 3 " pdb=" C2 BMA K 3 " ideal model delta sigma weight residual 1.519 1.603 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C1 BMA K 3 " pdb=" O5 BMA K 3 " ideal model delta sigma weight residual 1.410 1.468 -0.058 2.00e-02 2.50e+03 8.37e+00 bond pdb=" C PRO A1076 " pdb=" N PRO A1077 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.30e-02 5.92e+03 3.95e+00 bond pdb=" C1 BMA I 3 " pdb=" C2 BMA I 3 " ideal model delta sigma weight residual 1.519 1.555 -0.036 2.00e-02 2.50e+03 3.26e+00 ... (remaining 10122 not shown) Histogram of bond angle deviations from ideal: 100.33 - 107.06: 281 107.06 - 113.78: 5862 113.78 - 120.51: 3584 120.51 - 127.23: 3995 127.23 - 133.96: 79 Bond angle restraints: 13801 Sorted by residual: angle pdb=" C SER A 63 " pdb=" CA SER A 63 " pdb=" CB SER A 63 " ideal model delta sigma weight residual 116.54 109.72 6.82 1.15e+00 7.56e-01 3.51e+01 angle pdb=" CA SER A 63 " pdb=" C SER A 63 " pdb=" N THR A 64 " ideal model delta sigma weight residual 119.52 116.19 3.33 7.90e-01 1.60e+00 1.78e+01 angle pdb=" C GLN A 368 " pdb=" N VAL A 369 " pdb=" CA VAL A 369 " ideal model delta sigma weight residual 122.13 128.84 -6.71 1.85e+00 2.92e-01 1.32e+01 angle pdb=" C ASN A 688 " pdb=" N VAL A 689 " pdb=" CA VAL A 689 " ideal model delta sigma weight residual 121.97 127.74 -5.77 1.80e+00 3.09e-01 1.03e+01 angle pdb=" N SER A 63 " pdb=" CA SER A 63 " pdb=" C SER A 63 " ideal model delta sigma weight residual 108.31 113.13 -4.82 1.52e+00 4.33e-01 1.01e+01 ... (remaining 13796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.85: 6042 23.85 - 47.70: 285 47.70 - 71.54: 52 71.54 - 95.39: 58 95.39 - 119.24: 36 Dihedral angle restraints: 6473 sinusoidal: 2925 harmonic: 3548 Sorted by residual: dihedral pdb=" CB CYS A 920 " pdb=" SG CYS A 920 " pdb=" SG CYS A 931 " pdb=" CB CYS A 931 " ideal model delta sinusoidal sigma weight residual -86.00 -174.27 88.27 1 1.00e+01 1.00e-02 9.31e+01 dihedral pdb=" CB CYS A 230 " pdb=" SG CYS A 230 " pdb=" SG CYS A 234 " pdb=" CB CYS A 234 " ideal model delta sinusoidal sigma weight residual 93.00 144.54 -51.54 1 1.00e+01 1.00e-02 3.63e+01 dihedral pdb=" CB CYS A 808 " pdb=" SG CYS A 808 " pdb=" SG CYS A 830 " pdb=" CB CYS A 830 " ideal model delta sinusoidal sigma weight residual -86.00 -136.58 50.58 1 1.00e+01 1.00e-02 3.50e+01 ... (remaining 6470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1403 0.058 - 0.116: 260 0.116 - 0.175: 29 0.175 - 0.233: 4 0.233 - 0.291: 11 Chirality restraints: 1707 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN A1232 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 688 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 1704 not shown) Planarity restraints: 1746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 466 " 0.038 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO A 467 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 467 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 467 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 128 " 0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO A 129 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A1075 " -0.025 5.00e-02 4.00e+02 3.77e-02 2.27e+00 pdb=" N PRO A1076 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A1076 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1076 " -0.021 5.00e-02 4.00e+02 ... (remaining 1743 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 406 2.72 - 3.26: 10312 3.26 - 3.81: 16044 3.81 - 4.35: 19269 4.35 - 4.90: 32501 Nonbonded interactions: 78532 Sorted by model distance: nonbonded pdb=" O PRO A 498 " pdb=" OG1 THR A 650 " model vdw 2.170 2.440 nonbonded pdb=" O THR A 137 " pdb=" ND2 ASN A 140 " model vdw 2.197 2.520 nonbonded pdb=" O SER A 63 " pdb=" NE2 GLN A 205 " model vdw 2.199 2.520 nonbonded pdb=" OG1 THR A1234 " pdb=" OD1 ASP A1236 " model vdw 2.214 2.440 nonbonded pdb=" OD1 ASP A 265 " pdb=" N SER A 266 " model vdw 2.236 2.520 ... (remaining 78527 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 'B' selection = chain 'L' } ncs_group { reference = (chain 'D' and resid 1) selection = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'J' and resid 1) } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'K' } 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: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.300 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 33.060 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 10127 Z= 0.255 Angle : 0.688 7.214 13801 Z= 0.320 Chirality : 0.050 0.291 1707 Planarity : 0.003 0.058 1728 Dihedral : 18.856 119.240 4166 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.48 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.28 (0.25), residues: 1222 helix: 1.55 (0.36), residues: 221 sheet: -0.50 (0.31), residues: 300 loop : -0.57 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 189 HIS 0.002 0.000 HIS A 110 PHE 0.022 0.001 PHE A 100 TYR 0.007 0.001 TYR A1071 ARG 0.002 0.000 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 1.125 Fit side-chains REVERT: A 158 MET cc_start: 0.8753 (pmm) cc_final: 0.8552 (pmm) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1787 time to fit residues: 8.4451 Evaluate side-chains 19 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 6.9990 chunk 92 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 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 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10127 Z= 0.299 Angle : 0.646 9.300 13801 Z= 0.321 Chirality : 0.047 0.286 1707 Planarity : 0.004 0.067 1728 Dihedral : 15.594 105.015 2123 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.22 % Favored : 93.54 % Rotamer: Outliers : 0.19 % Allowed : 5.24 % Favored : 94.57 % 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: -0.46 (0.24), residues: 1222 helix: 1.47 (0.35), residues: 233 sheet: -0.54 (0.29), residues: 324 loop : -0.79 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 65 HIS 0.003 0.001 HIS A 110 PHE 0.013 0.001 PHE A 374 TYR 0.018 0.001 TYR A 563 ARG 0.002 0.000 ARG A 547 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 1.170 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.1747 time to fit residues: 8.0283 Evaluate side-chains 20 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 18 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 398 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 119 optimal weight: 0.0980 chunk 98 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 89 optimal weight: 0.0040 chunk 109 optimal weight: 3.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 GLN A 459 GLN ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10127 Z= 0.165 Angle : 0.585 9.306 13801 Z= 0.284 Chirality : 0.046 0.300 1707 Planarity : 0.004 0.072 1728 Dihedral : 11.692 103.617 2123 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.89 % Favored : 93.86 % Rotamer: Outliers : 1.33 % Allowed : 7.34 % Favored : 91.33 % 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: -0.36 (0.25), residues: 1222 helix: 1.66 (0.35), residues: 234 sheet: -0.46 (0.29), residues: 329 loop : -0.79 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 65 HIS 0.004 0.001 HIS A 157 PHE 0.012 0.001 PHE A 374 TYR 0.014 0.001 TYR A 563 ARG 0.002 0.000 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 19 time to evaluate : 1.144 Fit side-chains REVERT: A 795 GLU cc_start: 0.8138 (tp30) cc_final: 0.7924 (tp30) outliers start: 14 outliers final: 9 residues processed: 32 average time/residue: 0.1541 time to fit residues: 9.1680 Evaluate side-chains 26 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 17 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 991 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 58 optimal weight: 0.4980 chunk 105 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1120 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10127 Z= 0.338 Angle : 0.630 9.415 13801 Z= 0.310 Chirality : 0.046 0.302 1707 Planarity : 0.004 0.070 1728 Dihedral : 10.609 105.153 2123 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.06 % Favored : 93.70 % Rotamer: Outliers : 1.43 % Allowed : 8.96 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.24), residues: 1222 helix: 1.46 (0.35), residues: 238 sheet: -0.56 (0.29), residues: 326 loop : -0.88 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 65 HIS 0.004 0.001 HIS A 78 PHE 0.012 0.001 PHE A 374 TYR 0.014 0.001 TYR A 676 ARG 0.002 0.000 ARG A1090 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 18 time to evaluate : 1.070 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 12 residues processed: 32 average time/residue: 0.1513 time to fit residues: 9.0215 Evaluate side-chains 29 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 17 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1174 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10127 Z= 0.205 Angle : 0.574 9.398 13801 Z= 0.283 Chirality : 0.045 0.313 1707 Planarity : 0.004 0.068 1728 Dihedral : 10.162 104.097 2123 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.73 % Favored : 94.03 % Rotamer: Outliers : 1.53 % Allowed : 10.20 % Favored : 88.27 % 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: -0.44 (0.25), residues: 1222 helix: 1.61 (0.35), residues: 234 sheet: -0.52 (0.30), residues: 312 loop : -0.84 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 65 HIS 0.003 0.001 HIS A 110 PHE 0.011 0.001 PHE A 374 TYR 0.014 0.001 TYR A 563 ARG 0.001 0.000 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 18 time to evaluate : 1.067 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 34 average time/residue: 0.1518 time to fit residues: 9.5890 Evaluate side-chains 30 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 17 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1174 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 118 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10127 Z= 0.178 Angle : 0.562 9.467 13801 Z= 0.277 Chirality : 0.045 0.317 1707 Planarity : 0.004 0.065 1728 Dihedral : 9.594 103.190 2123 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.40 % Favored : 94.35 % Rotamer: Outliers : 2.00 % Allowed : 10.30 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.38 (0.25), residues: 1222 helix: 1.70 (0.35), residues: 235 sheet: -0.49 (0.30), residues: 311 loop : -0.82 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 65 HIS 0.002 0.001 HIS A 110 PHE 0.009 0.001 PHE A 374 TYR 0.015 0.001 TYR A 563 ARG 0.001 0.000 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 20 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: A 317 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8080 (pm20) outliers start: 21 outliers final: 17 residues processed: 41 average time/residue: 0.1587 time to fit residues: 11.8668 Evaluate side-chains 35 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 17 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1174 VAL Chi-restraints excluded: chain A residue 1176 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.9990 chunk 67 optimal weight: 0.3980 chunk 86 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1195 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10127 Z= 0.167 Angle : 0.553 9.492 13801 Z= 0.271 Chirality : 0.045 0.320 1707 Planarity : 0.003 0.062 1728 Dihedral : 9.229 102.528 2123 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.24 % Favored : 94.52 % Rotamer: Outliers : 1.81 % Allowed : 11.25 % Favored : 86.94 % 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: -0.37 (0.25), residues: 1222 helix: 1.73 (0.35), residues: 235 sheet: -0.50 (0.30), residues: 312 loop : -0.81 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 65 HIS 0.002 0.000 HIS A 110 PHE 0.010 0.001 PHE A 374 TYR 0.013 0.001 TYR A 563 ARG 0.001 0.000 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 20 time to evaluate : 1.020 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 16 residues processed: 39 average time/residue: 0.1432 time to fit residues: 10.1533 Evaluate side-chains 35 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 19 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1174 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.3980 chunk 70 optimal weight: 7.9990 chunk 35 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 0.0980 chunk 74 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10127 Z= 0.143 Angle : 0.548 9.533 13801 Z= 0.267 Chirality : 0.044 0.325 1707 Planarity : 0.003 0.060 1728 Dihedral : 8.945 101.378 2123 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.99 % Favored : 94.76 % Rotamer: Outliers : 2.10 % Allowed : 11.25 % Favored : 86.65 % 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: -0.32 (0.25), residues: 1222 helix: 1.82 (0.35), residues: 235 sheet: -0.44 (0.30), residues: 311 loop : -0.82 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 65 HIS 0.002 0.000 HIS A 110 PHE 0.008 0.001 PHE A 374 TYR 0.014 0.001 TYR A 563 ARG 0.001 0.000 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 22 time to evaluate : 1.239 Fit side-chains revert: symmetry clash REVERT: A 317 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7469 (pm20) outliers start: 22 outliers final: 20 residues processed: 44 average time/residue: 0.1957 time to fit residues: 14.2059 Evaluate side-chains 40 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 19 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1174 VAL Chi-restraints excluded: chain A residue 1176 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.6980 chunk 102 optimal weight: 0.1980 chunk 109 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 99 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 ASN ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10127 Z= 0.141 Angle : 0.556 9.556 13801 Z= 0.269 Chirality : 0.044 0.327 1707 Planarity : 0.004 0.059 1728 Dihedral : 8.739 100.719 2123 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.07 % Favored : 94.68 % Rotamer: Outliers : 2.38 % Allowed : 11.53 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.25), residues: 1222 helix: 1.86 (0.35), residues: 235 sheet: -0.43 (0.30), residues: 311 loop : -0.79 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 65 HIS 0.002 0.000 HIS A 110 PHE 0.009 0.001 PHE A 374 TYR 0.014 0.001 TYR A 563 ARG 0.013 0.000 ARG A1073 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 21 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7556 (pm20) REVERT: A 1238 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9172 (tp) outliers start: 25 outliers final: 21 residues processed: 45 average time/residue: 0.1350 time to fit residues: 10.9891 Evaluate side-chains 43 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 20 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1176 ASP Chi-restraints excluded: chain A residue 1232 ASN Chi-restraints excluded: chain A residue 1238 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 7.9990 chunk 54 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 96 optimal weight: 0.0370 chunk 10 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 ASN ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10127 Z= 0.150 Angle : 0.552 9.549 13801 Z= 0.267 Chirality : 0.045 0.328 1707 Planarity : 0.004 0.060 1728 Dihedral : 8.603 100.578 2123 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.83 % Favored : 94.93 % Rotamer: Outliers : 2.48 % Allowed : 11.63 % Favored : 85.89 % 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 (0.25), residues: 1222 helix: 1.87 (0.35), residues: 235 sheet: -0.38 (0.30), residues: 316 loop : -0.77 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 65 HIS 0.002 0.000 HIS A 110 PHE 0.009 0.001 PHE A 374 TYR 0.015 0.001 TYR A 563 ARG 0.013 0.000 ARG A1073 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 19 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7601 (pm20) outliers start: 26 outliers final: 22 residues processed: 45 average time/residue: 0.1467 time to fit residues: 11.8892 Evaluate side-chains 41 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 18 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1176 ASP Chi-restraints excluded: chain A residue 1232 ASN Chi-restraints excluded: chain A residue 1248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.1980 chunk 89 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 ASN ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.062902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.046595 restraints weight = 44215.417| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 4.83 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10127 Z= 0.238 Angle : 0.584 9.472 13801 Z= 0.284 Chirality : 0.045 0.326 1707 Planarity : 0.004 0.058 1728 Dihedral : 8.680 102.546 2123 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.07 % Favored : 94.68 % Rotamer: Outliers : 2.19 % Allowed : 11.82 % Favored : 85.99 % 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 (0.25), residues: 1222 helix: 1.75 (0.35), residues: 239 sheet: -0.47 (0.30), residues: 318 loop : -0.81 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 65 HIS 0.003 0.001 HIS A 110 PHE 0.011 0.001 PHE A 374 TYR 0.014 0.001 TYR A 563 ARG 0.012 0.000 ARG A1073 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1985.92 seconds wall clock time: 36 minutes 53.44 seconds (2213.44 seconds total)