Starting phenix.real_space_refine on Sun Dec 29 10:11:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y6u_33648/12_2024/7y6u_33648.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6u_33648/12_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/cci-nas-00/data/ceres_data/7y6u_33648/12_2024/7y6u_33648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6u_33648/12_2024/7y6u_33648.map" model { file = "/net/cci-nas-00/data/ceres_data/7y6u_33648/12_2024/7y6u_33648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6u_33648/12_2024/7y6u_33648.cif" } 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. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 6.75, per 1000 atoms: 0.68 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 3.04 Conformation dependent library (CDL) restraints added in 1.4 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: 1.44 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: 4.86 Time building geometry restraints manager: 3.46 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: 0.00 - 1.44: 13221 1.44 - 2.89: 426 2.89 - 4.33: 93 4.33 - 5.77: 45 5.77 - 7.21: 16 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 3.040 nonbonded pdb=" O THR A 137 " pdb=" ND2 ASN A 140 " model vdw 2.197 3.120 nonbonded pdb=" O SER A 63 " pdb=" NE2 GLN A 205 " model vdw 2.199 3.120 nonbonded pdb=" OG1 THR A1234 " pdb=" OD1 ASP A1236 " model vdw 2.214 3.040 nonbonded pdb=" OD1 ASP A 265 " pdb=" N SER A 266 " model vdw 2.236 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 27.880 Find NCS groups from input model: 0.190 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.290 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.993 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: 0.1918 time to fit residues: 8.8347 Evaluate side-chains 19 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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: 5.9990 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 276 ASN A 876 ASN ** A1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 10127 Z= 0.373 Angle : 0.685 8.995 13801 Z= 0.344 Chirality : 0.048 0.299 1707 Planarity : 0.004 0.068 1728 Dihedral : 15.751 106.085 2123 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.22 % Favored : 93.54 % Rotamer: Outliers : 0.19 % Allowed : 5.53 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.24), residues: 1222 helix: 1.32 (0.34), residues: 233 sheet: -0.65 (0.29), residues: 324 loop : -0.79 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 65 HIS 0.004 0.001 HIS A 110 PHE 0.013 0.001 PHE A 374 TYR 0.018 0.001 TYR A 563 ARG 0.004 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 to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 1.133 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.1719 time to fit residues: 8.0213 Evaluate side-chains 20 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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: 5.9990 chunk 34 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 89 optimal weight: 0.0070 chunk 109 optimal weight: 3.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 571 ASN A1120 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10127 Z= 0.180 Angle : 0.609 9.365 13801 Z= 0.299 Chirality : 0.047 0.314 1707 Planarity : 0.004 0.073 1728 Dihedral : 12.370 104.087 2123 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.81 % Favored : 93.94 % Rotamer: Outliers : 1.53 % Allowed : 7.53 % Favored : 90.94 % 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: -0.48 (0.24), residues: 1222 helix: 1.48 (0.34), residues: 234 sheet: -0.58 (0.29), residues: 329 loop : -0.80 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 65 HIS 0.004 0.001 HIS A 157 PHE 0.012 0.001 PHE A 374 TYR 0.016 0.001 TYR A 563 ARG 0.003 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 34 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 18 time to evaluate : 1.128 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 34 average time/residue: 0.1511 time to fit residues: 9.6215 Evaluate side-chains 26 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 17 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 1143 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 10127 Z= 0.354 Angle : 0.659 9.407 13801 Z= 0.327 Chirality : 0.047 0.314 1707 Planarity : 0.004 0.072 1728 Dihedral : 11.149 105.350 2123 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.81 % Favored : 93.94 % Rotamer: Outliers : 1.43 % Allowed : 9.06 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.59 (0.24), residues: 1222 helix: 1.28 (0.34), residues: 238 sheet: -0.66 (0.29), residues: 330 loop : -0.84 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 65 HIS 0.004 0.001 HIS A 110 PHE 0.012 0.001 PHE A 374 TYR 0.015 0.001 TYR A 563 ARG 0.001 0.000 ARG A 146 *********************** 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 34 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 19 time to evaluate : 1.021 Fit side-chains REVERT: A 317 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8291 (pm20) outliers start: 15 outliers final: 9 residues processed: 34 average time/residue: 0.1583 time to fit residues: 9.6709 Evaluate side-chains 28 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 18 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 166 ILE 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 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: 4.9990 chunk 1 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 0 optimal weight: 0.9980 chunk 60 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10127 Z= 0.336 Angle : 0.637 9.335 13801 Z= 0.319 Chirality : 0.047 0.325 1707 Planarity : 0.004 0.072 1728 Dihedral : 10.712 105.508 2123 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.81 % Favored : 93.94 % Rotamer: Outliers : 1.91 % Allowed : 10.96 % Favored : 87.13 % 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: -0.67 (0.24), residues: 1222 helix: 1.24 (0.34), residues: 239 sheet: -0.72 (0.30), residues: 320 loop : -0.90 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 65 HIS 0.004 0.001 HIS A 110 PHE 0.012 0.001 PHE A 374 TYR 0.015 0.001 TYR A 563 ARG 0.002 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 38 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 18 time to evaluate : 1.052 Fit side-chains REVERT: A 214 MET cc_start: 0.7904 (mtt) cc_final: 0.7654 (mmt) REVERT: A 317 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8289 (pm20) REVERT: A 635 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8785 (mm) outliers start: 20 outliers final: 14 residues processed: 37 average time/residue: 0.1546 time to fit residues: 10.3541 Evaluate side-chains 33 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 17 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 192 VAL 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 635 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10127 Z= 0.167 Angle : 0.582 9.467 13801 Z= 0.289 Chirality : 0.046 0.327 1707 Planarity : 0.004 0.070 1728 Dihedral : 10.293 103.895 2123 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.99 % Favored : 94.76 % Rotamer: Outliers : 1.91 % Allowed : 11.73 % Favored : 86.37 % 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: -0.49 (0.24), residues: 1222 helix: 1.50 (0.34), residues: 235 sheet: -0.58 (0.30), residues: 317 loop : -0.82 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 65 HIS 0.002 0.000 HIS A 249 PHE 0.010 0.001 PHE A 374 TYR 0.016 0.001 TYR A 563 ARG 0.002 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 40 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 20 time to evaluate : 1.076 Fit side-chains REVERT: A 317 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7898 (pm20) outliers start: 20 outliers final: 16 residues processed: 39 average time/residue: 0.1476 time to fit residues: 10.5301 Evaluate side-chains 34 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 17 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 166 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10127 Z= 0.240 Angle : 0.594 9.443 13801 Z= 0.295 Chirality : 0.046 0.327 1707 Planarity : 0.004 0.067 1728 Dihedral : 10.177 104.271 2123 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.56 % Favored : 94.11 % Rotamer: Outliers : 2.10 % Allowed : 12.11 % Favored : 85.80 % 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: -0.51 (0.24), residues: 1222 helix: 1.46 (0.34), residues: 235 sheet: -0.57 (0.30), residues: 317 loop : -0.85 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 65 HIS 0.003 0.001 HIS A 110 PHE 0.011 0.001 PHE A 374 TYR 0.015 0.001 TYR A 563 ARG 0.002 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 40 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 18 time to evaluate : 1.140 Fit side-chains REVERT: A 317 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7922 (pm20) REVERT: A 1238 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9131 (tp) outliers start: 22 outliers final: 17 residues processed: 39 average time/residue: 0.1523 time to fit residues: 11.0270 Evaluate side-chains 37 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 18 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 192 VAL 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 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 1238 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 92 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 ASN ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 10127 Z= 0.309 Angle : 0.623 9.384 13801 Z= 0.310 Chirality : 0.046 0.328 1707 Planarity : 0.004 0.065 1728 Dihedral : 10.183 105.162 2123 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.65 % Favored : 94.11 % Rotamer: Outliers : 2.48 % Allowed : 12.01 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.61 (0.24), residues: 1222 helix: 1.34 (0.34), residues: 239 sheet: -0.67 (0.30), residues: 314 loop : -0.89 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 439 HIS 0.004 0.001 HIS A 110 PHE 0.013 0.001 PHE A 374 TYR 0.016 0.001 TYR A 563 ARG 0.002 0.000 ARG A 146 *********************** 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 43 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 17 time to evaluate : 1.067 Fit side-chains revert: symmetry clash REVERT: A 317 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8301 (pm20) REVERT: A 635 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8795 (mm) REVERT: A 1238 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9109 (tp) outliers start: 26 outliers final: 19 residues processed: 42 average time/residue: 0.1519 time to fit residues: 11.8218 Evaluate side-chains 39 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 17 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 192 VAL 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 628 ILE Chi-restraints excluded: chain A residue 635 LEU 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 Chi-restraints excluded: chain A residue 1232 ASN Chi-restraints excluded: chain A residue 1238 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10127 Z= 0.179 Angle : 0.587 9.468 13801 Z= 0.290 Chirality : 0.046 0.329 1707 Planarity : 0.004 0.066 1728 Dihedral : 9.971 103.751 2123 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.99 % Favored : 94.68 % Rotamer: Outliers : 2.10 % Allowed : 12.20 % Favored : 85.70 % 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: -0.50 (0.24), residues: 1222 helix: 1.51 (0.34), residues: 235 sheet: -0.55 (0.30), residues: 317 loop : -0.87 (0.24), residues: 670 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 0.009 0.001 PHE A 374 TYR 0.017 0.001 TYR A 563 ARG 0.003 0.000 ARG A 146 *********************** 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 40 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 18 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: A 317 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7848 (pm20) REVERT: A 635 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8847 (mm) REVERT: A 1238 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9159 (tp) outliers start: 22 outliers final: 17 residues processed: 39 average time/residue: 0.1517 time to fit residues: 11.1416 Evaluate side-chains 37 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 17 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 192 VAL 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 635 LEU 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 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: 6.9990 chunk 54 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10127 Z= 0.213 Angle : 0.590 9.482 13801 Z= 0.291 Chirality : 0.046 0.330 1707 Planarity : 0.004 0.065 1728 Dihedral : 9.821 103.530 2123 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.48 % Favored : 94.19 % Rotamer: Outliers : 2.00 % Allowed : 12.30 % Favored : 85.70 % 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: -0.51 (0.24), residues: 1222 helix: 1.50 (0.34), residues: 239 sheet: -0.56 (0.30), residues: 317 loop : -0.89 (0.24), residues: 666 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 0.010 0.001 PHE A 374 TYR 0.016 0.001 TYR A 563 ARG 0.002 0.000 ARG A 146 ********************** 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 40 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 19 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 317 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7899 (pm20) REVERT: A 635 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8833 (mm) outliers start: 21 outliers final: 17 residues processed: 39 average time/residue: 0.1509 time to fit residues: 10.8397 Evaluate side-chains 35 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 16 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 192 VAL 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 635 LEU 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 1232 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.9990 chunk 89 optimal weight: 0.0170 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 99 optimal weight: 0.3980 chunk 12 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.063152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.047045 restraints weight = 44079.949| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 4.84 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10127 Z= 0.145 Angle : 0.578 9.527 13801 Z= 0.283 Chirality : 0.045 0.333 1707 Planarity : 0.004 0.064 1728 Dihedral : 9.404 101.693 2123 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.83 % Favored : 94.84 % Rotamer: Outliers : 1.91 % Allowed : 12.58 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.42 (0.25), residues: 1222 helix: 1.68 (0.35), residues: 235 sheet: -0.50 (0.30), residues: 316 loop : -0.86 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 65 HIS 0.003 0.000 HIS A 110 PHE 0.008 0.001 PHE A 374 TYR 0.031 0.001 TYR A 237 ARG 0.002 0.000 ARG A 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1955.36 seconds wall clock time: 37 minutes 21.62 seconds (2241.62 seconds total)