Starting phenix.real_space_refine on Thu Jul 2 21:13:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y6u_33648/07_2026/7y6u_33648.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6u_33648/07_2026/7y6u_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7y6u_33648/07_2026/7y6u_33648.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y6u_33648/07_2026/7y6u_33648.cif" model { file = "/net/cci-nas-00/data/ceres_data/7y6u_33648/07_2026/7y6u_33648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6u_33648/07_2026/7y6u_33648.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y6u_33648/07_2026/7y6u_33648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6u_33648/07_2026/7y6u_33648.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 7 Time building chain proxies: 1.97, per 1000 atoms: 0.20 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: 0.91 Conformation dependent library (CDL) restraints added in 262.0 milliseconds 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: 0.33 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: 1.89 Time building geometry restraints manager: 1.13 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 - 17.77: 5246 17.77 - 35.55: 336 35.55 - 53.32: 60 53.32 - 71.10: 10 71.10 - 88.87: 15 Dihedral angle restraints: 5667 sinusoidal: 2119 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 5664 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: 3.380 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.100 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 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 10180 Z= 0.200 Angle : 0.722 17.921 13947 Z= 0.329 Chirality : 0.050 0.291 1707 Planarity : 0.003 0.058 1728 Dihedral : 13.088 88.872 3360 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG A 146 TYR 0.007 0.001 TYR A1071 PHE 0.022 0.001 PHE A 100 TRP 0.002 0.000 TRP A 189 HIS 0.002 0.000 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.20 (10127) covalent geometry : angle 0.68821 / 0.32 (13801) SS BOND : bond 0.00233 / 0.12 ( 13) SS BOND : angle 1.56520 / 1.43 ( 26) hydrogen bonds : bond 0.22487 / 14.56 ( 345) hydrogen bonds : angle 8.58118 / 6.20 ( 1002) link_ALPHA1-3 : bond 0.00471 / 0.25 ( 1) link_ALPHA1-3 : angle 1.65082 / 1.14 ( 3) link_ALPHA1-6 : bond 0.00381 / 0.20 ( 1) link_ALPHA1-6 : angle 1.47043 / 1.20 ( 3) link_BETA1-4 : bond 0.01112 / 0.53 ( 16) link_BETA1-4 : angle 3.18265 / 1.66 ( 48) link_BETA1-6 : bond 0.00462 / 0.23 ( 4) link_BETA1-6 : angle 1.42485 / 0.95 ( 12) link_NAG-ASN : bond 0.00293 / 0.13 ( 18) link_NAG-ASN : angle 1.62152 / 1.30 ( 54) *********************** 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 : 0.369 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: 0.0728 time to fit residues: 3.4237 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 : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 876 ASN A1120 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.063596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.047432 restraints weight = 44583.374| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 4.78 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10180 Z= 0.134 Angle : 0.632 18.626 13947 Z= 0.313 Chirality : 0.046 0.329 1707 Planarity : 0.004 0.068 1728 Dihedral : 4.722 25.004 1317 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.48 % Favored : 94.19 % Rotamer: Outliers : 0.19 % Allowed : 4.58 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.24), residues: 1222 helix: 1.47 (0.34), residues: 233 sheet: -0.52 (0.29), residues: 327 loop : -0.70 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 547 TYR 0.019 0.001 TYR A 563 PHE 0.012 0.001 PHE A 296 TRP 0.005 0.001 TRP A 65 HIS 0.002 0.000 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (10127) covalent geometry : angle 0.59510 / 0.30 (13801) SS BOND : bond 0.00304 / 0.16 ( 13) SS BOND : angle 1.33117 / 1.14 ( 26) hydrogen bonds : bond 0.04943 / 3.26 ( 345) hydrogen bonds : angle 5.92991 / 4.37 ( 1002) link_ALPHA1-3 : bond 0.00533 / 0.28 ( 1) link_ALPHA1-3 : angle 1.62737 / 1.12 ( 3) link_ALPHA1-6 : bond 0.00529 / 0.28 ( 1) link_ALPHA1-6 : angle 1.53169 / 1.09 ( 3) link_BETA1-4 : bond 0.01220 / 0.57 ( 16) link_BETA1-4 : angle 3.22236 / 1.69 ( 48) link_BETA1-6 : bond 0.00334 / 0.16 ( 4) link_BETA1-6 : angle 1.16386 / 0.77 ( 12) link_NAG-ASN : bond 0.00307 / 0.15 ( 18) link_NAG-ASN : angle 1.39948 / 1.09 ( 54) *********************** 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 26 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.339 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 25 average time/residue: 0.0846 time to fit residues: 3.6615 Evaluate side-chains 21 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 13 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.062098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.045617 restraints weight = 44776.941| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 4.85 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10180 Z= 0.219 Angle : 0.656 17.812 13947 Z= 0.322 Chirality : 0.046 0.348 1707 Planarity : 0.004 0.074 1728 Dihedral : 4.961 26.879 1317 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.65 % Favored : 94.03 % Rotamer: Outliers : 1.33 % Allowed : 7.44 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.24), residues: 1222 helix: 1.27 (0.34), residues: 238 sheet: -0.65 (0.29), residues: 328 loop : -0.78 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1073 TYR 0.015 0.001 TYR A1071 PHE 0.013 0.001 PHE A 374 TRP 0.004 0.001 TRP A 65 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.22 (10127) covalent geometry : angle 0.61959 / 0.31 (13801) SS BOND : bond 0.00303 / 0.15 ( 13) SS BOND : angle 1.24445 / 1.05 ( 26) hydrogen bonds : bond 0.04587 / 3.04 ( 345) hydrogen bonds : angle 5.40146 / 3.96 ( 1002) link_ALPHA1-3 : bond 0.00355 / 0.19 ( 1) link_ALPHA1-3 : angle 1.77469 / 1.18 ( 3) link_ALPHA1-6 : bond 0.00246 / 0.13 ( 1) link_ALPHA1-6 : angle 1.53292 / 1.23 ( 3) link_BETA1-4 : bond 0.01323 / 0.61 ( 16) link_BETA1-4 : angle 3.13658 / 1.68 ( 48) link_BETA1-6 : bond 0.00281 / 0.14 ( 4) link_BETA1-6 : angle 1.35368 / 0.94 ( 12) link_NAG-ASN : bond 0.00322 / 0.15 ( 18) link_NAG-ASN : angle 1.68984 / 1.32 ( 54) *********************** 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 to be fit. rotamer outliers: 14 poor density : 19 time to evaluate : 0.355 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 33 average time/residue: 0.0645 time to fit residues: 3.8858 Evaluate side-chains 26 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 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 22 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 1 optimal weight: 0.2980 chunk 90 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 HIS A 276 ASN A 322 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.062520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.046217 restraints weight = 44915.009| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 4.80 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10180 Z= 0.142 Angle : 0.617 17.693 13947 Z= 0.304 Chirality : 0.045 0.346 1707 Planarity : 0.004 0.072 1728 Dihedral : 4.802 26.856 1317 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.40 % Favored : 94.27 % Rotamer: Outliers : 1.14 % Allowed : 8.87 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.24), residues: 1222 helix: 1.43 (0.34), residues: 235 sheet: -0.68 (0.29), residues: 316 loop : -0.75 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1073 TYR 0.016 0.001 TYR A 563 PHE 0.011 0.001 PHE A 374 TRP 0.005 0.001 TRP A 65 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (10127) covalent geometry : angle 0.58052 / 0.30 (13801) SS BOND : bond 0.00119 / 0.07 ( 13) SS BOND : angle 1.57643 / 1.46 ( 26) hydrogen bonds : bond 0.04002 / 2.67 ( 345) hydrogen bonds : angle 5.15277 / 3.77 ( 1002) link_ALPHA1-3 : bond 0.00503 / 0.26 ( 1) link_ALPHA1-3 : angle 1.67139 / 1.16 ( 3) link_ALPHA1-6 : bond 0.00320 / 0.17 ( 1) link_ALPHA1-6 : angle 1.46972 / 1.15 ( 3) link_BETA1-4 : bond 0.01240 / 0.57 ( 16) link_BETA1-4 : angle 3.01780 / 1.58 ( 48) link_BETA1-6 : bond 0.00328 / 0.16 ( 4) link_BETA1-6 : angle 1.22002 / 0.83 ( 12) link_NAG-ASN : bond 0.00259 / 0.12 ( 18) link_NAG-ASN : angle 1.48352 / 1.14 ( 54) *********************** 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 30 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 18 time to evaluate : 0.295 Fit side-chains REVERT: A 317 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7873 (pm20) outliers start: 12 outliers final: 8 residues processed: 29 average time/residue: 0.0586 time to fit residues: 3.1201 Evaluate side-chains 27 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 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 1174 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 41 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 73 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.062484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.046228 restraints weight = 44534.548| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 4.80 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10180 Z= 0.145 Angle : 0.597 17.632 13947 Z= 0.293 Chirality : 0.045 0.348 1707 Planarity : 0.004 0.069 1728 Dihedral : 4.722 27.490 1317 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.56 % Favored : 94.11 % Rotamer: Outliers : 1.53 % Allowed : 9.82 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.24), residues: 1222 helix: 1.51 (0.34), residues: 235 sheet: -0.53 (0.30), residues: 317 loop : -0.85 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1073 TYR 0.013 0.001 TYR A 563 PHE 0.010 0.001 PHE A 374 TRP 0.005 0.001 TRP A 65 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (10127) covalent geometry : angle 0.56245 / 0.29 (13801) SS BOND : bond 0.00255 / 0.13 ( 13) SS BOND : angle 1.04418 / 0.86 ( 26) hydrogen bonds : bond 0.03811 / 2.55 ( 345) hydrogen bonds : angle 4.96338 / 3.62 ( 1002) link_ALPHA1-3 : bond 0.00495 / 0.26 ( 1) link_ALPHA1-3 : angle 1.66631 / 1.18 ( 3) link_ALPHA1-6 : bond 0.00297 / 0.16 ( 1) link_ALPHA1-6 : angle 1.45835 / 1.17 ( 3) link_BETA1-4 : bond 0.01226 / 0.56 ( 16) link_BETA1-4 : angle 2.98576 / 1.56 ( 48) link_BETA1-6 : bond 0.00308 / 0.15 ( 4) link_BETA1-6 : angle 1.25204 / 0.86 ( 12) link_NAG-ASN : bond 0.00264 / 0.13 ( 18) link_NAG-ASN : angle 1.45573 / 1.12 ( 54) *********************** 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 36 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 20 time to evaluate : 0.268 Fit side-chains REVERT: A 214 MET cc_start: 0.8065 (mtt) cc_final: 0.7804 (mmt) REVERT: A 317 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.7857 (pm20) outliers start: 16 outliers final: 11 residues processed: 35 average time/residue: 0.0587 time to fit residues: 3.6399 Evaluate side-chains 31 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 19 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 52 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.060068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.043450 restraints weight = 45872.674| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 4.86 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.049 10180 Z= 0.414 Angle : 0.788 17.537 13947 Z= 0.388 Chirality : 0.049 0.352 1707 Planarity : 0.004 0.066 1728 Dihedral : 5.341 29.906 1317 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.71 % Favored : 93.04 % Rotamer: Outliers : 2.10 % Allowed : 10.87 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.24), residues: 1222 helix: 1.05 (0.34), residues: 238 sheet: -0.78 (0.30), residues: 312 loop : -0.96 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1073 TYR 0.015 0.002 TYR A 676 PHE 0.018 0.002 PHE A 438 TRP 0.009 0.001 TRP A 439 HIS 0.007 0.002 HIS A 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00928 / 0.41 (10127) covalent geometry : angle 0.75530 / 0.38 (13801) SS BOND : bond 0.00236 / 0.13 ( 13) SS BOND : angle 0.99940 / 0.74 ( 26) hydrogen bonds : bond 0.04712 / 3.12 ( 345) hydrogen bonds : angle 5.35178 / 3.91 ( 1002) link_ALPHA1-3 : bond 0.00040 / 0.02 ( 1) link_ALPHA1-3 : angle 2.38667 / 1.58 ( 3) link_ALPHA1-6 : bond 0.00044 / 0.02 ( 1) link_ALPHA1-6 : angle 1.55836 / 1.31 ( 3) link_BETA1-4 : bond 0.01269 / 0.59 ( 16) link_BETA1-4 : angle 3.16524 / 1.73 ( 48) link_BETA1-6 : bond 0.00188 / 0.09 ( 4) link_BETA1-6 : angle 1.62116 / 1.13 ( 12) link_NAG-ASN : bond 0.00551 / 0.28 ( 18) link_NAG-ASN : angle 2.00082 / 1.55 ( 54) *********************** 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 39 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 17 time to evaluate : 0.287 Fit side-chains REVERT: A 317 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8404 (pm20) REVERT: A 635 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8704 (mm) REVERT: A 795 GLU cc_start: 0.8472 (tp30) cc_final: 0.8266 (tp30) outliers start: 22 outliers final: 15 residues processed: 39 average time/residue: 0.0574 time to fit residues: 4.1025 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 : 0.331 ------------------------------------------------------------------------------- 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 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 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 30 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 11 optimal weight: 0.1980 chunk 94 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.062128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.045947 restraints weight = 44510.558| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 4.77 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10180 Z= 0.125 Angle : 0.620 17.674 13947 Z= 0.304 Chirality : 0.046 0.348 1707 Planarity : 0.004 0.067 1728 Dihedral : 4.948 28.515 1317 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.24 % Favored : 94.52 % Rotamer: Outliers : 1.72 % Allowed : 12.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.24), residues: 1222 helix: 1.45 (0.34), residues: 235 sheet: -0.75 (0.30), residues: 307 loop : -0.92 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 146 TYR 0.017 0.001 TYR A 563 PHE 0.010 0.001 PHE A 374 TRP 0.004 0.001 TRP A 65 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (10127) covalent geometry : angle 0.58837 / 0.30 (13801) SS BOND : bond 0.00138 / 0.09 ( 13) SS BOND : angle 0.80903 / 0.56 ( 26) hydrogen bonds : bond 0.03847 / 2.59 ( 345) hydrogen bonds : angle 4.97228 / 3.64 ( 1002) link_ALPHA1-3 : bond 0.00552 / 0.29 ( 1) link_ALPHA1-3 : angle 1.60969 / 1.14 ( 3) link_ALPHA1-6 : bond 0.00298 / 0.16 ( 1) link_ALPHA1-6 : angle 1.42478 / 1.14 ( 3) link_BETA1-4 : bond 0.01220 / 0.56 ( 16) link_BETA1-4 : angle 2.95740 / 1.54 ( 48) link_BETA1-6 : bond 0.00370 / 0.18 ( 4) link_BETA1-6 : angle 1.19319 / 0.82 ( 12) link_NAG-ASN : bond 0.00292 / 0.15 ( 18) link_NAG-ASN : angle 1.47246 / 1.12 ( 54) *********************** 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 36 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 18 time to evaluate : 0.231 Fit side-chains REVERT: A 214 MET cc_start: 0.8208 (mtt) cc_final: 0.7994 (mmt) REVERT: A 317 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7867 (pm20) REVERT: A 795 GLU cc_start: 0.8489 (tp30) cc_final: 0.8270 (tp30) outliers start: 18 outliers final: 15 residues processed: 35 average time/residue: 0.0572 time to fit residues: 3.5866 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 : 0.348 ------------------------------------------------------------------------------- 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 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 104 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 62 optimal weight: 0.3980 chunk 98 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.062223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.045970 restraints weight = 44431.508| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 4.81 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10180 Z= 0.130 Angle : 0.603 17.523 13947 Z= 0.293 Chirality : 0.045 0.350 1707 Planarity : 0.004 0.063 1728 Dihedral : 4.791 28.667 1317 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.24 % Favored : 94.44 % Rotamer: Outliers : 1.62 % Allowed : 12.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.24), residues: 1222 helix: 1.55 (0.34), residues: 235 sheet: -0.60 (0.30), residues: 317 loop : -0.90 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 146 TYR 0.016 0.001 TYR A 563 PHE 0.010 0.001 PHE A 374 TRP 0.004 0.001 TRP A 65 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (10127) covalent geometry : angle 0.57013 / 0.29 (13801) SS BOND : bond 0.00125 / 0.08 ( 13) SS BOND : angle 0.79130 / 0.53 ( 26) hydrogen bonds : bond 0.03664 / 2.46 ( 345) hydrogen bonds : angle 4.79704 / 3.51 ( 1002) link_ALPHA1-3 : bond 0.00499 / 0.26 ( 1) link_ALPHA1-3 : angle 1.62621 / 1.19 ( 3) link_ALPHA1-6 : bond 0.00304 / 0.16 ( 1) link_ALPHA1-6 : angle 1.42519 / 1.15 ( 3) link_BETA1-4 : bond 0.01204 / 0.56 ( 16) link_BETA1-4 : angle 2.93377 / 1.53 ( 48) link_BETA1-6 : bond 0.00306 / 0.15 ( 4) link_BETA1-6 : angle 1.25317 / 0.87 ( 12) link_NAG-ASN : bond 0.00259 / 0.12 ( 18) link_NAG-ASN : angle 1.46831 / 1.13 ( 54) *********************** 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 36 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 19 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 214 MET cc_start: 0.8176 (mtt) cc_final: 0.7960 (mmt) REVERT: A 317 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.7841 (pm20) REVERT: A 795 GLU cc_start: 0.8494 (tp30) cc_final: 0.8264 (tp30) outliers start: 17 outliers final: 16 residues processed: 35 average time/residue: 0.0606 time to fit residues: 3.8697 Evaluate side-chains 35 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 18 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 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 1232 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 50 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.061384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.045046 restraints weight = 44707.308| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 4.81 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10180 Z= 0.211 Angle : 0.639 17.478 13947 Z= 0.311 Chirality : 0.046 0.353 1707 Planarity : 0.004 0.062 1728 Dihedral : 4.916 29.392 1317 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.89 % Favored : 93.78 % Rotamer: Outliers : 2.19 % Allowed : 12.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.24), residues: 1222 helix: 1.26 (0.34), residues: 245 sheet: -0.67 (0.30), residues: 319 loop : -0.95 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 146 TYR 0.028 0.001 TYR A 237 PHE 0.012 0.001 PHE A 374 TRP 0.004 0.001 TRP A 439 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 (10127) covalent geometry : angle 0.60594 / 0.30 (13801) SS BOND : bond 0.00149 / 0.08 ( 13) SS BOND : angle 0.84237 / 0.58 ( 26) hydrogen bonds : bond 0.03908 / 2.62 ( 345) hydrogen bonds : angle 4.86651 / 3.56 ( 1002) link_ALPHA1-3 : bond 0.00325 / 0.17 ( 1) link_ALPHA1-3 : angle 1.82075 / 1.31 ( 3) link_ALPHA1-6 : bond 0.00227 / 0.12 ( 1) link_ALPHA1-6 : angle 1.46015 / 1.20 ( 3) link_BETA1-4 : bond 0.01202 / 0.55 ( 16) link_BETA1-4 : angle 2.97560 / 1.57 ( 48) link_BETA1-6 : bond 0.00242 / 0.12 ( 4) link_BETA1-6 : angle 1.36358 / 0.94 ( 12) link_NAG-ASN : bond 0.00308 / 0.14 ( 18) link_NAG-ASN : angle 1.60124 / 1.24 ( 54) *********************** 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 41 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 18 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 317 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.7896 (pm20) REVERT: A 795 GLU cc_start: 0.8546 (tp30) cc_final: 0.8327 (tp30) REVERT: A 1238 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9053 (tp) outliers start: 23 outliers final: 16 residues processed: 39 average time/residue: 0.0566 time to fit residues: 3.9743 Evaluate side-chains 36 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 18 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 94 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 60 optimal weight: 0.1980 chunk 102 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.062590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.046451 restraints weight = 43756.410| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 4.77 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10180 Z= 0.112 Angle : 0.598 17.604 13947 Z= 0.291 Chirality : 0.045 0.351 1707 Planarity : 0.004 0.064 1728 Dihedral : 4.707 28.845 1317 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.40 % Favored : 94.27 % Rotamer: Outliers : 1.91 % Allowed : 12.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.24), residues: 1222 helix: 1.62 (0.34), residues: 235 sheet: -0.54 (0.30), residues: 317 loop : -0.88 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 146 TYR 0.020 0.001 TYR A 237 PHE 0.008 0.001 PHE A 374 TRP 0.006 0.001 TRP A 65 HIS 0.003 0.000 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (10127) covalent geometry : angle 0.56700 / 0.28 (13801) SS BOND : bond 0.00131 / 0.08 ( 13) SS BOND : angle 0.77686 / 0.51 ( 26) hydrogen bonds : bond 0.03541 / 2.38 ( 345) hydrogen bonds : angle 4.69053 / 3.42 ( 1002) link_ALPHA1-3 : bond 0.00548 / 0.29 ( 1) link_ALPHA1-3 : angle 1.52223 / 1.12 ( 3) link_ALPHA1-6 : bond 0.00334 / 0.18 ( 1) link_ALPHA1-6 : angle 1.41606 / 1.13 ( 3) link_BETA1-4 : bond 0.01218 / 0.56 ( 16) link_BETA1-4 : angle 2.91130 / 1.51 ( 48) link_BETA1-6 : bond 0.00374 / 0.19 ( 4) link_BETA1-6 : angle 1.18872 / 0.81 ( 12) link_NAG-ASN : bond 0.00308 / 0.14 ( 18) link_NAG-ASN : angle 1.39674 / 1.05 ( 54) ********************** 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 41 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 21 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 317 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7836 (pm20) REVERT: A 795 GLU cc_start: 0.8506 (tp30) cc_final: 0.8272 (tp30) REVERT: A 1238 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9123 (tp) outliers start: 20 outliers final: 16 residues processed: 39 average time/residue: 0.0653 time to fit residues: 4.5383 Evaluate side-chains 37 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 19 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 790 MET 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 52 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 0.0670 chunk 73 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.062393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.046120 restraints weight = 44587.833| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 4.81 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10180 Z= 0.129 Angle : 0.601 17.571 13947 Z= 0.291 Chirality : 0.045 0.353 1707 Planarity : 0.004 0.063 1728 Dihedral : 4.667 29.087 1317 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.32 % Favored : 94.35 % Rotamer: Outliers : 1.72 % Allowed : 12.68 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.24), residues: 1222 helix: 1.47 (0.34), residues: 241 sheet: -0.53 (0.30), residues: 317 loop : -0.88 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 146 TYR 0.023 0.001 TYR A 237 PHE 0.010 0.001 PHE A 374 TRP 0.006 0.001 TRP A 65 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (10127) covalent geometry : angle 0.56913 / 0.28 (13801) SS BOND : bond 0.00131 / 0.08 ( 13) SS BOND : angle 0.80227 / 0.53 ( 26) hydrogen bonds : bond 0.03542 / 2.38 ( 345) hydrogen bonds : angle 4.62369 / 3.37 ( 1002) link_ALPHA1-3 : bond 0.00471 / 0.25 ( 1) link_ALPHA1-3 : angle 1.60688 / 1.21 ( 3) link_ALPHA1-6 : bond 0.00322 / 0.17 ( 1) link_ALPHA1-6 : angle 1.42628 / 1.15 ( 3) link_BETA1-4 : bond 0.01207 / 0.55 ( 16) link_BETA1-4 : angle 2.92404 / 1.52 ( 48) link_BETA1-6 : bond 0.00300 / 0.15 ( 4) link_BETA1-6 : angle 1.26530 / 0.87 ( 12) link_NAG-ASN : bond 0.00268 / 0.11 ( 18) link_NAG-ASN : angle 1.43649 / 1.09 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1783.53 seconds wall clock time: 31 minutes 38.53 seconds (1898.53 seconds total)