Starting phenix.real_space_refine on Wed Mar 4 02:57:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y6u_33648/03_2026/7y6u_33648.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6u_33648/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7y6u_33648/03_2026/7y6u_33648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6u_33648/03_2026/7y6u_33648.map" model { file = "/net/cci-nas-00/data/ceres_data/7y6u_33648/03_2026/7y6u_33648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6u_33648/03_2026/7y6u_33648.cif" } 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-5986/lib/python3.9/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 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: 2.33, per 1000 atoms: 0.23 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: 1.19 Conformation dependent library (CDL) restraints added in 482.7 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: 0.48 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: 2.27 Time building geometry restraints manager: 1.49 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: 4.290 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: 0.040 Set scattering table: 0.020 Process input model: 11.650 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.760 ------------------------------------------------------------------------------- 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 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 : 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 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 covalent geometry : bond 0.00401 (10127) covalent geometry : angle 0.68821 (13801) SS BOND : bond 0.00233 ( 13) SS BOND : angle 1.56520 ( 26) hydrogen bonds : bond 0.22487 ( 345) hydrogen bonds : angle 8.58118 ( 1002) link_ALPHA1-3 : bond 0.00471 ( 1) link_ALPHA1-3 : angle 1.65082 ( 3) link_ALPHA1-6 : bond 0.00381 ( 1) link_ALPHA1-6 : angle 1.47043 ( 3) link_BETA1-4 : bond 0.01112 ( 16) link_BETA1-4 : angle 3.18265 ( 48) link_BETA1-6 : bond 0.00462 ( 4) link_BETA1-6 : angle 1.42485 ( 12) link_NAG-ASN : bond 0.00293 ( 18) link_NAG-ASN : angle 1.62152 ( 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 : 0.367 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: 0.0759 time to fit residues: 3.5781 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 : 0.378 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.063608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.047499 restraints weight = 44586.641| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 4.79 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10180 Z= 0.140 Angle : 0.678 17.864 13947 Z= 0.326 Chirality : 0.048 0.307 1707 Planarity : 0.004 0.068 1728 Dihedral : 15.354 103.186 2123 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.56 % Favored : 94.11 % Rotamer: Outliers : 0.29 % Allowed : 4.58 % Favored : 95.14 % 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: -0.40 (0.24), residues: 1222 helix: 1.46 (0.34), residues: 233 sheet: -0.54 (0.29), residues: 327 loop : -0.71 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 547 TYR 0.018 0.001 TYR A 407 PHE 0.013 0.001 PHE A 296 TRP 0.005 0.001 TRP A 65 HIS 0.002 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00290 (10127) covalent geometry : angle 0.63852 (13801) SS BOND : bond 0.00340 ( 13) SS BOND : angle 1.36641 ( 26) hydrogen bonds : bond 0.04745 ( 345) hydrogen bonds : angle 5.90756 ( 1002) link_ALPHA1-3 : bond 0.00948 ( 1) link_ALPHA1-3 : angle 2.18774 ( 3) link_ALPHA1-6 : bond 0.00327 ( 1) link_ALPHA1-6 : angle 2.24133 ( 3) link_BETA1-4 : bond 0.01437 ( 16) link_BETA1-4 : angle 3.44626 ( 48) link_BETA1-6 : bond 0.00568 ( 4) link_BETA1-6 : angle 1.49180 ( 12) link_NAG-ASN : bond 0.00277 ( 18) link_NAG-ASN : angle 1.45559 ( 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 27 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.352 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 26 average time/residue: 0.0904 time to fit residues: 3.8784 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 : 0.357 ------------------------------------------------------------------------------- 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: 0.7980 chunk 16 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 322 ASN A 571 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.062311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.045858 restraints weight = 44767.171| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 4.85 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1323 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= 0.205 Angle : 0.688 18.332 13947 Z= 0.328 Chirality : 0.048 0.314 1707 Planarity : 0.004 0.074 1728 Dihedral : 12.152 105.571 2123 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.73 % Favored : 93.94 % Rotamer: Outliers : 1.43 % Allowed : 7.53 % Favored : 91.04 % 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: -0.53 (0.24), residues: 1222 helix: 1.32 (0.34), residues: 238 sheet: -0.64 (0.29), residues: 328 loop : -0.77 (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 covalent geometry : bond 0.00453 (10127) covalent geometry : angle 0.64549 (13801) SS BOND : bond 0.00271 ( 13) SS BOND : angle 1.20914 ( 26) hydrogen bonds : bond 0.04546 ( 345) hydrogen bonds : angle 5.35984 ( 1002) link_ALPHA1-3 : bond 0.00995 ( 1) link_ALPHA1-3 : angle 2.56344 ( 3) link_ALPHA1-6 : bond 0.00234 ( 1) link_ALPHA1-6 : angle 2.04777 ( 3) link_BETA1-4 : bond 0.01244 ( 16) link_BETA1-4 : angle 3.51441 ( 48) link_BETA1-6 : bond 0.00542 ( 4) link_BETA1-6 : angle 1.84238 ( 12) link_NAG-ASN : bond 0.00285 ( 18) link_NAG-ASN : angle 1.69948 ( 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: 15 poor density : 18 time to evaluate : 0.351 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 33 average time/residue: 0.0632 time to fit residues: 3.8452 Evaluate side-chains 25 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 17 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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: 3.9990 chunk 98 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.062145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.045762 restraints weight = 45110.032| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 4.83 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10180 Z= 0.194 Angle : 0.669 18.044 13947 Z= 0.321 Chirality : 0.047 0.320 1707 Planarity : 0.004 0.072 1728 Dihedral : 10.948 104.848 2123 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.73 % Favored : 93.94 % Rotamer: Outliers : 1.43 % Allowed : 8.58 % 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: -0.53 (0.24), residues: 1222 helix: 1.33 (0.34), residues: 239 sheet: -0.70 (0.29), residues: 317 loop : -0.76 (0.24), residues: 666 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 0.004 0.001 TRP A 65 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00428 (10127) covalent geometry : angle 0.62668 (13801) SS BOND : bond 0.00150 ( 13) SS BOND : angle 1.60667 ( 26) hydrogen bonds : bond 0.04139 ( 345) hydrogen bonds : angle 5.18772 ( 1002) link_ALPHA1-3 : bond 0.00997 ( 1) link_ALPHA1-3 : angle 2.80530 ( 3) link_ALPHA1-6 : bond 0.00376 ( 1) link_ALPHA1-6 : angle 2.13784 ( 3) link_BETA1-4 : bond 0.01264 ( 16) link_BETA1-4 : angle 3.37505 ( 48) link_BETA1-6 : bond 0.00567 ( 4) link_BETA1-6 : angle 1.81991 ( 12) link_NAG-ASN : bond 0.00247 ( 18) link_NAG-ASN : angle 1.59573 ( 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 34 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 19 time to evaluate : 0.365 Fit side-chains REVERT: A 317 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.7916 (pm20) outliers start: 15 outliers final: 9 residues processed: 33 average time/residue: 0.0676 time to fit residues: 4.0850 Evaluate side-chains 29 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 19 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 95 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 107 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 108 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 106 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.062749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.046442 restraints weight = 44605.210| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 4.81 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1589 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= 0.128 Angle : 0.624 18.014 13947 Z= 0.300 Chirality : 0.046 0.324 1707 Planarity : 0.004 0.070 1728 Dihedral : 10.420 103.593 2123 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.40 % Favored : 94.27 % Rotamer: Outliers : 1.62 % Allowed : 9.34 % Favored : 89.04 % 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: -0.46 (0.24), residues: 1222 helix: 1.52 (0.34), residues: 235 sheet: -0.54 (0.30), residues: 316 loop : -0.83 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1073 TYR 0.014 0.001 TYR A 563 PHE 0.011 0.001 PHE A 374 TRP 0.005 0.001 TRP A 65 HIS 0.003 0.000 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00272 (10127) covalent geometry : angle 0.58511 (13801) SS BOND : bond 0.00164 ( 13) SS BOND : angle 0.97129 ( 26) hydrogen bonds : bond 0.03818 ( 345) hydrogen bonds : angle 5.00016 ( 1002) link_ALPHA1-3 : bond 0.01073 ( 1) link_ALPHA1-3 : angle 2.39070 ( 3) link_ALPHA1-6 : bond 0.00484 ( 1) link_ALPHA1-6 : angle 2.08821 ( 3) link_BETA1-4 : bond 0.01249 ( 16) link_BETA1-4 : angle 3.23563 ( 48) link_BETA1-6 : bond 0.00254 ( 4) link_BETA1-6 : angle 1.35494 ( 12) link_NAG-ASN : bond 0.00235 ( 18) link_NAG-ASN : angle 1.50326 ( 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 37 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 20 time to evaluate : 0.388 Fit side-chains REVERT: A 214 MET cc_start: 0.8070 (mtt) cc_final: 0.7799 (mmt) REVERT: A 317 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.7860 (pm20) outliers start: 17 outliers final: 13 residues processed: 35 average time/residue: 0.0672 time to fit residues: 4.3010 Evaluate side-chains 32 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 18 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 406 VAL Chi-restraints excluded: chain A residue 563 TYR 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 52 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 120 optimal weight: 0.0000 chunk 65 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.061380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.045008 restraints weight = 45215.107| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 4.81 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 10180 Z= 0.248 Angle : 0.685 17.871 13947 Z= 0.331 Chirality : 0.047 0.323 1707 Planarity : 0.004 0.066 1728 Dihedral : 10.420 105.754 2123 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.81 % Favored : 93.86 % Rotamer: Outliers : 2.00 % Allowed : 10.49 % Favored : 87.51 % 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: -0.62 (0.24), residues: 1222 helix: 1.28 (0.34), residues: 239 sheet: -0.63 (0.30), residues: 319 loop : -0.89 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1073 TYR 0.013 0.001 TYR A 563 PHE 0.013 0.001 PHE A 374 TRP 0.007 0.001 TRP A 439 HIS 0.004 0.001 HIS A 78 Details of bonding type rmsd covalent geometry : bond 0.00552 (10127) covalent geometry : angle 0.64653 (13801) SS BOND : bond 0.00188 ( 13) SS BOND : angle 0.91661 ( 26) hydrogen bonds : bond 0.04211 ( 345) hydrogen bonds : angle 5.03659 ( 1002) link_ALPHA1-3 : bond 0.00861 ( 1) link_ALPHA1-3 : angle 3.20201 ( 3) link_ALPHA1-6 : bond 0.00351 ( 1) link_ALPHA1-6 : angle 2.14122 ( 3) link_BETA1-4 : bond 0.01264 ( 16) link_BETA1-4 : angle 3.27896 ( 48) link_BETA1-6 : bond 0.00254 ( 4) link_BETA1-6 : angle 1.48845 ( 12) link_NAG-ASN : bond 0.00345 ( 18) link_NAG-ASN : angle 1.77239 ( 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 40 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 19 time to evaluate : 0.354 Fit side-chains REVERT: A 214 MET cc_start: 0.8120 (mtt) cc_final: 0.7780 (mmt) REVERT: A 317 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8406 (pm20) REVERT: A 635 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8728 (mm) outliers start: 21 outliers final: 16 residues processed: 39 average time/residue: 0.0645 time to fit residues: 4.6006 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 : 0.403 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 79 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.061935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.045591 restraints weight = 44609.003| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 4.83 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10180 Z= 0.176 Angle : 0.640 17.887 13947 Z= 0.308 Chirality : 0.046 0.326 1707 Planarity : 0.004 0.065 1728 Dihedral : 10.243 104.921 2123 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.48 % Favored : 94.19 % Rotamer: Outliers : 1.62 % Allowed : 12.30 % 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: -0.55 (0.24), residues: 1222 helix: 1.39 (0.34), residues: 239 sheet: -0.59 (0.30), residues: 317 loop : -0.87 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 146 TYR 0.015 0.001 TYR A 563 PHE 0.011 0.001 PHE A 374 TRP 0.003 0.001 TRP A 65 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00387 (10127) covalent geometry : angle 0.60349 (13801) SS BOND : bond 0.00141 ( 13) SS BOND : angle 0.83164 ( 26) hydrogen bonds : bond 0.03906 ( 345) hydrogen bonds : angle 4.92607 ( 1002) link_ALPHA1-3 : bond 0.00880 ( 1) link_ALPHA1-3 : angle 2.57102 ( 3) link_ALPHA1-6 : bond 0.00450 ( 1) link_ALPHA1-6 : angle 2.14930 ( 3) link_BETA1-4 : bond 0.01260 ( 16) link_BETA1-4 : angle 3.18584 ( 48) link_BETA1-6 : bond 0.00235 ( 4) link_BETA1-6 : angle 1.32900 ( 12) link_NAG-ASN : bond 0.00247 ( 18) link_NAG-ASN : angle 1.58200 ( 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 35 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 18 time to evaluate : 0.363 Fit side-chains REVERT: A 214 MET cc_start: 0.8148 (mtt) cc_final: 0.7877 (mmt) REVERT: A 317 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.7986 (pm20) outliers start: 17 outliers final: 16 residues processed: 34 average time/residue: 0.0649 time to fit residues: 4.0695 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 : 0.351 ------------------------------------------------------------------------------- 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 1087 ILE 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: 0.4980 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.062783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.046470 restraints weight = 44206.411| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 4.83 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1897 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= 0.116 Angle : 0.612 17.901 13947 Z= 0.293 Chirality : 0.046 0.329 1707 Planarity : 0.004 0.063 1728 Dihedral : 9.937 103.141 2123 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.99 % Favored : 94.68 % 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: -0.44 (0.25), residues: 1222 helix: 1.61 (0.34), residues: 235 sheet: -0.53 (0.30), residues: 317 loop : -0.84 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1073 TYR 0.015 0.001 TYR A 563 PHE 0.009 0.001 PHE A 374 TRP 0.005 0.001 TRP A 65 HIS 0.003 0.000 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00245 (10127) covalent geometry : angle 0.57556 (13801) SS BOND : bond 0.00122 ( 13) SS BOND : angle 0.80002 ( 26) hydrogen bonds : bond 0.03578 ( 345) hydrogen bonds : angle 4.72249 ( 1002) link_ALPHA1-3 : bond 0.00898 ( 1) link_ALPHA1-3 : angle 2.13911 ( 3) link_ALPHA1-6 : bond 0.00563 ( 1) link_ALPHA1-6 : angle 2.12280 ( 3) link_BETA1-4 : bond 0.01260 ( 16) link_BETA1-4 : angle 3.14670 ( 48) link_BETA1-6 : bond 0.00285 ( 4) link_BETA1-6 : angle 1.28322 ( 12) link_NAG-ASN : bond 0.00266 ( 18) link_NAG-ASN : angle 1.46320 ( 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 39 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 21 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 214 MET cc_start: 0.8159 (mtt) cc_final: 0.7947 (mmt) REVERT: A 317 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.7909 (pm20) outliers start: 18 outliers final: 16 residues processed: 38 average time/residue: 0.0662 time to fit residues: 4.5957 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 : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 50 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.062403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.046025 restraints weight = 44424.246| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 4.84 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10180 Z= 0.148 Angle : 0.619 17.843 13947 Z= 0.296 Chirality : 0.046 0.330 1707 Planarity : 0.004 0.062 1728 Dihedral : 9.863 103.519 2123 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.56 % Favored : 94.11 % Rotamer: Outliers : 2.29 % Allowed : 12.01 % 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 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: -0.44 (0.24), residues: 1222 helix: 1.56 (0.34), residues: 239 sheet: -0.50 (0.30), residues: 317 loop : -0.85 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 146 TYR 0.026 0.001 TYR A 237 PHE 0.011 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 covalent geometry : bond 0.00323 (10127) covalent geometry : angle 0.58251 (13801) SS BOND : bond 0.00126 ( 13) SS BOND : angle 0.81146 ( 26) hydrogen bonds : bond 0.03651 ( 345) hydrogen bonds : angle 4.70324 ( 1002) link_ALPHA1-3 : bond 0.00768 ( 1) link_ALPHA1-3 : angle 2.39609 ( 3) link_ALPHA1-6 : bond 0.00549 ( 1) link_ALPHA1-6 : angle 2.14675 ( 3) link_BETA1-4 : bond 0.01268 ( 16) link_BETA1-4 : angle 3.14165 ( 48) link_BETA1-6 : bond 0.00257 ( 4) link_BETA1-6 : angle 1.33899 ( 12) link_NAG-ASN : bond 0.00242 ( 18) link_NAG-ASN : angle 1.50965 ( 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 42 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 18 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 317 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.7947 (pm20) REVERT: A 635 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8784 (mm) REVERT: A 1238 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9122 (tp) outliers start: 24 outliers final: 16 residues processed: 41 average time/residue: 0.0638 time to fit residues: 4.7342 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 : 0.381 ------------------------------------------------------------------------------- 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 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 94 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 60 optimal weight: 0.4980 chunk 102 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.062963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.046612 restraints weight = 43704.969| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 4.87 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10180 Z= 0.116 Angle : 0.611 17.904 13947 Z= 0.290 Chirality : 0.045 0.331 1707 Planarity : 0.004 0.062 1728 Dihedral : 9.553 102.323 2123 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.32 % Favored : 94.35 % Rotamer: Outliers : 1.91 % Allowed : 12.11 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.25), residues: 1222 helix: 1.63 (0.34), residues: 239 sheet: -0.48 (0.30), residues: 316 loop : -0.82 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 146 TYR 0.020 0.001 TYR A 237 PHE 0.009 0.001 PHE A 374 TRP 0.018 0.001 TRP A 65 HIS 0.003 0.000 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00248 (10127) covalent geometry : angle 0.57582 (13801) SS BOND : bond 0.00126 ( 13) SS BOND : angle 0.75759 ( 26) hydrogen bonds : bond 0.03473 ( 345) hydrogen bonds : angle 4.59532 ( 1002) link_ALPHA1-3 : bond 0.00782 ( 1) link_ALPHA1-3 : angle 1.96519 ( 3) link_ALPHA1-6 : bond 0.00739 ( 1) link_ALPHA1-6 : angle 1.82003 ( 3) link_BETA1-4 : bond 0.01279 ( 16) link_BETA1-4 : angle 3.12023 ( 48) link_BETA1-6 : bond 0.00299 ( 4) link_BETA1-6 : angle 1.27708 ( 12) link_NAG-ASN : bond 0.00273 ( 18) link_NAG-ASN : angle 1.41830 ( 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 39 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 19 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 317 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.7920 (pm20) outliers start: 20 outliers final: 16 residues processed: 38 average time/residue: 0.0641 time to fit residues: 4.4423 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 : 0.357 ------------------------------------------------------------------------------- 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 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 1232 ASN 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: 0.0670 chunk 109 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 73 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 83 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.062787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.046488 restraints weight = 44310.038| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 4.88 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10180 Z= 0.126 Angle : 0.612 17.839 13947 Z= 0.290 Chirality : 0.045 0.333 1707 Planarity : 0.004 0.061 1728 Dihedral : 9.375 102.473 2123 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.99 % Favored : 94.68 % Rotamer: Outliers : 1.81 % Allowed : 12.01 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.62 (0.34), residues: 239 sheet: -0.51 (0.30), residues: 314 loop : -0.79 (0.24), residues: 669 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 0.015 0.001 TRP A 65 HIS 0.003 0.000 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00271 (10127) covalent geometry : angle 0.57666 (13801) SS BOND : bond 0.00122 ( 13) SS BOND : angle 0.78292 ( 26) hydrogen bonds : bond 0.03481 ( 345) hydrogen bonds : angle 4.56784 ( 1002) link_ALPHA1-3 : bond 0.00741 ( 1) link_ALPHA1-3 : angle 1.97878 ( 3) link_ALPHA1-6 : bond 0.00839 ( 1) link_ALPHA1-6 : angle 1.45792 ( 3) link_BETA1-4 : bond 0.01267 ( 16) link_BETA1-4 : angle 3.12982 ( 48) link_BETA1-6 : bond 0.00282 ( 4) link_BETA1-6 : angle 1.31547 ( 12) link_NAG-ASN : bond 0.00246 ( 18) link_NAG-ASN : angle 1.45391 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1993.43 seconds wall clock time: 35 minutes 13.26 seconds (2113.26 seconds total)