Starting phenix.real_space_refine on Sun Jun 22 13:16:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uuo_42592/06_2025/8uuo_42592.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uuo_42592/06_2025/8uuo_42592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uuo_42592/06_2025/8uuo_42592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uuo_42592/06_2025/8uuo_42592.map" model { file = "/net/cci-nas-00/data/ceres_data/8uuo_42592/06_2025/8uuo_42592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uuo_42592/06_2025/8uuo_42592.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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 114 5.16 5 C 16239 2.51 5 N 4210 2.21 5 O 4902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25465 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8354 Classifications: {'peptide': 1067} Link IDs: {'PTRANS': 57, 'TRANS': 1009} Chain breaks: 6 Chain: "B" Number of atoms: 8390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1074, 8390 Classifications: {'peptide': 1074} Link IDs: {'PTRANS': 57, 'TRANS': 1016} Chain breaks: 5 Chain: "C" Number of atoms: 8425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8425 Classifications: {'peptide': 1077} Link IDs: {'PTRANS': 57, 'TRANS': 1019} Chain breaks: 5 Chain: "E" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'MAN': 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: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'MAN': 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: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'MAN': 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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "B" 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 Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 3} 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 Time building chain proxies: 16.10, per 1000 atoms: 0.63 Number of scatterers: 25465 At special positions: 0 Unit cell: (144.309, 159.36, 200.971, 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 114 16.00 O 4902 8.00 N 4210 7.00 C 16239 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.01 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 ALPHA1-4 " NAG D 1 " - " MAN D 2 " " NAG E 1 " - " MAN E 2 " " NAG F 1 " - " MAN F 2 " NAG-ASN " NAG F 1 " - " ASN A1098 " Time building additional restraints: 6.60 Conformation dependent library (CDL) restraints added in 3.6 seconds 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6032 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 48 sheets defined 24.4% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.25 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.819A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.512A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.767A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.745A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.636A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.925A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.906A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.574A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.519A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 4.110A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 918' Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.920A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.126A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1149 removed outlier: 3.848A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.683A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.586A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.605A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.625A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.683A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.505A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.570A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.639A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.615A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.555A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.528A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.672A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.513A pdb=" N ILE B 923 " --> pdb=" O ASN B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.368A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.573A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1033 removed outlier: 3.537A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1148 removed outlier: 4.146A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.840A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.648A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.806A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA C 411 " --> pdb=" O ARG C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.678A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 623 Processing helix chain 'C' and resid 634 through 638 removed outlier: 3.804A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.546A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.528A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.653A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.610A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.832A pdb=" N ILE C 923 " --> pdb=" O ASN C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 957 removed outlier: 4.535A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 4.009A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.062A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1149 removed outlier: 4.211A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 10.379A pdb=" N ASN A 61 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLY A 268 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR A 63 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR A 266 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE A 65 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ALA A 264 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA A 67 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 262 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.949A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.233A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.035A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 144 removed outlier: 7.835A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET A 153 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.625A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 6.912A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.513A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.712A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 712 Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.855A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.328A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.617A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.717A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.534A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.726A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.182A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 9.520A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.548A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 11.716A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.643A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 141 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL B 143 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.182A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 9.520A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.634A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.860A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC9, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.036A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.686A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.003A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.003A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.141A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 10.108A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.185A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.921A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.098A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 142 through 144 removed outlier: 6.296A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.583A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.583A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.414A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.838A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.223A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.132A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1029 hydrogen bonds defined for protein. 2772 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: 12.84 Time building geometry restraints manager: 7.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8072 1.34 - 1.47: 6618 1.47 - 1.59: 11226 1.59 - 1.72: 0 1.72 - 1.85: 143 Bond restraints: 26059 Sorted by residual: bond pdb=" C VAL C 620 " pdb=" N PRO C 621 " ideal model delta sigma weight residual 1.334 1.423 -0.089 1.51e-02 4.39e+03 3.48e+01 bond pdb=" N ILE A 235 " pdb=" CA ILE A 235 " ideal model delta sigma weight residual 1.458 1.513 -0.054 1.08e-02 8.57e+03 2.54e+01 bond pdb=" N ARG A 237 " pdb=" CA ARG A 237 " ideal model delta sigma weight residual 1.454 1.511 -0.056 1.33e-02 5.65e+03 1.79e+01 bond pdb=" CA GLN B 965 " pdb=" C GLN B 965 " ideal model delta sigma weight residual 1.523 1.469 0.054 1.41e-02 5.03e+03 1.46e+01 bond pdb=" N ILE A 231 " pdb=" CA ILE A 231 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.37e+01 ... (remaining 26054 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.24: 35191 4.24 - 8.48: 259 8.48 - 12.72: 24 12.72 - 16.95: 6 16.95 - 21.19: 1 Bond angle restraints: 35481 Sorted by residual: angle pdb=" N GLY C 526 " pdb=" CA GLY C 526 " pdb=" C GLY C 526 " ideal model delta sigma weight residual 112.34 133.53 -21.19 2.04e+00 2.40e-01 1.08e+02 angle pdb=" N SER A 316 " pdb=" CA SER A 316 " pdb=" C SER A 316 " ideal model delta sigma weight residual 111.39 124.69 -13.30 1.38e+00 5.25e-01 9.29e+01 angle pdb=" N ARG A 237 " pdb=" CA ARG A 237 " pdb=" C ARG A 237 " ideal model delta sigma weight residual 109.41 122.68 -13.27 1.52e+00 4.33e-01 7.62e+01 angle pdb=" N ILE A 235 " pdb=" CA ILE A 235 " pdb=" C ILE A 235 " ideal model delta sigma weight residual 108.44 121.15 -12.71 1.55e+00 4.16e-01 6.73e+01 angle pdb=" N GLU C 96 " pdb=" CA GLU C 96 " pdb=" C GLU C 96 " ideal model delta sigma weight residual 108.75 122.27 -13.52 1.71e+00 3.42e-01 6.25e+01 ... (remaining 35476 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.74: 14934 23.74 - 47.48: 735 47.48 - 71.22: 99 71.22 - 94.96: 39 94.96 - 118.70: 23 Dihedral angle restraints: 15830 sinusoidal: 6458 harmonic: 9372 Sorted by residual: dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 28.09 64.91 1 1.00e+01 1.00e-02 5.53e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual -86.00 -24.36 -61.64 1 1.00e+01 1.00e-02 5.04e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 34.92 58.08 1 1.00e+01 1.00e-02 4.52e+01 ... (remaining 15827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 3500 0.090 - 0.180: 524 0.180 - 0.270: 31 0.270 - 0.359: 6 0.359 - 0.449: 4 Chirality restraints: 4065 Sorted by residual: chirality pdb=" CB ILE C1115 " pdb=" CA ILE C1115 " pdb=" CG1 ILE C1115 " pdb=" CG2 ILE C1115 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 5.05e+00 chirality pdb=" CA THR A 236 " pdb=" N THR A 236 " pdb=" C THR A 236 " pdb=" CB THR A 236 " both_signs ideal model delta sigma weight residual False 2.53 2.08 0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" CA SER A 316 " pdb=" N SER A 316 " pdb=" C SER A 316 " pdb=" CB SER A 316 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.76e+00 ... (remaining 4062 not shown) Planarity restraints: 4575 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 152 " 0.035 2.00e-02 2.50e+03 2.18e-02 1.19e+01 pdb=" CG TRP C 152 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP C 152 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP C 152 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 152 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 152 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP C 152 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 152 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 152 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 152 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 958 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C ALA A 958 " 0.057 2.00e-02 2.50e+03 pdb=" O ALA A 958 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU A 959 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 956 " 0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C ALA A 956 " -0.057 2.00e-02 2.50e+03 pdb=" O ALA A 956 " 0.022 2.00e-02 2.50e+03 pdb=" N GLN A 957 " 0.019 2.00e-02 2.50e+03 ... (remaining 4572 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1076 2.70 - 3.25: 23998 3.25 - 3.80: 41534 3.80 - 4.35: 47931 4.35 - 4.90: 82411 Nonbonded interactions: 196950 Sorted by model distance: nonbonded pdb=" OD1 ASN A 234 " pdb=" N ILE A 235 " model vdw 2.155 3.120 nonbonded pdb=" OD2 ASP B 420 " pdb=" OH TYR C 369 " model vdw 2.204 3.040 nonbonded pdb=" OE1 GLN B 115 " pdb=" OG1 THR B 167 " model vdw 2.215 3.040 nonbonded pdb=" OG1 THR C 912 " pdb=" OE1 GLN C1106 " model vdw 2.233 3.040 nonbonded pdb=" OG1 THR A 33 " pdb=" O GLY A 219 " model vdw 2.248 3.040 ... (remaining 196945 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 'A' and (resid 14 through 622 or resid 635 through 827 or resid 852 throu \ gh 1148 or resid 1302 through 1304)) selection = (chain 'B' and (resid 14 through 176 or resid 185 through 622 or resid 635 throu \ gh 827 or resid 852 through 1148 or resid 1303 through 1305)) selection = (chain 'C' and (resid 14 through 176 or resid 185 through 622 or resid 635 throu \ gh 1148 or resid 1302 through 1304)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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 group one per residue 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: 5.400 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: 0.030 Extract box with map and model: 1.020 Check model and map are aligned: 0.180 Set scattering table: 0.200 Process input model: 63.180 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.119 26104 Z= 0.375 Angle : 1.099 21.192 35575 Z= 0.619 Chirality : 0.062 0.449 4065 Planarity : 0.007 0.078 4574 Dihedral : 15.131 118.697 9675 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.00 % Favored : 94.97 % Rotamer: Outliers : 0.11 % Allowed : 0.57 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.14), residues: 3180 helix: 0.01 (0.20), residues: 648 sheet: -0.26 (0.20), residues: 621 loop : -2.06 (0.12), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP C 152 HIS 0.012 0.002 HIS A1064 PHE 0.049 0.003 PHE C 559 TYR 0.040 0.003 TYR C 873 ARG 0.015 0.001 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00938 ( 1) link_NAG-ASN : angle 6.24728 ( 3) link_ALPHA1-4 : bond 0.00948 ( 3) link_ALPHA1-4 : angle 3.03106 ( 9) hydrogen bonds : bond 0.15662 ( 1000) hydrogen bonds : angle 7.50125 ( 2772) SS BOND : bond 0.00542 ( 41) SS BOND : angle 1.53458 ( 82) covalent geometry : bond 0.00758 (26059) covalent geometry : angle 1.09523 (35481) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 2.734 Fit side-chains REVERT: A 229 LEU cc_start: 0.8956 (mt) cc_final: 0.8629 (tt) REVERT: A 725 GLU cc_start: 0.7976 (mp0) cc_final: 0.7664 (mp0) REVERT: A 740 MET cc_start: 0.9448 (tpt) cc_final: 0.9155 (tpp) REVERT: A 763 LEU cc_start: 0.9567 (mt) cc_final: 0.9271 (mt) REVERT: B 177 MET cc_start: 0.6664 (ppp) cc_final: 0.5983 (ppp) REVERT: B 238 PHE cc_start: 0.8678 (p90) cc_final: 0.8286 (p90) REVERT: C 177 MET cc_start: 0.5012 (ptt) cc_final: 0.4549 (ptt) REVERT: C 780 GLU cc_start: 0.9323 (tm-30) cc_final: 0.9100 (tm-30) REVERT: C 957 GLN cc_start: 0.8947 (tt0) cc_final: 0.8599 (tm-30) REVERT: C 1050 MET cc_start: 0.8514 (tpp) cc_final: 0.8312 (mmt) outliers start: 3 outliers final: 2 residues processed: 64 average time/residue: 0.3296 time to fit residues: 38.4695 Evaluate side-chains 49 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 270 optimal weight: 3.9990 chunk 242 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 163 optimal weight: 0.9990 chunk 129 optimal weight: 20.0000 chunk 250 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 152 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 290 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 914 ASN C 487 ASN C 919 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.050466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.037136 restraints weight = 244667.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.038117 restraints weight = 128610.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.038728 restraints weight = 83485.968| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 26104 Z= 0.191 Angle : 0.654 10.014 35575 Z= 0.341 Chirality : 0.044 0.238 4065 Planarity : 0.005 0.070 4574 Dihedral : 9.952 102.900 3904 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.18 % Allowed : 4.57 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.14), residues: 3180 helix: 1.00 (0.20), residues: 659 sheet: -0.32 (0.20), residues: 637 loop : -1.88 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 152 HIS 0.008 0.001 HIS A1064 PHE 0.021 0.001 PHE C 559 TYR 0.018 0.001 TYR C1067 ARG 0.006 0.001 ARG A1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 1) link_NAG-ASN : angle 3.72568 ( 3) link_ALPHA1-4 : bond 0.00755 ( 3) link_ALPHA1-4 : angle 2.93911 ( 9) hydrogen bonds : bond 0.05105 ( 1000) hydrogen bonds : angle 6.00289 ( 2772) SS BOND : bond 0.00292 ( 41) SS BOND : angle 1.00296 ( 82) covalent geometry : bond 0.00404 (26059) covalent geometry : angle 0.65027 (35481) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 725 GLU cc_start: 0.7884 (mp0) cc_final: 0.7638 (mp0) REVERT: A 740 MET cc_start: 0.9345 (tpt) cc_final: 0.9133 (tpp) REVERT: B 177 MET cc_start: 0.6540 (ppp) cc_final: 0.5844 (ppp) REVERT: B 238 PHE cc_start: 0.8683 (p90) cc_final: 0.8232 (p90) REVERT: B 1050 MET cc_start: 0.8550 (ptp) cc_final: 0.8097 (ptp) REVERT: C 177 MET cc_start: 0.5127 (ptt) cc_final: 0.4413 (ptt) outliers start: 5 outliers final: 2 residues processed: 57 average time/residue: 0.3249 time to fit residues: 33.8702 Evaluate side-chains 46 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 2.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain C residue 487 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 313 optimal weight: 5.9990 chunk 316 optimal weight: 3.9990 chunk 153 optimal weight: 20.0000 chunk 272 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 141 optimal weight: 0.0670 chunk 306 optimal weight: 7.9990 chunk 121 optimal weight: 30.0000 chunk 36 optimal weight: 30.0000 overall best weight: 3.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** C 487 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 = 0.3478 r_free = 0.3478 target = 0.050146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.036772 restraints weight = 245045.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.037737 restraints weight = 129331.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.038412 restraints weight = 84624.122| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 26104 Z= 0.185 Angle : 0.604 9.025 35575 Z= 0.313 Chirality : 0.043 0.222 4065 Planarity : 0.004 0.063 4574 Dihedral : 8.628 99.989 3901 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.53 % Allowed : 7.12 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.14), residues: 3180 helix: 1.36 (0.20), residues: 679 sheet: -0.31 (0.20), residues: 619 loop : -1.74 (0.13), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 152 HIS 0.005 0.001 HIS A1064 PHE 0.015 0.001 PHE C 133 TYR 0.018 0.001 TYR C1067 ARG 0.003 0.000 ARG A1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 1) link_NAG-ASN : angle 3.27202 ( 3) link_ALPHA1-4 : bond 0.00916 ( 3) link_ALPHA1-4 : angle 2.29815 ( 9) hydrogen bonds : bond 0.04755 ( 1000) hydrogen bonds : angle 5.61629 ( 2772) SS BOND : bond 0.00291 ( 41) SS BOND : angle 0.91878 ( 82) covalent geometry : bond 0.00396 (26059) covalent geometry : angle 0.60115 (35481) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 4.869 Fit side-chains revert: symmetry clash REVERT: A 725 GLU cc_start: 0.7997 (mp0) cc_final: 0.7686 (mp0) REVERT: A 762 GLN cc_start: 0.8693 (pp30) cc_final: 0.8418 (pp30) REVERT: B 177 MET cc_start: 0.6618 (ppp) cc_final: 0.5883 (ppp) REVERT: B 238 PHE cc_start: 0.8680 (p90) cc_final: 0.8239 (p90) REVERT: B 780 GLU cc_start: 0.9074 (tm-30) cc_final: 0.8657 (tm-30) REVERT: B 1050 MET cc_start: 0.8492 (ptp) cc_final: 0.8131 (ptp) REVERT: C 177 MET cc_start: 0.5128 (ptt) cc_final: 0.4605 (ptt) outliers start: 15 outliers final: 7 residues processed: 60 average time/residue: 0.3913 time to fit residues: 44.8510 Evaluate side-chains 50 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 3.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 980 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 221 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 186 optimal weight: 9.9990 chunk 47 optimal weight: 50.0000 chunk 293 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 273 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 chunk 147 optimal weight: 20.0000 chunk 183 optimal weight: 0.0470 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.050583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.037304 restraints weight = 245926.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.038301 restraints weight = 129170.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.038969 restraints weight = 83988.002| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26104 Z= 0.137 Angle : 0.552 8.860 35575 Z= 0.283 Chirality : 0.043 0.213 4065 Planarity : 0.004 0.059 4574 Dihedral : 7.482 87.443 3901 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.78 % Allowed : 8.61 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.15), residues: 3180 helix: 1.78 (0.21), residues: 667 sheet: -0.15 (0.21), residues: 594 loop : -1.68 (0.13), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 152 HIS 0.004 0.001 HIS A1064 PHE 0.013 0.001 PHE C 133 TYR 0.018 0.001 TYR C1067 ARG 0.008 0.000 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00174 ( 1) link_NAG-ASN : angle 2.81351 ( 3) link_ALPHA1-4 : bond 0.01345 ( 3) link_ALPHA1-4 : angle 2.74385 ( 9) hydrogen bonds : bond 0.04282 ( 1000) hydrogen bonds : angle 5.26443 ( 2772) SS BOND : bond 0.00220 ( 41) SS BOND : angle 0.77710 ( 82) covalent geometry : bond 0.00297 (26059) covalent geometry : angle 0.54864 (35481) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 45 time to evaluate : 2.752 Fit side-chains revert: symmetry clash REVERT: A 725 GLU cc_start: 0.8016 (mp0) cc_final: 0.7696 (mp0) REVERT: A 762 GLN cc_start: 0.8693 (pp30) cc_final: 0.8458 (pp30) REVERT: B 177 MET cc_start: 0.6618 (ppp) cc_final: 0.5893 (ppp) REVERT: B 238 PHE cc_start: 0.8731 (p90) cc_final: 0.8265 (p90) REVERT: B 780 GLU cc_start: 0.9072 (tm-30) cc_final: 0.8704 (tm-30) REVERT: C 177 MET cc_start: 0.4909 (ptt) cc_final: 0.4367 (ptt) outliers start: 22 outliers final: 13 residues processed: 65 average time/residue: 0.3102 time to fit residues: 38.0362 Evaluate side-chains 58 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 980 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 217 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 51 optimal weight: 0.8980 chunk 180 optimal weight: 0.0570 chunk 310 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 289 optimal weight: 0.2980 chunk 231 optimal weight: 9.9990 chunk 270 optimal weight: 1.9990 chunk 313 optimal weight: 4.9990 overall best weight: 1.4502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 935 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.051043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.037913 restraints weight = 245940.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.038913 restraints weight = 128321.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.039597 restraints weight = 83051.602| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 26104 Z= 0.105 Angle : 0.519 8.826 35575 Z= 0.265 Chirality : 0.042 0.215 4065 Planarity : 0.004 0.057 4574 Dihedral : 6.803 86.113 3901 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.96 % Allowed : 9.85 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.15), residues: 3180 helix: 2.13 (0.21), residues: 662 sheet: -0.02 (0.20), residues: 634 loop : -1.59 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 152 HIS 0.003 0.001 HIS B1083 PHE 0.012 0.001 PHE C 133 TYR 0.017 0.001 TYR A1067 ARG 0.002 0.000 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00108 ( 1) link_NAG-ASN : angle 2.46583 ( 3) link_ALPHA1-4 : bond 0.01168 ( 3) link_ALPHA1-4 : angle 2.28767 ( 9) hydrogen bonds : bond 0.03914 ( 1000) hydrogen bonds : angle 4.97380 ( 2772) SS BOND : bond 0.00186 ( 41) SS BOND : angle 0.68562 ( 82) covalent geometry : bond 0.00230 (26059) covalent geometry : angle 0.51704 (35481) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 50 time to evaluate : 2.929 Fit side-chains revert: symmetry clash REVERT: A 725 GLU cc_start: 0.8011 (mp0) cc_final: 0.7655 (mp0) REVERT: A 762 GLN cc_start: 0.8681 (pp30) cc_final: 0.8433 (pp30) REVERT: B 177 MET cc_start: 0.6504 (ppp) cc_final: 0.5785 (ppp) REVERT: B 238 PHE cc_start: 0.8782 (p90) cc_final: 0.8301 (p90) REVERT: C 177 MET cc_start: 0.4676 (ptt) cc_final: 0.4137 (ptt) REVERT: C 387 LEU cc_start: 0.9659 (mt) cc_final: 0.9412 (mt) REVERT: C 901 GLN cc_start: 0.9492 (OUTLIER) cc_final: 0.9212 (pp30) outliers start: 27 outliers final: 15 residues processed: 74 average time/residue: 0.3182 time to fit residues: 43.8954 Evaluate side-chains 62 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 980 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 255 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 287 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 269 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 243 optimal weight: 0.7980 chunk 183 optimal weight: 0.0010 chunk 234 optimal weight: 1.9990 overall best weight: 1.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.050982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.037875 restraints weight = 244277.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.038871 restraints weight = 127873.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.039536 restraints weight = 82853.281| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 26104 Z= 0.105 Angle : 0.516 8.676 35575 Z= 0.263 Chirality : 0.042 0.229 4065 Planarity : 0.004 0.057 4574 Dihedral : 6.499 83.480 3901 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.92 % Allowed : 10.28 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 3180 helix: 2.26 (0.21), residues: 663 sheet: 0.06 (0.20), residues: 634 loop : -1.52 (0.14), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 152 HIS 0.004 0.001 HIS A1064 PHE 0.016 0.001 PHE A 392 TYR 0.017 0.001 TYR A1067 ARG 0.003 0.000 ARG A1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00058 ( 1) link_NAG-ASN : angle 2.42893 ( 3) link_ALPHA1-4 : bond 0.01149 ( 3) link_ALPHA1-4 : angle 2.07512 ( 9) hydrogen bonds : bond 0.03830 ( 1000) hydrogen bonds : angle 4.88457 ( 2772) SS BOND : bond 0.00314 ( 41) SS BOND : angle 0.71327 ( 82) covalent geometry : bond 0.00233 (26059) covalent geometry : angle 0.51354 (35481) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 49 time to evaluate : 3.086 Fit side-chains revert: symmetry clash REVERT: A 725 GLU cc_start: 0.8161 (mp0) cc_final: 0.7832 (mp0) REVERT: A 740 MET cc_start: 0.9074 (tpp) cc_final: 0.8773 (tpp) REVERT: A 762 GLN cc_start: 0.8639 (pp30) cc_final: 0.8380 (pp30) REVERT: B 177 MET cc_start: 0.6524 (ppp) cc_final: 0.5851 (ppp) REVERT: B 238 PHE cc_start: 0.8783 (p90) cc_final: 0.8252 (p90) REVERT: C 177 MET cc_start: 0.4549 (ptt) cc_final: 0.4022 (ptt) REVERT: C 387 LEU cc_start: 0.9665 (mt) cc_final: 0.9418 (mt) outliers start: 26 outliers final: 18 residues processed: 72 average time/residue: 0.3261 time to fit residues: 42.9230 Evaluate side-chains 65 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 980 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 82 optimal weight: 7.9990 chunk 77 optimal weight: 0.1980 chunk 128 optimal weight: 0.1980 chunk 261 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 12 optimal weight: 30.0000 chunk 85 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 154 optimal weight: 6.9990 chunk 243 optimal weight: 0.0270 chunk 296 optimal weight: 4.9990 overall best weight: 2.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 913 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.050514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.037388 restraints weight = 245783.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.038322 restraints weight = 129418.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.038963 restraints weight = 84212.148| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 26104 Z= 0.129 Angle : 0.530 8.909 35575 Z= 0.271 Chirality : 0.042 0.209 4065 Planarity : 0.004 0.056 4574 Dihedral : 6.359 84.222 3901 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.13 % Allowed : 10.63 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 3180 helix: 2.32 (0.21), residues: 665 sheet: -0.03 (0.20), residues: 618 loop : -1.47 (0.14), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 152 HIS 0.003 0.001 HIS A1064 PHE 0.013 0.001 PHE B 133 TYR 0.016 0.001 TYR A1067 ARG 0.003 0.000 ARG A1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00135 ( 1) link_NAG-ASN : angle 2.49892 ( 3) link_ALPHA1-4 : bond 0.00930 ( 3) link_ALPHA1-4 : angle 2.19365 ( 9) hydrogen bonds : bond 0.03889 ( 1000) hydrogen bonds : angle 4.87056 ( 2772) SS BOND : bond 0.00235 ( 41) SS BOND : angle 0.70905 ( 82) covalent geometry : bond 0.00284 (26059) covalent geometry : angle 0.52784 (35481) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 46 time to evaluate : 2.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 725 GLU cc_start: 0.8280 (mp0) cc_final: 0.7964 (mp0) REVERT: A 740 MET cc_start: 0.9066 (tpp) cc_final: 0.8749 (tpp) REVERT: A 762 GLN cc_start: 0.8670 (pp30) cc_final: 0.8405 (pp30) REVERT: B 177 MET cc_start: 0.6668 (ppp) cc_final: 0.5992 (ppp) REVERT: B 238 PHE cc_start: 0.8818 (p90) cc_final: 0.8318 (p90) REVERT: B 347 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.8136 (m-10) REVERT: C 177 MET cc_start: 0.4560 (ptt) cc_final: 0.4058 (ptt) REVERT: C 901 GLN cc_start: 0.9521 (OUTLIER) cc_final: 0.9152 (pp30) outliers start: 32 outliers final: 19 residues processed: 73 average time/residue: 0.3092 time to fit residues: 41.6649 Evaluate side-chains 66 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 45 time to evaluate : 3.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 980 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 298 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 174 optimal weight: 0.9980 chunk 258 optimal weight: 0.0570 chunk 124 optimal weight: 8.9990 chunk 38 optimal weight: 50.0000 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 0.0370 chunk 117 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 overall best weight: 1.1978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.047993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.033044 restraints weight = 220490.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.034049 restraints weight = 124551.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.034752 restraints weight = 84594.595| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 26104 Z= 0.097 Angle : 0.509 8.986 35575 Z= 0.258 Chirality : 0.042 0.245 4065 Planarity : 0.004 0.057 4574 Dihedral : 6.035 79.571 3901 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.99 % Allowed : 11.06 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.15), residues: 3180 helix: 2.39 (0.21), residues: 664 sheet: 0.12 (0.20), residues: 645 loop : -1.42 (0.14), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 152 HIS 0.003 0.000 HIS A1064 PHE 0.013 0.001 PHE B 133 TYR 0.016 0.001 TYR A1067 ARG 0.005 0.000 ARG A1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00001 ( 1) link_NAG-ASN : angle 2.28596 ( 3) link_ALPHA1-4 : bond 0.00882 ( 3) link_ALPHA1-4 : angle 2.45941 ( 9) hydrogen bonds : bond 0.03692 ( 1000) hydrogen bonds : angle 4.73611 ( 2772) SS BOND : bond 0.00190 ( 41) SS BOND : angle 0.62641 ( 82) covalent geometry : bond 0.00214 (26059) covalent geometry : angle 0.50722 (35481) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 49 time to evaluate : 3.059 Fit side-chains revert: symmetry clash REVERT: A 725 GLU cc_start: 0.8269 (mp0) cc_final: 0.7906 (mp0) REVERT: A 762 GLN cc_start: 0.8685 (pp30) cc_final: 0.8458 (pp30) REVERT: B 177 MET cc_start: 0.6903 (ppp) cc_final: 0.6214 (ppp) REVERT: B 238 PHE cc_start: 0.8909 (p90) cc_final: 0.8387 (p90) REVERT: B 347 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.8237 (m-10) REVERT: B 697 MET cc_start: 0.8047 (mmm) cc_final: 0.7604 (mmp) REVERT: C 177 MET cc_start: 0.4726 (ptt) cc_final: 0.4043 (ptt) REVERT: C 901 GLN cc_start: 0.9503 (OUTLIER) cc_final: 0.9154 (pp30) outliers start: 28 outliers final: 18 residues processed: 73 average time/residue: 0.3028 time to fit residues: 41.9745 Evaluate side-chains 64 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 980 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 74 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 223 optimal weight: 10.0000 chunk 264 optimal weight: 1.9990 chunk 292 optimal weight: 10.0000 chunk 276 optimal weight: 7.9990 chunk 304 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 chunk 189 optimal weight: 0.9980 chunk 45 optimal weight: 30.0000 chunk 228 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 HIS B 125 ASN C 913 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.049835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.036554 restraints weight = 246254.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.037497 restraints weight = 130410.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.038139 restraints weight = 85267.009| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 26104 Z= 0.178 Angle : 0.574 9.899 35575 Z= 0.291 Chirality : 0.042 0.178 4065 Planarity : 0.004 0.056 4574 Dihedral : 6.430 87.064 3901 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.10 % Allowed : 11.20 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.15), residues: 3180 helix: 2.33 (0.21), residues: 662 sheet: -0.02 (0.20), residues: 620 loop : -1.49 (0.14), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 152 HIS 0.004 0.001 HIS C1048 PHE 0.014 0.001 PHE B 347 TYR 0.016 0.001 TYR A1067 ARG 0.004 0.000 ARG A1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00031 ( 1) link_NAG-ASN : angle 2.67082 ( 3) link_ALPHA1-4 : bond 0.00794 ( 3) link_ALPHA1-4 : angle 2.30023 ( 9) hydrogen bonds : bond 0.04053 ( 1000) hydrogen bonds : angle 4.95317 ( 2772) SS BOND : bond 0.00247 ( 41) SS BOND : angle 0.78017 ( 82) covalent geometry : bond 0.00386 (26059) covalent geometry : angle 0.57139 (35481) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 41 time to evaluate : 3.213 Fit side-chains revert: symmetry clash REVERT: A 762 GLN cc_start: 0.8720 (pp30) cc_final: 0.8458 (pp30) REVERT: B 177 MET cc_start: 0.6785 (ppp) cc_final: 0.6152 (ppp) REVERT: B 238 PHE cc_start: 0.8868 (p90) cc_final: 0.8377 (p90) REVERT: C 177 MET cc_start: 0.4769 (ptt) cc_final: 0.4283 (ptt) REVERT: C 901 GLN cc_start: 0.9537 (OUTLIER) cc_final: 0.9068 (pp30) outliers start: 31 outliers final: 24 residues processed: 68 average time/residue: 0.3388 time to fit residues: 42.8821 Evaluate side-chains 64 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 39 time to evaluate : 3.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 169 optimal weight: 7.9990 chunk 171 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 276 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 162 optimal weight: 7.9990 chunk 186 optimal weight: 0.0270 chunk 190 optimal weight: 5.9990 chunk 210 optimal weight: 0.7980 chunk 290 optimal weight: 5.9990 chunk 165 optimal weight: 0.3980 overall best weight: 2.6442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 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 = 0.3479 r_free = 0.3479 target = 0.050233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.037032 restraints weight = 245328.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.037966 restraints weight = 129476.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.038647 restraints weight = 84248.751| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 26104 Z= 0.137 Angle : 0.538 10.174 35575 Z= 0.272 Chirality : 0.042 0.208 4065 Planarity : 0.004 0.057 4574 Dihedral : 6.324 85.502 3901 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.99 % Allowed : 11.55 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 3180 helix: 2.41 (0.21), residues: 661 sheet: -0.01 (0.20), residues: 658 loop : -1.43 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 152 HIS 0.005 0.001 HIS A1064 PHE 0.013 0.001 PHE B 133 TYR 0.016 0.001 TYR C1067 ARG 0.003 0.000 ARG A1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00056 ( 1) link_NAG-ASN : angle 2.47056 ( 3) link_ALPHA1-4 : bond 0.00838 ( 3) link_ALPHA1-4 : angle 2.46882 ( 9) hydrogen bonds : bond 0.03892 ( 1000) hydrogen bonds : angle 4.85117 ( 2772) SS BOND : bond 0.00220 ( 41) SS BOND : angle 0.72000 ( 82) covalent geometry : bond 0.00301 (26059) covalent geometry : angle 0.53578 (35481) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 43 time to evaluate : 3.152 Fit side-chains revert: symmetry clash REVERT: A 762 GLN cc_start: 0.8702 (pp30) cc_final: 0.8430 (pp30) REVERT: B 177 MET cc_start: 0.6685 (ppp) cc_final: 0.6101 (ppp) REVERT: B 238 PHE cc_start: 0.8843 (p90) cc_final: 0.8374 (p90) REVERT: C 176 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8633 (tp) REVERT: C 177 MET cc_start: 0.4711 (ptt) cc_final: 0.3543 (ptt) REVERT: C 901 GLN cc_start: 0.9535 (OUTLIER) cc_final: 0.9121 (pp30) outliers start: 28 outliers final: 25 residues processed: 67 average time/residue: 0.3190 time to fit residues: 40.0335 Evaluate side-chains 70 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 43 time to evaluate : 3.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 980 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 136 optimal weight: 3.9990 chunk 285 optimal weight: 1.9990 chunk 223 optimal weight: 8.9990 chunk 15 optimal weight: 30.0000 chunk 184 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 239 optimal weight: 0.0040 chunk 49 optimal weight: 20.0000 chunk 157 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 262 optimal weight: 5.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN B 913 GLN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.047922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.033185 restraints weight = 219528.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.034215 restraints weight = 124710.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.034905 restraints weight = 84887.041| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 26104 Z= 0.096 Angle : 0.518 11.905 35575 Z= 0.260 Chirality : 0.042 0.246 4065 Planarity : 0.004 0.058 4574 Dihedral : 5.927 79.715 3901 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.99 % Allowed : 11.66 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.15), residues: 3180 helix: 2.50 (0.21), residues: 660 sheet: 0.13 (0.20), residues: 660 loop : -1.35 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 152 HIS 0.002 0.000 HIS B1083 PHE 0.015 0.001 PHE B 133 TYR 0.015 0.001 TYR C1067 ARG 0.004 0.000 ARG A1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00124 ( 1) link_NAG-ASN : angle 2.17422 ( 3) link_ALPHA1-4 : bond 0.00779 ( 3) link_ALPHA1-4 : angle 2.60719 ( 9) hydrogen bonds : bond 0.03639 ( 1000) hydrogen bonds : angle 4.67385 ( 2772) SS BOND : bond 0.00185 ( 41) SS BOND : angle 0.62966 ( 82) covalent geometry : bond 0.00213 (26059) covalent geometry : angle 0.51595 (35481) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10006.06 seconds wall clock time: 175 minutes 45.78 seconds (10545.78 seconds total)