Starting phenix.real_space_refine on Mon Aug 25 06:38:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uuo_42592/08_2025/8uuo_42592.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uuo_42592/08_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_42592/08_2025/8uuo_42592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uuo_42592/08_2025/8uuo_42592.map" model { file = "/net/cci-nas-00/data/ceres_data/8uuo_42592/08_2025/8uuo_42592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uuo_42592/08_2025/8uuo_42592.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 6.44, per 1000 atoms: 0.25 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: 2.17 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.31 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: 6.98 Time building geometry restraints manager: 2.88 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: 4.550 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: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.910 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.060 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.400 ------------------------------------------------------------------------------- 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 : 6.62 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.015 0.001 ARG A 466 TYR 0.040 0.003 TYR C 873 PHE 0.049 0.003 PHE C 559 TRP 0.058 0.003 TRP C 152 HIS 0.012 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00758 (26059) covalent geometry : angle 1.09523 (35481) SS BOND : bond 0.00542 ( 41) SS BOND : angle 1.53458 ( 82) hydrogen bonds : bond 0.15662 ( 1000) hydrogen bonds : angle 7.50125 ( 2772) link_ALPHA1-4 : bond 0.00948 ( 3) link_ALPHA1-4 : angle 3.03106 ( 9) link_NAG-ASN : bond 0.00938 ( 1) link_NAG-ASN : angle 6.24728 ( 3) *********************** 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 : 1.021 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: 0.9156 (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: 0.1637 time to fit residues: 18.8315 Evaluate side-chains 50 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.8980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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** B 914 ASN B 935 GLN 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 = 0.3438 r_free = 0.3438 target = 0.048243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.033099 restraints weight = 218749.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.034147 restraints weight = 122745.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.034859 restraints weight = 82944.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.035318 restraints weight = 63157.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.035666 restraints weight = 52468.642| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26104 Z= 0.140 Angle : 0.615 9.592 35575 Z= 0.320 Chirality : 0.044 0.252 4065 Planarity : 0.005 0.065 4574 Dihedral : 9.612 100.019 3904 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.18 % Allowed : 4.43 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.14), residues: 3180 helix: 1.04 (0.20), residues: 659 sheet: -0.26 (0.20), residues: 634 loop : -1.84 (0.13), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1019 TYR 0.018 0.001 TYR C1067 PHE 0.019 0.001 PHE C 133 TRP 0.018 0.001 TRP C 152 HIS 0.008 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00290 (26059) covalent geometry : angle 0.61203 (35481) SS BOND : bond 0.00265 ( 41) SS BOND : angle 0.92024 ( 82) hydrogen bonds : bond 0.04967 ( 1000) hydrogen bonds : angle 5.82487 ( 2772) link_ALPHA1-4 : bond 0.01121 ( 3) link_ALPHA1-4 : angle 3.04169 ( 9) link_NAG-ASN : bond 0.00150 ( 1) link_NAG-ASN : angle 3.31610 ( 3) *********************** 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 61 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9009 (mt) cc_final: 0.8728 (tp) REVERT: A 740 MET cc_start: 0.9370 (tpt) cc_final: 0.9144 (tpp) REVERT: B 177 MET cc_start: 0.6469 (ppp) cc_final: 0.5691 (ppp) REVERT: B 238 PHE cc_start: 0.8670 (p90) cc_final: 0.8209 (p90) REVERT: B 1050 MET cc_start: 0.8427 (ptp) cc_final: 0.8145 (ptp) REVERT: C 177 MET cc_start: 0.5034 (ptt) cc_final: 0.4371 (ptt) outliers start: 5 outliers final: 2 residues processed: 60 average time/residue: 0.1639 time to fit residues: 17.4148 Evaluate side-chains 47 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 90 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 206 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 39 optimal weight: 30.0000 chunk 181 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 253 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 184 optimal weight: 2.9990 chunk 295 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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** A1135 ASN B 239 GLN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3476 r_free = 0.3476 target = 0.050065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.036685 restraints weight = 247641.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.037651 restraints weight = 130655.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.038305 restraints weight = 85162.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.038756 restraints weight = 63621.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.038992 restraints weight = 52418.287| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 26104 Z= 0.204 Angle : 0.621 9.341 35575 Z= 0.320 Chirality : 0.044 0.219 4065 Planarity : 0.004 0.060 4574 Dihedral : 8.579 100.665 3901 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.46 % Allowed : 7.30 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.14), residues: 3180 helix: 1.37 (0.20), residues: 682 sheet: -0.31 (0.20), residues: 621 loop : -1.73 (0.13), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 765 TYR 0.018 0.001 TYR C1067 PHE 0.015 0.001 PHE C 559 TRP 0.018 0.001 TRP C 152 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00438 (26059) covalent geometry : angle 0.61865 (35481) SS BOND : bond 0.00293 ( 41) SS BOND : angle 0.90993 ( 82) hydrogen bonds : bond 0.04764 ( 1000) hydrogen bonds : angle 5.58072 ( 2772) link_ALPHA1-4 : bond 0.01128 ( 3) link_ALPHA1-4 : angle 2.41712 ( 9) link_NAG-ASN : bond 0.00387 ( 1) link_NAG-ASN : angle 3.36448 ( 3) *********************** 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 59 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 762 GLN cc_start: 0.8714 (pp30) cc_final: 0.8411 (pp30) REVERT: B 177 MET cc_start: 0.6480 (ppp) cc_final: 0.5745 (ppp) REVERT: B 238 PHE cc_start: 0.8684 (p90) cc_final: 0.8232 (p90) REVERT: B 1050 MET cc_start: 0.8540 (ptp) cc_final: 0.8180 (ptp) REVERT: C 177 MET cc_start: 0.4897 (ptt) cc_final: 0.4394 (ptt) outliers start: 13 outliers final: 6 residues processed: 58 average time/residue: 0.1448 time to fit residues: 15.6433 Evaluate side-chains 48 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 213 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 980 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 218 optimal weight: 9.9990 chunk 162 optimal weight: 6.9990 chunk 217 optimal weight: 7.9990 chunk 245 optimal weight: 10.0000 chunk 14 optimal weight: 0.0040 chunk 154 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 313 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 overall best weight: 3.6000 ------------------------------------------------------------------------------- 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** B 613 GLN C 52 GLN C1134 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.050013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.036656 restraints weight = 245328.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.037621 restraints weight = 130093.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.038259 restraints weight = 84814.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.038621 restraints weight = 63548.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.038964 restraints weight = 52824.355| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 26104 Z= 0.181 Angle : 0.587 9.013 35575 Z= 0.301 Chirality : 0.043 0.195 4065 Planarity : 0.004 0.058 4574 Dihedral : 7.612 89.661 3901 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.96 % Allowed : 8.82 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.15), residues: 3180 helix: 1.65 (0.21), residues: 677 sheet: -0.24 (0.20), residues: 606 loop : -1.69 (0.13), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1019 TYR 0.018 0.001 TYR C1067 PHE 0.014 0.001 PHE B 347 TRP 0.019 0.001 TRP C 152 HIS 0.007 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00391 (26059) covalent geometry : angle 0.58410 (35481) SS BOND : bond 0.00248 ( 41) SS BOND : angle 0.82454 ( 82) hydrogen bonds : bond 0.04446 ( 1000) hydrogen bonds : angle 5.37340 ( 2772) link_ALPHA1-4 : bond 0.01337 ( 3) link_ALPHA1-4 : angle 2.78114 ( 9) link_NAG-ASN : bond 0.00297 ( 1) link_NAG-ASN : angle 2.99671 ( 3) *********************** 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 72 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 45 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: A 740 MET cc_start: 0.9104 (tpp) cc_final: 0.8784 (tpp) REVERT: A 762 GLN cc_start: 0.8690 (pp30) cc_final: 0.8424 (pp30) REVERT: B 177 MET cc_start: 0.6524 (ppp) cc_final: 0.5876 (ppp) REVERT: B 238 PHE cc_start: 0.8800 (p90) cc_final: 0.8331 (p90) REVERT: C 1134 ASN cc_start: 0.8856 (OUTLIER) cc_final: 0.8498 (m110) outliers start: 27 outliers final: 15 residues processed: 70 average time/residue: 0.1415 time to fit residues: 18.2638 Evaluate side-chains 60 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 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 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 980 ILE Chi-restraints excluded: chain C residue 1134 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 176 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 219 optimal weight: 20.0000 chunk 90 optimal weight: 0.0060 chunk 30 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 42 optimal weight: 0.0040 chunk 16 optimal weight: 20.0000 chunk 292 optimal weight: 0.8980 chunk 186 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 overall best weight: 0.9812 ------------------------------------------------------------------------------- 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 ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.051138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.038005 restraints weight = 243560.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.039012 restraints weight = 127357.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.039700 restraints weight = 82562.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.040131 restraints weight = 61314.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.040407 restraints weight = 50180.531| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 26104 Z= 0.099 Angle : 0.525 8.706 35575 Z= 0.268 Chirality : 0.043 0.234 4065 Planarity : 0.004 0.058 4574 Dihedral : 6.863 85.251 3901 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.82 % Allowed : 9.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.15), residues: 3180 helix: 2.10 (0.21), residues: 662 sheet: -0.03 (0.20), residues: 628 loop : -1.60 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1019 TYR 0.017 0.001 TYR A1067 PHE 0.013 0.001 PHE C 133 TRP 0.018 0.001 TRP C 152 HIS 0.004 0.000 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00214 (26059) covalent geometry : angle 0.52281 (35481) SS BOND : bond 0.00190 ( 41) SS BOND : angle 0.69254 ( 82) hydrogen bonds : bond 0.04008 ( 1000) hydrogen bonds : angle 5.00687 ( 2772) link_ALPHA1-4 : bond 0.01271 ( 3) link_ALPHA1-4 : angle 2.39252 ( 9) link_NAG-ASN : bond 0.00017 ( 1) link_NAG-ASN : angle 2.47925 ( 3) *********************** 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 71 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 48 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: B 177 MET cc_start: 0.6452 (ppp) cc_final: 0.5816 (ppp) REVERT: B 238 PHE cc_start: 0.8756 (p90) cc_final: 0.8308 (p90) REVERT: C 104 TRP cc_start: 0.7111 (m-90) cc_final: 0.6873 (m-90) REVERT: C 241 LEU cc_start: 0.9352 (mp) cc_final: 0.8976 (tt) REVERT: C 901 GLN cc_start: 0.9483 (OUTLIER) cc_final: 0.9215 (pp30) outliers start: 23 outliers final: 12 residues processed: 69 average time/residue: 0.1328 time to fit residues: 17.0210 Evaluate side-chains 57 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 159 VAL Chi-restraints excluded: chain C residue 587 ILE 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 52 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 270 optimal weight: 0.3980 chunk 155 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 139 optimal weight: 9.9990 chunk 5 optimal weight: 30.0000 chunk 22 optimal weight: 7.9990 chunk 285 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 overall best weight: 6.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 HIS ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS B 125 ASN B 239 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.046053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.031294 restraints weight = 222426.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.032241 restraints weight = 126493.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.032900 restraints weight = 86560.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.033345 restraints weight = 66320.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 72)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.033657 restraints weight = 55162.094| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.133 26104 Z= 0.301 Angle : 0.692 9.465 35575 Z= 0.354 Chirality : 0.044 0.156 4065 Planarity : 0.004 0.056 4574 Dihedral : 7.614 99.078 3901 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.28 % Allowed : 10.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.15), residues: 3180 helix: 1.65 (0.20), residues: 674 sheet: -0.28 (0.20), residues: 623 loop : -1.72 (0.13), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 319 TYR 0.017 0.002 TYR B 396 PHE 0.030 0.002 PHE A 392 TRP 0.017 0.002 TRP C 436 HIS 0.006 0.002 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00645 (26059) covalent geometry : angle 0.68990 (35481) SS BOND : bond 0.00369 ( 41) SS BOND : angle 1.03107 ( 82) hydrogen bonds : bond 0.04750 ( 1000) hydrogen bonds : angle 5.51732 ( 2772) link_ALPHA1-4 : bond 0.01412 ( 3) link_ALPHA1-4 : angle 2.10145 ( 9) link_NAG-ASN : bond 0.00586 ( 1) link_NAG-ASN : angle 3.29936 ( 3) *********************** 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 77 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 41 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: B 177 MET cc_start: 0.6715 (ppp) cc_final: 0.6134 (ppp) REVERT: B 238 PHE cc_start: 0.8921 (p90) cc_final: 0.8438 (p90) REVERT: C 177 MET cc_start: 0.4396 (ptt) cc_final: 0.4116 (ptt) REVERT: C 241 LEU cc_start: 0.9549 (mp) cc_final: 0.9202 (tt) outliers start: 36 outliers final: 23 residues processed: 72 average time/residue: 0.1398 time to fit residues: 18.4312 Evaluate side-chains 62 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 39 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE 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 954 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 15 CYS 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 297 optimal weight: 4.9990 chunk 219 optimal weight: 20.0000 chunk 279 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 206 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 241 optimal weight: 7.9990 chunk 175 optimal weight: 0.8980 chunk 74 optimal weight: 0.0470 chunk 5 optimal weight: 9.9990 chunk 44 optimal weight: 50.0000 overall best weight: 1.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 717 ASN ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.047504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.032623 restraints weight = 221440.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.033612 restraints weight = 127555.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.034293 restraints weight = 87554.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.034737 restraints weight = 67412.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.035027 restraints weight = 56262.741| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 26104 Z= 0.110 Angle : 0.535 9.272 35575 Z= 0.273 Chirality : 0.043 0.239 4065 Planarity : 0.004 0.059 4574 Dihedral : 6.667 85.227 3901 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.03 % Allowed : 11.20 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.15), residues: 3180 helix: 2.14 (0.21), residues: 671 sheet: -0.11 (0.20), residues: 618 loop : -1.57 (0.14), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 577 TYR 0.017 0.001 TYR C1067 PHE 0.012 0.001 PHE B 133 TRP 0.019 0.001 TRP C 152 HIS 0.003 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00239 (26059) covalent geometry : angle 0.53240 (35481) SS BOND : bond 0.00211 ( 41) SS BOND : angle 0.75089 ( 82) hydrogen bonds : bond 0.04107 ( 1000) hydrogen bonds : angle 5.02079 ( 2772) link_ALPHA1-4 : bond 0.01149 ( 3) link_ALPHA1-4 : angle 2.18107 ( 9) link_NAG-ASN : bond 0.00107 ( 1) link_NAG-ASN : angle 2.52059 ( 3) *********************** 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 74 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 45 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7482 (tt) REVERT: A 762 GLN cc_start: 0.8710 (pp30) cc_final: 0.8508 (pp30) REVERT: A 964 LYS cc_start: 0.9429 (mmmt) cc_final: 0.9221 (ptpp) REVERT: B 177 MET cc_start: 0.6881 (ppp) cc_final: 0.6215 (ppp) REVERT: B 238 PHE cc_start: 0.8870 (p90) cc_final: 0.8365 (p90) REVERT: B 298 GLU cc_start: 0.9536 (OUTLIER) cc_final: 0.9251 (mt-10) REVERT: C 177 MET cc_start: 0.4265 (ptt) cc_final: 0.4063 (ptt) REVERT: C 241 LEU cc_start: 0.9438 (mp) cc_final: 0.9076 (tt) REVERT: C 901 GLN cc_start: 0.9510 (OUTLIER) cc_final: 0.9085 (pp30) outliers start: 29 outliers final: 17 residues processed: 71 average time/residue: 0.1424 time to fit residues: 17.7513 Evaluate side-chains 62 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 42 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 320 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 298 GLU 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 B residue 731 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 121 optimal weight: 20.0000 chunk 215 optimal weight: 4.9990 chunk 135 optimal weight: 0.6980 chunk 265 optimal weight: 20.0000 chunk 100 optimal weight: 6.9990 chunk 301 optimal weight: 5.9990 chunk 281 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 183 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN C 146 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.049121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.035815 restraints weight = 247096.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.036737 restraints weight = 131799.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.037367 restraints weight = 86243.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.037804 restraints weight = 64692.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.038076 restraints weight = 53396.277| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 26104 Z= 0.209 Angle : 0.599 9.849 35575 Z= 0.305 Chirality : 0.043 0.243 4065 Planarity : 0.004 0.056 4574 Dihedral : 7.010 93.507 3901 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.38 % Allowed : 11.30 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.15), residues: 3180 helix: 2.05 (0.21), residues: 668 sheet: -0.28 (0.20), residues: 624 loop : -1.60 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 408 TYR 0.015 0.001 TYR C1067 PHE 0.021 0.001 PHE B 135 TRP 0.027 0.002 TRP C 152 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00453 (26059) covalent geometry : angle 0.59642 (35481) SS BOND : bond 0.00286 ( 41) SS BOND : angle 0.83918 ( 82) hydrogen bonds : bond 0.04333 ( 1000) hydrogen bonds : angle 5.20223 ( 2772) link_ALPHA1-4 : bond 0.00853 ( 3) link_ALPHA1-4 : angle 2.11929 ( 9) link_NAG-ASN : bond 0.00429 ( 1) link_NAG-ASN : angle 2.87288 ( 3) *********************** 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 82 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 43 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 762 GLN cc_start: 0.8716 (pp30) cc_final: 0.8505 (pp30) REVERT: B 177 MET cc_start: 0.6858 (ppp) cc_final: 0.6312 (ppp) REVERT: B 238 PHE cc_start: 0.8921 (p90) cc_final: 0.8473 (p90) REVERT: B 298 GLU cc_start: 0.9528 (OUTLIER) cc_final: 0.9235 (mt-10) REVERT: C 176 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8597 (tp) REVERT: C 177 MET cc_start: 0.4194 (ptt) cc_final: 0.3389 (ptt) REVERT: C 241 LEU cc_start: 0.9434 (mp) cc_final: 0.9083 (tt) REVERT: C 901 GLN cc_start: 0.9525 (OUTLIER) cc_final: 0.9124 (pp30) outliers start: 39 outliers final: 26 residues processed: 77 average time/residue: 0.1400 time to fit residues: 19.7230 Evaluate side-chains 71 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 42 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE 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 582 LEU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 298 GLU 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 117 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 304 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 chunk 268 optimal weight: 6.9990 chunk 245 optimal weight: 10.0000 chunk 238 optimal weight: 6.9990 chunk 313 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.048852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.035556 restraints weight = 247375.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.036461 restraints weight = 131465.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.037095 restraints weight = 86283.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.037520 restraints weight = 64732.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.037801 restraints weight = 53530.905| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 26104 Z= 0.216 Angle : 0.615 11.615 35575 Z= 0.313 Chirality : 0.043 0.262 4065 Planarity : 0.004 0.057 4574 Dihedral : 7.124 93.979 3901 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.17 % Allowed : 11.91 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.15), residues: 3180 helix: 1.95 (0.21), residues: 673 sheet: -0.35 (0.20), residues: 635 loop : -1.67 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 408 TYR 0.016 0.001 TYR C1067 PHE 0.015 0.001 PHE B 347 TRP 0.019 0.001 TRP C 152 HIS 0.004 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00468 (26059) covalent geometry : angle 0.61306 (35481) SS BOND : bond 0.00268 ( 41) SS BOND : angle 0.90934 ( 82) hydrogen bonds : bond 0.04451 ( 1000) hydrogen bonds : angle 5.28476 ( 2772) link_ALPHA1-4 : bond 0.00841 ( 3) link_ALPHA1-4 : angle 2.20353 ( 9) link_NAG-ASN : bond 0.00346 ( 1) link_NAG-ASN : angle 2.85422 ( 3) *********************** 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 76 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 43 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: A 762 GLN cc_start: 0.8717 (pp30) cc_final: 0.8496 (pp30) REVERT: B 177 MET cc_start: 0.6875 (ppp) cc_final: 0.6488 (ppp) REVERT: B 238 PHE cc_start: 0.8967 (p90) cc_final: 0.8532 (p90) REVERT: B 298 GLU cc_start: 0.9547 (OUTLIER) cc_final: 0.9236 (mt-10) REVERT: C 153 MET cc_start: 0.8771 (pmm) cc_final: 0.8453 (pmm) REVERT: C 176 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8640 (tp) REVERT: C 177 MET cc_start: 0.4350 (ptt) cc_final: 0.3742 (ptt) REVERT: C 241 LEU cc_start: 0.9452 (mp) cc_final: 0.9099 (tt) REVERT: C 901 GLN cc_start: 0.9537 (OUTLIER) cc_final: 0.9219 (pp30) outliers start: 33 outliers final: 26 residues processed: 70 average time/residue: 0.1391 time to fit residues: 18.0249 Evaluate side-chains 69 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 40 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 582 LEU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 298 GLU 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 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 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 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 990 GLU 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 85 optimal weight: 6.9990 chunk 38 optimal weight: 50.0000 chunk 212 optimal weight: 7.9990 chunk 214 optimal weight: 5.9990 chunk 173 optimal weight: 8.9990 chunk 200 optimal weight: 6.9990 chunk 247 optimal weight: 10.0000 chunk 259 optimal weight: 20.0000 chunk 240 optimal weight: 10.0000 chunk 297 optimal weight: 0.7980 chunk 18 optimal weight: 30.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 211 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 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 = 0.3416 r_free = 0.3416 target = 0.048062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.034736 restraints weight = 247659.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.035639 restraints weight = 132649.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.036262 restraints weight = 87759.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.036694 restraints weight = 66058.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.036989 restraints weight = 54530.184| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 26104 Z= 0.273 Angle : 0.682 12.083 35575 Z= 0.347 Chirality : 0.044 0.285 4065 Planarity : 0.004 0.055 4574 Dihedral : 7.507 97.828 3901 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.20 % Allowed : 12.12 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.15), residues: 3180 helix: 1.69 (0.20), residues: 673 sheet: -0.48 (0.20), residues: 634 loop : -1.80 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 905 TYR 0.017 0.002 TYR C1067 PHE 0.053 0.002 PHE B 135 TRP 0.024 0.002 TRP C 436 HIS 0.006 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00587 (26059) covalent geometry : angle 0.67981 (35481) SS BOND : bond 0.00353 ( 41) SS BOND : angle 1.03613 ( 82) hydrogen bonds : bond 0.04783 ( 1000) hydrogen bonds : angle 5.56296 ( 2772) link_ALPHA1-4 : bond 0.00833 ( 3) link_ALPHA1-4 : angle 2.22582 ( 9) link_NAG-ASN : bond 0.00596 ( 1) link_NAG-ASN : angle 3.09641 ( 3) ********************** 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 75 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 41 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 762 GLN cc_start: 0.8791 (pp30) cc_final: 0.8533 (pp30) REVERT: B 238 PHE cc_start: 0.9070 (p90) cc_final: 0.8616 (p90) REVERT: B 298 GLU cc_start: 0.9554 (OUTLIER) cc_final: 0.9196 (mt-10) REVERT: B 697 MET cc_start: 0.8363 (mmm) cc_final: 0.8000 (mmp) REVERT: C 153 MET cc_start: 0.8743 (pmm) cc_final: 0.8402 (pmm) REVERT: C 176 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8731 (tp) REVERT: C 177 MET cc_start: 0.4747 (ptt) cc_final: 0.4132 (ptt) REVERT: C 241 LEU cc_start: 0.9468 (mp) cc_final: 0.9136 (tt) REVERT: C 901 GLN cc_start: 0.9536 (OUTLIER) cc_final: 0.9250 (pp30) outliers start: 34 outliers final: 27 residues processed: 70 average time/residue: 0.1370 time to fit residues: 17.7148 Evaluate side-chains 70 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 40 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE 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 731 MET Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 298 GLU 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 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 62 VAL 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 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 83 optimal weight: 3.9990 chunk 214 optimal weight: 8.9990 chunk 235 optimal weight: 20.0000 chunk 149 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 212 optimal weight: 7.9990 chunk 289 optimal weight: 0.6980 chunk 50 optimal weight: 7.9990 chunk 59 optimal weight: 20.0000 chunk 25 optimal weight: 0.9990 chunk 257 optimal weight: 20.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 949 GLN ** 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 = 0.3359 r_free = 0.3359 target = 0.045845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.031220 restraints weight = 218278.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.032187 restraints weight = 123922.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.032840 restraints weight = 84657.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.033267 restraints weight = 64825.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.033601 restraints weight = 53940.441| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 26104 Z= 0.209 Angle : 0.616 11.157 35575 Z= 0.313 Chirality : 0.044 0.184 4065 Planarity : 0.004 0.057 4574 Dihedral : 7.204 92.960 3901 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.24 % Allowed : 12.23 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.15), residues: 3180 helix: 1.87 (0.21), residues: 673 sheet: -0.48 (0.20), residues: 628 loop : -1.76 (0.14), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 577 TYR 0.017 0.001 TYR C1067 PHE 0.038 0.001 PHE B 135 TRP 0.021 0.001 TRP C 152 HIS 0.005 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00454 (26059) covalent geometry : angle 0.61347 (35481) SS BOND : bond 0.00294 ( 41) SS BOND : angle 0.89306 ( 82) hydrogen bonds : bond 0.04484 ( 1000) hydrogen bonds : angle 5.38620 ( 2772) link_ALPHA1-4 : bond 0.00871 ( 3) link_ALPHA1-4 : angle 2.30199 ( 9) link_NAG-ASN : bond 0.00411 ( 1) link_NAG-ASN : angle 2.80302 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5390.88 seconds wall clock time: 93 minutes 38.98 seconds (5618.98 seconds total)