Starting phenix.real_space_refine on Wed Jun 18 13:42:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tpi_26056/06_2025/7tpi_26056.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tpi_26056/06_2025/7tpi_26056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tpi_26056/06_2025/7tpi_26056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tpi_26056/06_2025/7tpi_26056.map" model { file = "/net/cci-nas-00/data/ceres_data/7tpi_26056/06_2025/7tpi_26056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tpi_26056/06_2025/7tpi_26056.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.089 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 96 5.16 5 C 13644 2.51 5 N 3516 2.21 5 O 3912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21168 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 954, 6804 Classifications: {'peptide': 954} Incomplete info: {'truncation_to_alanine': 233} Link IDs: {'PTRANS': 53, 'TRANS': 900} Chain breaks: 13 Unresolved non-hydrogen bonds: 698 Unresolved non-hydrogen angles: 879 Unresolved non-hydrogen dihedrals: 535 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 15, 'TYR:plan': 4, 'ASN:plan1': 19, 'ASP:plan': 29, 'PHE:plan': 3, 'GLU:plan': 21, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 389 Chain: "B" Number of atoms: 6804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 954, 6804 Classifications: {'peptide': 954} Incomplete info: {'truncation_to_alanine': 233} Link IDs: {'PTRANS': 53, 'TRANS': 900} Chain breaks: 13 Unresolved non-hydrogen bonds: 698 Unresolved non-hydrogen angles: 879 Unresolved non-hydrogen dihedrals: 535 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 15, 'TYR:plan': 4, 'ASN:plan1': 19, 'ASP:plan': 29, 'PHE:plan': 3, 'GLU:plan': 21, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 389 Chain: "C" Number of atoms: 6804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 954, 6804 Classifications: {'peptide': 954} Incomplete info: {'truncation_to_alanine': 233} Link IDs: {'PTRANS': 53, 'TRANS': 900} Chain breaks: 13 Unresolved non-hydrogen bonds: 698 Unresolved non-hydrogen angles: 879 Unresolved non-hydrogen dihedrals: 535 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 15, 'TYR:plan': 4, 'ASN:plan1': 19, 'ASP:plan': 29, 'PHE:plan': 3, 'GLU:plan': 21, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 389 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 15.00, per 1000 atoms: 0.71 Number of scatterers: 21168 At special positions: 0 Unit cell: (127, 124, 167, 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 96 16.00 O 3912 8.00 N 3516 7.00 C 13644 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.11 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 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=2.11 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.11 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 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.11 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.11 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.11 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 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.11 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 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=2.11 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.11 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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=3, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 657 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A1098 " " NAG A1305 " - " ASN A1134 " " NAG A1306 " - " ASN A 234 " " NAG A1307 " - " ASN A 282 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A 603 " " NAG A1310 " - " ASN A 165 " " NAG A1311 " - " ASN A 122 " " NAG A1312 " - " ASN A 61 " " NAG A1313 " - " ASN A 331 " " NAG A1314 " - " ASN A 343 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 657 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B1098 " " NAG B1305 " - " ASN B1134 " " NAG B1306 " - " ASN B 234 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 603 " " NAG B1310 " - " ASN B 165 " " NAG B1311 " - " ASN B 122 " " NAG B1312 " - " ASN B 61 " " NAG B1313 " - " ASN B 331 " " NAG B1314 " - " ASN B 343 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 657 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C1098 " " NAG C1305 " - " ASN C1134 " " NAG C1306 " - " ASN C 234 " " NAG C1307 " - " ASN C 282 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 603 " " NAG C1310 " - " ASN C 165 " " NAG C1311 " - " ASN C 122 " " NAG C1312 " - " ASN C 61 " " NAG C1313 " - " ASN C 331 " " NAG C1314 " - " ASN C 343 " " NAG D 1 " - " ASN A 801 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN B 801 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN C 801 " " NAG I 1 " - " ASN C 717 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.42 Conformation dependent library (CDL) restraints added in 2.8 seconds 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5400 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 42 sheets defined 26.8% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.36 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.906A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.736A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.813A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.635A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.026A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 940 through 944 removed outlier: 6.586A pdb=" N SER A 943 " --> pdb=" O SER A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.989A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.757A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.905A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.736A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 744 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: 3.813A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.635A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.026A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 940 through 944 removed outlier: 6.586A pdb=" N SER B 943 " --> pdb=" O SER B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.989A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.757A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.906A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.736A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 744 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: 3.813A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.635A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.027A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 940 through 944 removed outlier: 6.586A pdb=" N SER C 943 " --> pdb=" O SER C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.989A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.757A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 7.895A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.738A 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: 4.212A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.364A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.558A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.299A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.459A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 7.727A pdb=" N ASN A 394 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 10.065A pdb=" N ALA A 522 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.504A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) 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 654 through 655 removed outlier: 6.609A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.723A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.723A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.992A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.736A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 29 through 30 removed outlier: 7.895A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.365A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.557A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.299A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.458A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 7.727A pdb=" N ASN B 394 " --> pdb=" O ALA B 522 " (cutoff:3.500A) removed outlier: 10.065A pdb=" N ALA B 522 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.504A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.608A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.723A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.723A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.737A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 29 through 30 removed outlier: 7.895A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.365A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.557A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.299A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 7.727A pdb=" N ASN C 394 " --> pdb=" O ALA C 522 " (cutoff:3.500A) removed outlier: 10.065A pdb=" N ALA C 522 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.504A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.608A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.723A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.723A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.737A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1068 hydrogen bonds defined for protein. 2925 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: 10.40 Time building geometry restraints manager: 6.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.23: 233 1.23 - 1.38: 8205 1.38 - 1.54: 12240 1.54 - 1.70: 850 1.70 - 1.86: 120 Bond restraints: 21648 Sorted by residual: bond pdb=" C PRO B 527 " pdb=" N LYS B 528 " ideal model delta sigma weight residual 1.331 1.066 0.265 1.23e-02 6.61e+03 4.63e+02 bond pdb=" C PRO C 527 " pdb=" N LYS C 528 " ideal model delta sigma weight residual 1.331 1.066 0.265 1.23e-02 6.61e+03 4.63e+02 bond pdb=" C PRO A 527 " pdb=" N LYS A 528 " ideal model delta sigma weight residual 1.331 1.067 0.265 1.23e-02 6.61e+03 4.63e+02 bond pdb=" C CYS C1082 " pdb=" O CYS C1082 " ideal model delta sigma weight residual 1.236 1.296 -0.060 1.24e-02 6.50e+03 2.32e+01 bond pdb=" C CYS B1082 " pdb=" O CYS B1082 " ideal model delta sigma weight residual 1.236 1.295 -0.059 1.24e-02 6.50e+03 2.30e+01 ... (remaining 21643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.18: 29514 6.18 - 12.35: 117 12.35 - 18.53: 9 18.53 - 24.71: 9 24.71 - 30.88: 6 Bond angle restraints: 29655 Sorted by residual: angle pdb=" CA PRO C 527 " pdb=" C PRO C 527 " pdb=" N LYS C 528 " ideal model delta sigma weight residual 115.71 146.59 -30.88 1.19e+00 7.06e-01 6.73e+02 angle pdb=" CA PRO B 527 " pdb=" C PRO B 527 " pdb=" N LYS B 528 " ideal model delta sigma weight residual 115.71 146.57 -30.86 1.19e+00 7.06e-01 6.73e+02 angle pdb=" CA PRO A 527 " pdb=" C PRO A 527 " pdb=" N LYS A 528 " ideal model delta sigma weight residual 115.71 146.56 -30.85 1.19e+00 7.06e-01 6.72e+02 angle pdb=" O PRO C 527 " pdb=" C PRO C 527 " pdb=" N LYS C 528 " ideal model delta sigma weight residual 122.98 97.38 25.60 1.09e+00 8.42e-01 5.52e+02 angle pdb=" O PRO A 527 " pdb=" C PRO A 527 " pdb=" N LYS A 528 " ideal model delta sigma weight residual 122.98 97.38 25.60 1.09e+00 8.42e-01 5.51e+02 ... (remaining 29650 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 12816 17.52 - 35.03: 447 35.03 - 52.55: 75 52.55 - 70.06: 45 70.06 - 87.58: 15 Dihedral angle restraints: 13398 sinusoidal: 5064 harmonic: 8334 Sorted by residual: dihedral pdb=" C PRO A 527 " pdb=" N PRO A 527 " pdb=" CA PRO A 527 " pdb=" CB PRO A 527 " ideal model delta harmonic sigma weight residual -120.70 -90.50 -30.20 0 2.50e+00 1.60e-01 1.46e+02 dihedral pdb=" C PRO B 527 " pdb=" N PRO B 527 " pdb=" CA PRO B 527 " pdb=" CB PRO B 527 " ideal model delta harmonic sigma weight residual -120.70 -90.51 -30.19 0 2.50e+00 1.60e-01 1.46e+02 dihedral pdb=" C PRO C 527 " pdb=" N PRO C 527 " pdb=" CA PRO C 527 " pdb=" CB PRO C 527 " ideal model delta harmonic sigma weight residual -120.70 -90.52 -30.18 0 2.50e+00 1.60e-01 1.46e+02 ... (remaining 13395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.175: 3386 0.175 - 0.351: 202 0.351 - 0.526: 48 0.526 - 0.701: 3 0.701 - 0.877: 3 Chirality restraints: 3642 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.99e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.89e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.87e+01 ... (remaining 3639 not shown) Planarity restraints: 3831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " 0.112 2.00e-02 2.50e+03 1.19e-01 1.78e+02 pdb=" CG ASN B 343 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " -0.049 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " -0.175 2.00e-02 2.50e+03 pdb=" C1 NAG B1314 " 0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " 0.112 2.00e-02 2.50e+03 1.19e-01 1.78e+02 pdb=" CG ASN A 343 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.049 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " -0.175 2.00e-02 2.50e+03 pdb=" C1 NAG A1314 " 0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 343 " 0.112 2.00e-02 2.50e+03 1.19e-01 1.77e+02 pdb=" CG ASN C 343 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN C 343 " -0.049 2.00e-02 2.50e+03 pdb=" ND2 ASN C 343 " -0.175 2.00e-02 2.50e+03 pdb=" C1 NAG C1314 " 0.154 2.00e-02 2.50e+03 ... (remaining 3828 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 162 2.66 - 3.22: 18771 3.22 - 3.78: 31638 3.78 - 4.34: 44917 4.34 - 4.90: 71623 Nonbonded interactions: 167111 Sorted by model distance: nonbonded pdb=" O PRO A 527 " pdb=" CB PRO A 527 " model vdw 2.100 2.752 nonbonded pdb=" O PRO B 527 " pdb=" CB PRO B 527 " model vdw 2.100 2.752 nonbonded pdb=" O PRO C 527 " pdb=" CB PRO C 527 " model vdw 2.100 2.752 nonbonded pdb=" O PRO C 527 " pdb=" CA LYS C 528 " model vdw 2.313 2.776 nonbonded pdb=" O PRO A 527 " pdb=" CA LYS A 528 " model vdw 2.313 2.776 ... (remaining 167106 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 54.590 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.110 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:13.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 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 : 0.014 0.446 21741 Z= 0.925 Angle : 1.569 30.883 29889 Z= 1.079 Chirality : 0.102 0.877 3642 Planarity : 0.006 0.037 3783 Dihedral : 10.363 87.581 7890 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.49 % Allowed : 1.04 % Favored : 98.47 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.14), residues: 2778 helix: 0.29 (0.18), residues: 672 sheet: 1.41 (0.20), residues: 564 loop : -0.18 (0.14), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.005 TRP C 886 HIS 0.005 0.002 HIS B1088 PHE 0.039 0.004 PHE B 565 TYR 0.062 0.005 TYR A 495 ARG 0.004 0.001 ARG B1019 Details of bonding type rmsd link_NAG-ASN : bond 0.06198 ( 48) link_NAG-ASN : angle 3.52241 ( 144) link_BETA1-4 : bond 0.07381 ( 6) link_BETA1-4 : angle 3.28700 ( 18) hydrogen bonds : bond 0.17224 ( 1014) hydrogen bonds : angle 8.88377 ( 2925) SS BOND : bond 0.04032 ( 36) SS BOND : angle 2.24143 ( 72) covalent geometry : bond 0.01298 (21648) covalent geometry : angle 1.55026 (29655) Misc. bond : bond 0.44547 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 281 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 ASN cc_start: 0.7927 (m-40) cc_final: 0.7688 (m-40) REVERT: A 356 LYS cc_start: 0.7716 (tptt) cc_final: 0.7482 (tptm) REVERT: A 697 MET cc_start: 0.7796 (ptm) cc_final: 0.7596 (ptm) REVERT: A 1029 MET cc_start: 0.9129 (tpp) cc_final: 0.8218 (tpp) REVERT: B 355 ARG cc_start: 0.7578 (ttm170) cc_final: 0.7052 (ttt180) REVERT: B 424 LYS cc_start: 0.6989 (tttp) cc_final: 0.6771 (tttp) REVERT: B 1029 MET cc_start: 0.9077 (tpp) cc_final: 0.8733 (tpp) outliers start: 9 outliers final: 6 residues processed: 290 average time/residue: 1.3557 time to fit residues: 446.6275 Evaluate side-chains 224 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 218 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 331 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 3.9990 chunk 216 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 73 optimal weight: 0.5980 chunk 145 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 223 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 166 optimal weight: 0.5980 chunk 258 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 901 GLN A 957 GLN A1002 GLN A1088 HIS B 542 ASN B 804 GLN B 901 GLN B 957 GLN B1002 GLN C 804 GLN C 901 GLN C1002 GLN C1101 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.215471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.202107 restraints weight = 16978.606| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 0.44 r_work: 0.4099 rms_B_bonded: 0.80 restraints_weight: 0.5000 r_work: 0.4057 rms_B_bonded: 1.23 restraints_weight: 0.2500 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21741 Z= 0.159 Angle : 0.609 5.977 29889 Z= 0.327 Chirality : 0.048 0.219 3642 Planarity : 0.004 0.032 3783 Dihedral : 5.413 39.693 4143 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.53 % Allowed : 5.13 % Favored : 93.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.15), residues: 2778 helix: 1.78 (0.20), residues: 660 sheet: 1.04 (0.19), residues: 675 loop : -0.25 (0.15), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 886 HIS 0.009 0.002 HIS B1064 PHE 0.016 0.002 PHE C 898 TYR 0.025 0.002 TYR C1067 ARG 0.005 0.001 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 48) link_NAG-ASN : angle 2.40794 ( 144) link_BETA1-4 : bond 0.00615 ( 6) link_BETA1-4 : angle 1.90679 ( 18) hydrogen bonds : bond 0.06329 ( 1014) hydrogen bonds : angle 6.52826 ( 2925) SS BOND : bond 0.00160 ( 36) SS BOND : angle 0.77465 ( 72) covalent geometry : bond 0.00321 (21648) covalent geometry : angle 0.58519 (29655) Misc. bond : bond 0.00021 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 230 time to evaluate : 2.100 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.7070 (tt0) REVERT: A 697 MET cc_start: 0.8434 (ptm) cc_final: 0.8123 (ptt) REVERT: A 1029 MET cc_start: 0.9098 (tpp) cc_final: 0.8045 (tpp) REVERT: B 740 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7339 (tmm) REVERT: C 356 LYS cc_start: 0.7098 (OUTLIER) cc_final: 0.6872 (tptp) outliers start: 28 outliers final: 7 residues processed: 241 average time/residue: 1.1870 time to fit residues: 329.5987 Evaluate side-chains 207 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 197 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 724 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 200 optimal weight: 5.9990 chunk 179 optimal weight: 0.3980 chunk 145 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 282 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 167 optimal weight: 0.4980 chunk 71 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 935 GLN A 957 GLN A1002 GLN A1071 GLN B 388 ASN B 607 GLN B 613 GLN B 872 GLN B 957 GLN B1002 GLN C 388 ASN C 957 GLN C1071 GLN C1088 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.214093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.201116 restraints weight = 16885.693| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 0.43 r_work: 0.4084 rms_B_bonded: 0.80 restraints_weight: 0.5000 r_work: 0.4024 rms_B_bonded: 1.59 restraints_weight: 0.2500 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 21741 Z= 0.158 Angle : 0.592 13.733 29889 Z= 0.311 Chirality : 0.047 0.237 3642 Planarity : 0.004 0.035 3783 Dihedral : 4.733 31.000 4134 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.47 % Allowed : 5.95 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.15), residues: 2778 helix: 2.25 (0.20), residues: 639 sheet: 1.00 (0.19), residues: 681 loop : -0.22 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 886 HIS 0.006 0.002 HIS B1064 PHE 0.019 0.002 PHE C 898 TYR 0.024 0.002 TYR C1067 ARG 0.005 0.001 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00442 ( 48) link_NAG-ASN : angle 2.35458 ( 144) link_BETA1-4 : bond 0.00794 ( 6) link_BETA1-4 : angle 1.74455 ( 18) hydrogen bonds : bond 0.06280 ( 1014) hydrogen bonds : angle 6.21182 ( 2925) SS BOND : bond 0.00150 ( 36) SS BOND : angle 1.01298 ( 72) covalent geometry : bond 0.00322 (21648) covalent geometry : angle 0.56716 (29655) Misc. bond : bond 0.00072 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 2.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.7101 (tt0) REVERT: A 697 MET cc_start: 0.8415 (ptm) cc_final: 0.8122 (ptt) REVERT: A 740 MET cc_start: 0.8184 (tpp) cc_final: 0.7981 (tmt) REVERT: A 1029 MET cc_start: 0.9104 (tpp) cc_final: 0.8044 (tpp) REVERT: B 740 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7423 (tmm) outliers start: 27 outliers final: 7 residues processed: 211 average time/residue: 1.1697 time to fit residues: 287.1031 Evaluate side-chains 196 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 187 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 724 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 115 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 257 optimal weight: 0.4980 chunk 128 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 181 optimal weight: 0.6980 chunk 282 optimal weight: 0.6980 chunk 264 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 chunk 258 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 957 GLN A1002 GLN B 388 ASN B 613 GLN B 872 GLN B 957 GLN B1002 GLN C 388 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 957 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.213790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.200693 restraints weight = 16998.084| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 0.44 r_work: 0.4081 rms_B_bonded: 0.81 restraints_weight: 0.5000 r_work: 0.4037 rms_B_bonded: 1.25 restraints_weight: 0.2500 r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21741 Z= 0.148 Angle : 0.572 11.365 29889 Z= 0.301 Chirality : 0.047 0.229 3642 Planarity : 0.004 0.036 3783 Dihedral : 4.422 26.210 4134 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.15 % Allowed : 6.71 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.15), residues: 2778 helix: 2.37 (0.20), residues: 642 sheet: 1.02 (0.18), residues: 717 loop : -0.24 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 886 HIS 0.006 0.002 HIS B 655 PHE 0.019 0.002 PHE C 898 TYR 0.023 0.001 TYR B1067 ARG 0.005 0.000 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00514 ( 48) link_NAG-ASN : angle 2.30330 ( 144) link_BETA1-4 : bond 0.00571 ( 6) link_BETA1-4 : angle 1.61226 ( 18) hydrogen bonds : bond 0.05958 ( 1014) hydrogen bonds : angle 5.94692 ( 2925) SS BOND : bond 0.00338 ( 36) SS BOND : angle 0.95740 ( 72) covalent geometry : bond 0.00302 (21648) covalent geometry : angle 0.54791 (29655) Misc. bond : bond 0.00055 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.6998 (tt0) REVERT: A 697 MET cc_start: 0.8376 (ptm) cc_final: 0.8071 (ptt) REVERT: A 1029 MET cc_start: 0.9117 (tpp) cc_final: 0.8048 (tpp) REVERT: B 740 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7299 (tmm) REVERT: B 1017 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.8000 (tt0) outliers start: 21 outliers final: 7 residues processed: 196 average time/residue: 1.2014 time to fit residues: 274.6092 Evaluate side-chains 183 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 173 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 724 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 34 optimal weight: 0.6980 chunk 274 optimal weight: 1.9990 chunk 254 optimal weight: 0.0000 chunk 119 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 201 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 21 optimal weight: 0.0870 chunk 215 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 overall best weight: 0.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 957 GLN A1002 GLN B 388 ASN B 872 GLN B 957 GLN B1002 GLN C 388 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.214454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.201551 restraints weight = 17030.139| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 0.43 r_work: 0.4094 rms_B_bonded: 0.77 restraints_weight: 0.5000 r_work: 0.4049 rms_B_bonded: 1.26 restraints_weight: 0.2500 r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 21741 Z= 0.121 Angle : 0.525 9.494 29889 Z= 0.275 Chirality : 0.046 0.302 3642 Planarity : 0.004 0.036 3783 Dihedral : 4.104 23.061 4134 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.31 % Allowed : 6.87 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.16), residues: 2778 helix: 2.61 (0.21), residues: 624 sheet: 1.07 (0.18), residues: 708 loop : -0.21 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 436 HIS 0.004 0.001 HIS B 655 PHE 0.018 0.001 PHE C 898 TYR 0.021 0.001 TYR B1067 ARG 0.006 0.000 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 48) link_NAG-ASN : angle 1.94712 ( 144) link_BETA1-4 : bond 0.00499 ( 6) link_BETA1-4 : angle 1.43444 ( 18) hydrogen bonds : bond 0.05356 ( 1014) hydrogen bonds : angle 5.69745 ( 2925) SS BOND : bond 0.00389 ( 36) SS BOND : angle 1.17902 ( 72) covalent geometry : bond 0.00242 (21648) covalent geometry : angle 0.50452 (29655) Misc. bond : bond 0.00028 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8337 (ptm) cc_final: 0.8055 (ptt) REVERT: A 1029 MET cc_start: 0.9003 (tpp) cc_final: 0.8007 (tpp) REVERT: B 740 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7269 (tmm) outliers start: 24 outliers final: 11 residues processed: 193 average time/residue: 1.0930 time to fit residues: 246.7590 Evaluate side-chains 187 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 724 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 127 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 264 optimal weight: 1.9990 chunk 190 optimal weight: 10.0000 chunk 237 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 182 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 644 GLN A 658 ASN A 957 GLN A1002 GLN B 388 ASN B 872 GLN B1002 GLN B1088 HIS C 388 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.211879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.198827 restraints weight = 16841.204| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 0.43 r_work: 0.4058 rms_B_bonded: 0.81 restraints_weight: 0.5000 r_work: 0.4015 rms_B_bonded: 1.23 restraints_weight: 0.2500 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 21741 Z= 0.265 Angle : 0.700 9.378 29889 Z= 0.373 Chirality : 0.053 0.305 3642 Planarity : 0.005 0.047 3783 Dihedral : 4.880 28.125 4134 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.58 % Allowed : 6.93 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.15), residues: 2778 helix: 2.21 (0.20), residues: 621 sheet: 0.95 (0.18), residues: 717 loop : -0.46 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 886 HIS 0.009 0.003 HIS C1064 PHE 0.027 0.003 PHE C 898 TYR 0.022 0.003 TYR C1067 ARG 0.006 0.001 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00420 ( 48) link_NAG-ASN : angle 2.28869 ( 144) link_BETA1-4 : bond 0.00585 ( 6) link_BETA1-4 : angle 1.86485 ( 18) hydrogen bonds : bond 0.07568 ( 1014) hydrogen bonds : angle 6.16548 ( 2925) SS BOND : bond 0.00541 ( 36) SS BOND : angle 1.61723 ( 72) covalent geometry : bond 0.00580 (21648) covalent geometry : angle 0.67798 (29655) Misc. bond : bond 0.00084 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 2.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7343 (mtpp) REVERT: A 697 MET cc_start: 0.8317 (ptm) cc_final: 0.8021 (ptt) REVERT: A 1029 MET cc_start: 0.9212 (tpp) cc_final: 0.8175 (tpp) REVERT: B 740 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7405 (tmm) REVERT: B 791 THR cc_start: 0.7322 (OUTLIER) cc_final: 0.6994 (m) REVERT: B 1017 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7967 (tt0) outliers start: 29 outliers final: 16 residues processed: 201 average time/residue: 1.2277 time to fit residues: 289.3582 Evaluate side-chains 199 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 826 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 189 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 157 optimal weight: 0.2980 chunk 199 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 223 optimal weight: 0.3980 chunk 8 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 chunk 217 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 613 GLN A 957 GLN B 388 ASN B 872 GLN B 957 GLN B1002 GLN C 388 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.212615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.199976 restraints weight = 16856.686| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 0.42 r_work: 0.4071 rms_B_bonded: 0.77 restraints_weight: 0.5000 r_work: 0.4030 rms_B_bonded: 1.17 restraints_weight: 0.2500 r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 21741 Z= 0.201 Angle : 0.617 9.242 29889 Z= 0.328 Chirality : 0.049 0.284 3642 Planarity : 0.004 0.039 3783 Dihedral : 4.595 27.894 4134 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.15 % Allowed : 8.24 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.15), residues: 2778 helix: 2.26 (0.20), residues: 624 sheet: 0.85 (0.18), residues: 711 loop : -0.50 (0.15), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.007 0.002 HIS C1064 PHE 0.023 0.002 PHE C 898 TYR 0.023 0.002 TYR C1067 ARG 0.006 0.001 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 48) link_NAG-ASN : angle 2.08129 ( 144) link_BETA1-4 : bond 0.00494 ( 6) link_BETA1-4 : angle 1.56651 ( 18) hydrogen bonds : bond 0.06580 ( 1014) hydrogen bonds : angle 5.98330 ( 2925) SS BOND : bond 0.00434 ( 36) SS BOND : angle 1.43604 ( 72) covalent geometry : bond 0.00431 (21648) covalent geometry : angle 0.59678 (29655) Misc. bond : bond 0.00063 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 2.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8304 (ptm) cc_final: 0.8078 (ptt) REVERT: A 1029 MET cc_start: 0.9168 (tpp) cc_final: 0.8123 (tpp) REVERT: B 740 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7380 (tmm) REVERT: B 791 THR cc_start: 0.7354 (OUTLIER) cc_final: 0.7002 (m) REVERT: B 1017 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7937 (tt0) outliers start: 21 outliers final: 13 residues processed: 197 average time/residue: 1.0527 time to fit residues: 242.6544 Evaluate side-chains 195 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 826 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 29 optimal weight: 5.9990 chunk 284 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 188 optimal weight: 0.6980 chunk 48 optimal weight: 0.2980 chunk 139 optimal weight: 0.8980 chunk 209 optimal weight: 0.9990 chunk 281 optimal weight: 0.3980 chunk 234 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 388 ASN B 872 GLN B 957 GLN B1002 GLN C 388 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.213666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.200797 restraints weight = 16985.593| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 0.44 r_work: 0.4079 rms_B_bonded: 0.82 restraints_weight: 0.5000 r_work: 0.4030 rms_B_bonded: 1.38 restraints_weight: 0.2500 r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 21741 Z= 0.146 Angle : 0.555 9.505 29889 Z= 0.292 Chirality : 0.047 0.273 3642 Planarity : 0.004 0.040 3783 Dihedral : 4.293 22.529 4134 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.15 % Allowed : 8.35 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.15), residues: 2778 helix: 2.52 (0.21), residues: 624 sheet: 0.83 (0.18), residues: 729 loop : -0.42 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.004 0.001 HIS B 655 PHE 0.020 0.002 PHE C 898 TYR 0.021 0.001 TYR C1067 ARG 0.006 0.000 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 48) link_NAG-ASN : angle 1.98991 ( 144) link_BETA1-4 : bond 0.00514 ( 6) link_BETA1-4 : angle 1.38574 ( 18) hydrogen bonds : bond 0.05856 ( 1014) hydrogen bonds : angle 5.78158 ( 2925) SS BOND : bond 0.00368 ( 36) SS BOND : angle 1.26365 ( 72) covalent geometry : bond 0.00303 (21648) covalent geometry : angle 0.53514 (29655) Misc. bond : bond 0.00040 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 2.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8348 (ptm) cc_final: 0.8090 (ptt) REVERT: A 1029 MET cc_start: 0.9106 (tpp) cc_final: 0.7942 (tpp) REVERT: B 740 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7435 (tmm) REVERT: B 791 THR cc_start: 0.7317 (OUTLIER) cc_final: 0.6970 (m) outliers start: 21 outliers final: 11 residues processed: 189 average time/residue: 1.3799 time to fit residues: 305.3543 Evaluate side-chains 185 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 3.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 724 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 26 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 238 optimal weight: 1.9990 chunk 198 optimal weight: 20.0000 chunk 81 optimal weight: 0.6980 chunk 248 optimal weight: 0.9980 chunk 202 optimal weight: 5.9990 chunk 278 optimal weight: 0.1980 chunk 163 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 872 GLN B1002 GLN C 388 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.212810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.199307 restraints weight = 16868.594| |-----------------------------------------------------------------------------| r_work (start): 0.4170 rms_B_bonded: 0.47 r_work: 0.4058 rms_B_bonded: 0.87 restraints_weight: 0.5000 r_work: 0.4011 rms_B_bonded: 1.36 restraints_weight: 0.2500 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 21741 Z= 0.178 Angle : 0.593 9.690 29889 Z= 0.314 Chirality : 0.048 0.275 3642 Planarity : 0.004 0.039 3783 Dihedral : 4.434 25.121 4134 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.09 % Allowed : 8.51 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.15), residues: 2778 helix: 2.39 (0.21), residues: 624 sheet: 0.80 (0.18), residues: 729 loop : -0.45 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 886 HIS 0.006 0.002 HIS C1064 PHE 0.023 0.002 PHE C 898 TYR 0.024 0.002 TYR C1067 ARG 0.004 0.000 ARG B 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 48) link_NAG-ASN : angle 1.99267 ( 144) link_BETA1-4 : bond 0.00553 ( 6) link_BETA1-4 : angle 1.40333 ( 18) hydrogen bonds : bond 0.06448 ( 1014) hydrogen bonds : angle 5.87663 ( 2925) SS BOND : bond 0.00385 ( 36) SS BOND : angle 1.29353 ( 72) covalent geometry : bond 0.00377 (21648) covalent geometry : angle 0.57415 (29655) Misc. bond : bond 0.00054 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 2.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8374 (ptm) cc_final: 0.8125 (ptt) REVERT: A 1029 MET cc_start: 0.9164 (tpp) cc_final: 0.8073 (tpp) REVERT: B 587 ILE cc_start: 0.7744 (mt) cc_final: 0.7492 (mt) REVERT: B 740 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7420 (tmm) REVERT: B 791 THR cc_start: 0.7395 (OUTLIER) cc_final: 0.7046 (m) REVERT: C 740 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7520 (tmm) outliers start: 20 outliers final: 14 residues processed: 189 average time/residue: 1.1330 time to fit residues: 255.2841 Evaluate side-chains 187 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 2.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 740 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 109 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 265 optimal weight: 0.8980 chunk 274 optimal weight: 0.9990 chunk 196 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 872 GLN B1002 GLN C 388 ASN C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.211934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.198677 restraints weight = 16828.171| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 0.41 r_work: 0.4062 rms_B_bonded: 0.78 restraints_weight: 0.5000 r_work: 0.4021 rms_B_bonded: 1.16 restraints_weight: 0.2500 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 21741 Z= 0.231 Angle : 0.656 9.903 29889 Z= 0.349 Chirality : 0.051 0.281 3642 Planarity : 0.005 0.041 3783 Dihedral : 4.715 29.662 4134 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.25 % Allowed : 8.57 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.15), residues: 2778 helix: 2.16 (0.20), residues: 624 sheet: 0.77 (0.19), residues: 699 loop : -0.54 (0.15), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 886 HIS 0.007 0.002 HIS C1064 PHE 0.025 0.003 PHE C 823 TYR 0.023 0.002 TYR C1067 ARG 0.006 0.001 ARG B 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 48) link_NAG-ASN : angle 2.13209 ( 144) link_BETA1-4 : bond 0.00492 ( 6) link_BETA1-4 : angle 1.54450 ( 18) hydrogen bonds : bond 0.07080 ( 1014) hydrogen bonds : angle 6.03317 ( 2925) SS BOND : bond 0.00430 ( 36) SS BOND : angle 1.38257 ( 72) covalent geometry : bond 0.00501 (21648) covalent geometry : angle 0.63717 (29655) Misc. bond : bond 0.00075 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 2.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8358 (ptm) cc_final: 0.8067 (ptt) REVERT: A 1029 MET cc_start: 0.9205 (tpp) cc_final: 0.8118 (tpp) REVERT: B 587 ILE cc_start: 0.7753 (mt) cc_final: 0.7509 (mt) REVERT: B 740 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7436 (tmm) REVERT: B 791 THR cc_start: 0.7385 (OUTLIER) cc_final: 0.7009 (m) REVERT: C 740 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7448 (tmm) outliers start: 23 outliers final: 17 residues processed: 188 average time/residue: 1.1196 time to fit residues: 246.8797 Evaluate side-chains 190 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 30 optimal weight: 0.0030 chunk 37 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 109 optimal weight: 0.4980 chunk 139 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 143 optimal weight: 0.0040 chunk 277 optimal weight: 0.6980 chunk 279 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 overall best weight: 0.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A 957 GLN A1011 GLN B 394 ASN B 872 GLN B1002 GLN C 388 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN C 957 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.214792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.201177 restraints weight = 17040.376| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 0.46 r_work: 0.4081 rms_B_bonded: 0.86 restraints_weight: 0.5000 r_work: 0.4035 rms_B_bonded: 1.38 restraints_weight: 0.2500 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 21741 Z= 0.115 Angle : 0.516 9.781 29889 Z= 0.270 Chirality : 0.046 0.262 3642 Planarity : 0.004 0.040 3783 Dihedral : 4.069 21.811 4134 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.04 % Allowed : 8.73 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.16), residues: 2778 helix: 2.75 (0.21), residues: 606 sheet: 0.90 (0.19), residues: 699 loop : -0.40 (0.15), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS B 655 PHE 0.018 0.001 PHE C 898 TYR 0.019 0.001 TYR A1067 ARG 0.006 0.000 ARG B 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 48) link_NAG-ASN : angle 1.76152 ( 144) link_BETA1-4 : bond 0.00488 ( 6) link_BETA1-4 : angle 1.26398 ( 18) hydrogen bonds : bond 0.05168 ( 1014) hydrogen bonds : angle 5.59184 ( 2925) SS BOND : bond 0.00373 ( 36) SS BOND : angle 1.20015 ( 72) covalent geometry : bond 0.00233 (21648) covalent geometry : angle 0.49831 (29655) Misc. bond : bond 0.00028 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16254.02 seconds wall clock time: 280 minutes 33.68 seconds (16833.68 seconds total)