Starting phenix.real_space_refine on Sat Jul 4 13:51:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tpi_26056/07_2026/7tpi_26056.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tpi_26056/07_2026/7tpi_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_26056/07_2026/7tpi_26056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tpi_26056/07_2026/7tpi_26056.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tpi_26056/07_2026/7tpi_26056.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tpi_26056/07_2026/7tpi_26056.cif" model { file = "/net/cci-nas-00/data/ceres_data/7tpi_26056/07_2026/7tpi_26056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tpi_26056/07_2026/7tpi_26056.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ASP:plan': 29, 'ASN:plan1': 19, 'GLU:plan': 21, 'ARG:plan': 11, 'GLN:plan1': 15, 'PHE:plan': 3, 'TYR:plan': 4} 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: {'ASP:plan': 29, 'ASN:plan1': 19, 'GLU:plan': 21, 'ARG:plan': 11, 'GLN:plan1': 15, 'PHE:plan': 3, 'TYR:plan': 4} 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: {'ASP:plan': 29, 'ASN:plan1': 19, 'GLU:plan': 21, 'ARG:plan': 11, 'GLN:plan1': 15, 'PHE:plan': 3, 'TYR:plan': 4} 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 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 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 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 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 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 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 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 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 chiralities: 14 Time building chain proxies: 4.43, per 1000 atoms: 0.21 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: 1.63 Conformation dependent library (CDL) restraints added in 1.2 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: 1.06 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: 5.04 Time building geometry restraints manager: 2.20 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: 11787 17.52 - 35.03: 357 35.03 - 52.55: 66 52.55 - 70.06: 39 70.06 - 87.58: 15 Dihedral angle restraints: 12264 sinusoidal: 3930 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 12261 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: 0.04 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: 12.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 21.390 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:7.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 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 : 10.499 87.581 6756 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (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 ARG 0.004 0.001 ARG B1019 TYR 0.062 0.005 TYR A 495 PHE 0.039 0.004 PHE B 565 TRP 0.019 0.005 TRP C 886 HIS 0.005 0.002 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.01298 / 0.74 (21648) covalent geometry : angle 1.55026 / 1.08 (29655) SS BOND : bond 0.04032 / 2.79 ( 36) SS BOND : angle 2.24143 / 1.49 ( 72) hydrogen bonds : bond 0.17224 / 11.90 ( 1014) hydrogen bonds : angle 8.88377 / 6.28 ( 2925) Misc. bond : bond 0.44547 / 19.84 ( 3) link_BETA1-4 : bond 0.07381 / 4.44 ( 6) link_BETA1-4 : angle 3.28700 / 1.96 ( 18) link_NAG-ASN : bond 0.06198 / 3.79 ( 48) link_NAG-ASN : angle 3.52241 / 2.23 ( 144) *********************** 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 : 0.673 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: 0.5727 time to fit residues: 187.8752 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 : 0.706 ------------------------------------------------------------------------------- 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 197 optimal weight: 8.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.0970 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.4980 chunk 111 optimal weight: 0.8980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 804 GLN A 901 GLN A 957 GLN A1002 GLN 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.216411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.203146 restraints weight = 17133.084| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 0.44 r_work: 0.4110 rms_B_bonded: 0.80 restraints_weight: 0.5000 r_work: 0.4066 rms_B_bonded: 1.27 restraints_weight: 0.2500 r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21741 Z= 0.144 Angle : 0.597 5.759 29889 Z= 0.318 Chirality : 0.048 0.218 3642 Planarity : 0.004 0.030 3783 Dihedral : 4.527 25.665 3009 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 1.25 % Allowed : 5.18 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.15), residues: 2778 helix: 1.85 (0.20), residues: 663 sheet: 1.05 (0.19), residues: 654 loop : -0.21 (0.15), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 567 TYR 0.024 0.001 TYR A1067 PHE 0.016 0.002 PHE C 898 TRP 0.017 0.002 TRP B 886 HIS 0.007 0.002 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (21648) covalent geometry : angle 0.57243 / 0.31 (29655) SS BOND : bond 0.00267 / 0.14 ( 36) SS BOND : angle 0.75357 / 0.51 ( 72) hydrogen bonds : bond 0.06253 / 4.36 ( 1014) hydrogen bonds : angle 6.55102 / 4.64 ( 2925) Misc. bond : bond 0.00767 / 0.34 ( 3) link_BETA1-4 : bond 0.00607 / 0.37 ( 6) link_BETA1-4 : angle 1.77176 / 1.02 ( 18) link_NAG-ASN : bond 0.00396 / 0.24 ( 48) link_NAG-ASN : angle 2.41881 / 1.62 ( 144) *********************** 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 247 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 224 time to evaluate : 0.738 Fit side-chains REVERT: A 282 ASN cc_start: 0.7519 (m-40) cc_final: 0.7312 (m-40) REVERT: A 314 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.7119 (tt0) REVERT: A 697 MET cc_start: 0.8430 (ptm) cc_final: 0.8121 (ptt) REVERT: A 1029 MET cc_start: 0.9081 (tpp) cc_final: 0.8126 (tpp) REVERT: B 740 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7348 (tmm) REVERT: B 1029 MET cc_start: 0.9074 (tpp) cc_final: 0.8759 (tpp) REVERT: C 356 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.6904 (tptp) outliers start: 23 outliers final: 6 residues processed: 233 average time/residue: 0.5211 time to fit residues: 139.8666 Evaluate side-chains 205 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 196 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 121 optimal weight: 0.9980 chunk 205 optimal weight: 20.0000 chunk 27 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 179 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 195 optimal weight: 3.9990 chunk 277 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 221 optimal weight: 0.0870 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN A 935 GLN A 957 GLN A1002 GLN A1088 HIS B 607 GLN B 613 GLN B 655 HIS B 872 GLN B 957 GLN B1002 GLN C 957 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.214003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.201124 restraints weight = 16958.054| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 0.43 r_work: 0.4086 rms_B_bonded: 0.76 restraints_weight: 0.5000 r_work: 0.4043 rms_B_bonded: 1.19 restraints_weight: 0.2500 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21741 Z= 0.169 Angle : 0.612 15.282 29889 Z= 0.321 Chirality : 0.048 0.221 3642 Planarity : 0.004 0.035 3783 Dihedral : 4.426 22.232 3000 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.58 % Allowed : 5.67 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.15), residues: 2778 helix: 2.20 (0.20), residues: 639 sheet: 1.05 (0.19), residues: 681 loop : -0.23 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 567 TYR 0.026 0.002 TYR C1067 PHE 0.018 0.002 PHE B 898 TRP 0.015 0.001 TRP B 886 HIS 0.007 0.002 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (21648) covalent geometry : angle 0.58675 / 0.32 (29655) SS BOND : bond 0.00252 / 0.18 ( 36) SS BOND : angle 1.05961 / 0.63 ( 72) hydrogen bonds : bond 0.06469 / 4.51 ( 1014) hydrogen bonds : angle 6.25485 / 4.42 ( 2925) Misc. bond : bond 0.00237 / 0.10 ( 3) link_BETA1-4 : bond 0.00628 / 0.37 ( 6) link_BETA1-4 : angle 1.64345 / 0.96 ( 18) link_NAG-ASN : bond 0.00267 / 0.17 ( 48) link_NAG-ASN : angle 2.41503 / 1.59 ( 144) *********************** 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 224 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7071 (tt0) REVERT: A 697 MET cc_start: 0.8379 (ptm) cc_final: 0.8068 (ptt) REVERT: A 740 MET cc_start: 0.8087 (tpp) cc_final: 0.7873 (tmt) REVERT: A 1029 MET cc_start: 0.9130 (tpp) cc_final: 0.8068 (tpp) REVERT: B 740 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7313 (tmm) REVERT: B 1017 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.8000 (tt0) outliers start: 29 outliers final: 8 residues processed: 210 average time/residue: 0.4828 time to fit residues: 117.1263 Evaluate side-chains 189 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 178 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 565 PHE 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 724 THR Chi-restraints excluded: chain C residue 1017 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 182 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 217 optimal weight: 3.9990 chunk 274 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 258 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 198 optimal weight: 30.0000 chunk 190 optimal weight: 10.0000 chunk 219 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN A 613 GLN A 644 GLN A 655 HIS A 658 ASN A 957 GLN A1002 GLN B 388 ASN B 613 GLN B 872 GLN B 957 GLN B1002 GLN B1088 HIS C 388 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS C 957 GLN C1071 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.210168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.196988 restraints weight = 16959.269| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 0.42 r_work: 0.4048 rms_B_bonded: 0.75 restraints_weight: 0.5000 r_work: 0.4005 rms_B_bonded: 1.17 restraints_weight: 0.2500 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.107 21741 Z= 0.401 Angle : 0.865 13.584 29889 Z= 0.465 Chirality : 0.060 0.294 3642 Planarity : 0.006 0.067 3783 Dihedral : 5.352 23.742 3000 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.51 % Favored : 98.45 % Rotamer: Outliers : 1.85 % Allowed : 5.95 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.15), residues: 2778 helix: 1.59 (0.20), residues: 618 sheet: 0.86 (0.18), residues: 690 loop : -0.66 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1019 TYR 0.024 0.004 TYR C1067 PHE 0.038 0.004 PHE C 855 TRP 0.024 0.003 TRP C 886 HIS 0.015 0.004 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00891 / 0.40 (21648) covalent geometry : angle 0.84139 / 0.46 (29655) SS BOND : bond 0.00526 / 0.36 ( 36) SS BOND : angle 1.52489 / 0.93 ( 72) hydrogen bonds : bond 0.08717 / 6.07 ( 1014) hydrogen bonds : angle 6.57594 / 4.67 ( 2925) Misc. bond : bond 0.00121 / 0.05 ( 3) link_BETA1-4 : bond 0.00581 / 0.33 ( 6) link_BETA1-4 : angle 2.06995 / 1.21 ( 18) link_NAG-ASN : bond 0.00751 / 0.43 ( 48) link_NAG-ASN : angle 2.79976 / 1.88 ( 144) *********************** 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 227 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 0.650 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: 0.8355 (ptm) cc_final: 0.8082 (ptt) REVERT: A 1029 MET cc_start: 0.9247 (tpp) cc_final: 0.8083 (tpp) REVERT: B 740 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7477 (tmm) REVERT: B 1113 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8198 (mt0) REVERT: C 773 GLU cc_start: 0.7770 (tt0) cc_final: 0.7537 (tt0) REVERT: C 821 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8211 (tt) outliers start: 34 outliers final: 17 residues processed: 209 average time/residue: 0.4167 time to fit residues: 102.9697 Evaluate side-chains 196 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 LYS 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 1113 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 1017 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 192 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 152 optimal weight: 0.5980 chunk 187 optimal weight: 0.0870 chunk 51 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 190 optimal weight: 8.9990 chunk 278 optimal weight: 0.1980 overall best weight: 0.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN A 957 GLN A1071 GLN B 388 ASN B 872 GLN B 957 GLN B1002 GLN C 388 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.212744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.199404 restraints weight = 16869.080| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 0.48 r_work: 0.4053 rms_B_bonded: 0.91 restraints_weight: 0.5000 r_work: 0.4006 rms_B_bonded: 1.43 restraints_weight: 0.2500 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2938 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= 0.144 Angle : 0.580 11.339 29889 Z= 0.305 Chirality : 0.047 0.260 3642 Planarity : 0.004 0.041 3783 Dihedral : 4.494 23.801 3000 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.98 % Allowed : 7.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.15), residues: 2778 helix: 2.30 (0.20), residues: 624 sheet: 0.83 (0.18), residues: 717 loop : -0.48 (0.15), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1019 TYR 0.022 0.001 TYR C1067 PHE 0.021 0.001 PHE C 898 TRP 0.007 0.001 TRP B 886 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (21648) covalent geometry : angle 0.55875 / 0.30 (29655) SS BOND : bond 0.00264 / 0.20 ( 36) SS BOND : angle 1.12728 / 0.75 ( 72) hydrogen bonds : bond 0.06053 / 4.23 ( 1014) hydrogen bonds : angle 6.01202 / 4.26 ( 2925) Misc. bond : bond 0.00034 / 0.01 ( 3) link_BETA1-4 : bond 0.00496 / 0.28 ( 6) link_BETA1-4 : angle 1.33653 / 0.79 ( 18) link_NAG-ASN : bond 0.00342 / 0.20 ( 48) link_NAG-ASN : angle 2.14238 / 1.45 ( 144) *********************** 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 209 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8354 (ptm) cc_final: 0.8140 (ptt) REVERT: A 1029 MET cc_start: 0.9120 (tpp) cc_final: 0.8035 (tpp) REVERT: B 587 ILE cc_start: 0.7766 (mt) cc_final: 0.7512 (mt) REVERT: B 740 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7501 (tmm) REVERT: B 791 THR cc_start: 0.7168 (t) cc_final: 0.6876 (m) REVERT: B 1017 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7898 (tt0) outliers start: 18 outliers final: 9 residues processed: 198 average time/residue: 0.4753 time to fit residues: 109.7689 Evaluate side-chains 195 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 184 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL 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 386 LYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 1017 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 76 optimal weight: 0.5980 chunk 31 optimal weight: 0.0060 chunk 51 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 131 optimal weight: 8.9990 chunk 180 optimal weight: 0.5980 chunk 222 optimal weight: 5.9990 chunk 212 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 175 optimal weight: 1.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN 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** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.212728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.199452 restraints weight = 16849.043| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 0.42 r_work: 0.4071 rms_B_bonded: 0.79 restraints_weight: 0.5000 r_work: 0.4027 rms_B_bonded: 1.26 restraints_weight: 0.2500 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21741 Z= 0.159 Angle : 0.574 9.717 29889 Z= 0.303 Chirality : 0.047 0.197 3642 Planarity : 0.004 0.041 3783 Dihedral : 4.396 22.562 3000 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.36 % Allowed : 7.64 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.15), residues: 2778 helix: 2.43 (0.21), residues: 624 sheet: 0.85 (0.18), residues: 711 loop : -0.47 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 509 TYR 0.023 0.002 TYR C1067 PHE 0.021 0.002 PHE C 898 TRP 0.006 0.001 TRP C 886 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (21648) covalent geometry : angle 0.55804 / 0.30 (29655) SS BOND : bond 0.00277 / 0.21 ( 36) SS BOND : angle 1.03309 / 0.69 ( 72) hydrogen bonds : bond 0.06229 / 4.35 ( 1014) hydrogen bonds : angle 5.92497 / 4.19 ( 2925) Misc. bond : bond 0.00037 / 0.02 ( 3) link_BETA1-4 : bond 0.00494 / 0.29 ( 6) link_BETA1-4 : angle 1.22850 / 0.73 ( 18) link_NAG-ASN : bond 0.00325 / 0.19 ( 48) link_NAG-ASN : angle 1.91112 / 1.28 ( 144) *********************** 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 212 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.701 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: 0.8333 (ptm) cc_final: 0.8081 (ptt) REVERT: A 740 MET cc_start: 0.8244 (tpp) cc_final: 0.7959 (tmt) REVERT: A 1029 MET cc_start: 0.9134 (tpp) cc_final: 0.8048 (tpp) REVERT: B 740 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7464 (tmm) REVERT: B 791 THR cc_start: 0.7141 (t) cc_final: 0.6851 (m) REVERT: B 859 THR cc_start: 0.8601 (p) cc_final: 0.8377 (p) REVERT: B 1017 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7925 (tt0) outliers start: 25 outliers final: 12 residues processed: 196 average time/residue: 0.4843 time to fit residues: 110.7807 Evaluate side-chains 191 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 1017 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 71 optimal weight: 0.0980 chunk 2 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 chunk 139 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 213 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1002 GLN B 388 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.211841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.198730 restraints weight = 16843.409| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 0.43 r_work: 0.4063 rms_B_bonded: 0.77 restraints_weight: 0.5000 r_work: 0.4021 rms_B_bonded: 1.18 restraints_weight: 0.2500 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 21741 Z= 0.214 Angle : 0.645 11.869 29889 Z= 0.342 Chirality : 0.050 0.338 3642 Planarity : 0.004 0.041 3783 Dihedral : 4.615 22.011 3000 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.36 % Allowed : 8.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.15), residues: 2778 helix: 2.21 (0.21), residues: 624 sheet: 0.67 (0.18), residues: 735 loop : -0.56 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1019 TYR 0.023 0.002 TYR C1067 PHE 0.025 0.002 PHE C 898 TRP 0.010 0.001 TRP C 886 HIS 0.007 0.002 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.21 (21648) covalent geometry : angle 0.62661 / 0.34 (29655) SS BOND : bond 0.00467 / 0.34 ( 36) SS BOND : angle 1.50046 / 0.99 ( 72) hydrogen bonds : bond 0.06950 / 4.85 ( 1014) hydrogen bonds : angle 6.06455 / 4.29 ( 2925) Misc. bond : bond 0.00064 / 0.03 ( 3) link_BETA1-4 : bond 0.00457 / 0.26 ( 6) link_BETA1-4 : angle 1.30630 / 0.77 ( 18) link_NAG-ASN : bond 0.00351 / 0.21 ( 48) link_NAG-ASN : angle 2.03589 / 1.37 ( 144) *********************** 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: 25 poor density : 182 time to evaluate : 0.714 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 386 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7491 (mtpp) REVERT: A 697 MET cc_start: 0.8307 (ptm) cc_final: 0.8011 (ptt) REVERT: A 1029 MET cc_start: 0.9207 (tpp) cc_final: 0.8099 (tpp) REVERT: B 587 ILE cc_start: 0.7765 (mt) cc_final: 0.7507 (mt) REVERT: B 740 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7470 (tmm) REVERT: B 791 THR cc_start: 0.7093 (t) cc_final: 0.6780 (m) REVERT: B 859 THR cc_start: 0.8615 (p) cc_final: 0.8386 (p) REVERT: C 740 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7583 (tmm) outliers start: 25 outliers final: 17 residues processed: 197 average time/residue: 0.4756 time to fit residues: 109.8603 Evaluate side-chains 198 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR 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 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 432 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 1017 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 69 optimal weight: 0.9980 chunk 177 optimal weight: 0.6980 chunk 227 optimal weight: 10.0000 chunk 170 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 190 optimal weight: 10.0000 chunk 202 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 172 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1002 GLN B 872 GLN B1002 GLN C 388 ASN C 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.212685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.199781 restraints weight = 16843.379| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 0.42 r_work: 0.4073 rms_B_bonded: 0.77 restraints_weight: 0.5000 r_work: 0.4032 rms_B_bonded: 1.17 restraints_weight: 0.2500 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 21741 Z= 0.173 Angle : 0.600 12.501 29889 Z= 0.316 Chirality : 0.049 0.340 3642 Planarity : 0.004 0.041 3783 Dihedral : 4.402 21.188 3000 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.69 % Allowed : 7.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.15), residues: 2778 helix: 2.40 (0.21), residues: 624 sheet: 0.76 (0.18), residues: 699 loop : -0.52 (0.15), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1019 TYR 0.021 0.002 TYR C1067 PHE 0.022 0.002 PHE C 898 TRP 0.008 0.001 TRP C 886 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (21648) covalent geometry : angle 0.57905 / 0.31 (29655) SS BOND : bond 0.00558 / 0.37 ( 36) SS BOND : angle 1.66803 / 1.06 ( 72) hydrogen bonds : bond 0.06263 / 4.38 ( 1014) hydrogen bonds : angle 5.90019 / 4.18 ( 2925) Misc. bond : bond 0.00043 / 0.02 ( 3) link_BETA1-4 : bond 0.00453 / 0.26 ( 6) link_BETA1-4 : angle 1.16463 / 0.69 ( 18) link_NAG-ASN : bond 0.00309 / 0.19 ( 48) link_NAG-ASN : angle 2.05327 / 1.39 ( 144) *********************** 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 211 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 0.642 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: 0.8312 (ptm) cc_final: 0.8072 (ptt) REVERT: A 1029 MET cc_start: 0.9151 (tpp) cc_final: 0.8060 (tpp) REVERT: B 740 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7469 (tmm) REVERT: B 791 THR cc_start: 0.7176 (t) cc_final: 0.6873 (m) REVERT: B 859 THR cc_start: 0.8622 (p) cc_final: 0.8383 (p) REVERT: B 1017 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7922 (tt0) REVERT: C 740 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7529 (tmm) outliers start: 31 outliers final: 19 residues processed: 196 average time/residue: 0.4361 time to fit residues: 100.5312 Evaluate side-chains 198 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 615 VAL 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 1096 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 1017 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 222 optimal weight: 0.9990 chunk 219 optimal weight: 0.9990 chunk 213 optimal weight: 4.9990 chunk 266 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 212 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 171 optimal weight: 0.5980 chunk 159 optimal weight: 0.0980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1002 GLN B 872 GLN B1002 GLN C 388 ASN C 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.213438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.200434 restraints weight = 16907.622| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 0.42 r_work: 0.4080 rms_B_bonded: 0.76 restraints_weight: 0.5000 r_work: 0.4038 rms_B_bonded: 1.18 restraints_weight: 0.2500 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 21741 Z= 0.146 Angle : 0.572 13.122 29889 Z= 0.299 Chirality : 0.048 0.431 3642 Planarity : 0.004 0.042 3783 Dihedral : 4.217 19.965 3000 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.31 % Allowed : 8.35 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.16), residues: 2778 helix: 2.63 (0.21), residues: 606 sheet: 0.83 (0.19), residues: 693 loop : -0.47 (0.15), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 509 TYR 0.021 0.001 TYR C1067 PHE 0.020 0.001 PHE C 898 TRP 0.007 0.001 TRP B 436 HIS 0.004 0.001 HIS C1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (21648) covalent geometry : angle 0.54741 / 0.29 (29655) SS BOND : bond 0.00493 / 0.33 ( 36) SS BOND : angle 1.56397 / 0.96 ( 72) hydrogen bonds : bond 0.05798 / 4.05 ( 1014) hydrogen bonds : angle 5.74203 / 4.06 ( 2925) Misc. bond : bond 0.00036 / 0.02 ( 3) link_BETA1-4 : bond 0.00436 / 0.25 ( 6) link_BETA1-4 : angle 1.04368 / 0.61 ( 18) link_NAG-ASN : bond 0.00286 / 0.17 ( 48) link_NAG-ASN : angle 2.21825 / 1.50 ( 144) *********************** 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 211 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.786 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: 0.8308 (ptm) cc_final: 0.8048 (ptt) REVERT: A 1029 MET cc_start: 0.9108 (tpp) cc_final: 0.7938 (tpp) REVERT: B 740 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7460 (tmm) REVERT: B 791 THR cc_start: 0.7241 (t) cc_final: 0.6921 (m) REVERT: B 859 THR cc_start: 0.8610 (p) cc_final: 0.8358 (p) REVERT: B 1017 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7901 (tt0) outliers start: 24 outliers final: 17 residues processed: 197 average time/residue: 0.4654 time to fit residues: 107.6976 Evaluate side-chains 195 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 615 VAL 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 1096 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 1017 GLU 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 1017 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 103 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 218 optimal weight: 1.9990 chunk 187 optimal weight: 0.5980 chunk 171 optimal weight: 0.9980 chunk 253 optimal weight: 0.8980 chunk 186 optimal weight: 0.5980 chunk 188 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 228 optimal weight: 4.9990 chunk 162 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1002 GLN B 872 GLN B1002 GLN C 388 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.213068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.199846 restraints weight = 16948.180| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 0.42 r_work: 0.4075 rms_B_bonded: 0.77 restraints_weight: 0.5000 r_work: 0.4033 rms_B_bonded: 1.23 restraints_weight: 0.2500 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 21741 Z= 0.158 Angle : 0.590 17.285 29889 Z= 0.308 Chirality : 0.048 0.542 3642 Planarity : 0.004 0.041 3783 Dihedral : 4.283 19.997 3000 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.31 % Allowed : 8.73 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.16), residues: 2778 helix: 2.56 (0.21), residues: 606 sheet: 0.82 (0.19), residues: 693 loop : -0.47 (0.15), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 509 TYR 0.022 0.001 TYR C1067 PHE 0.021 0.002 PHE C 898 TRP 0.007 0.001 TRP B 436 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (21648) covalent geometry : angle 0.56273 / 0.30 (29655) SS BOND : bond 0.00497 / 0.33 ( 36) SS BOND : angle 1.50731 / 0.94 ( 72) hydrogen bonds : bond 0.06066 / 4.24 ( 1014) hydrogen bonds : angle 5.77188 / 4.08 ( 2925) Misc. bond : bond 0.00040 / 0.02 ( 3) link_BETA1-4 : bond 0.00446 / 0.26 ( 6) link_BETA1-4 : angle 1.04645 / 0.61 ( 18) link_NAG-ASN : bond 0.00316 / 0.20 ( 48) link_NAG-ASN : angle 2.39982 / 1.63 ( 144) ********************** 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 201 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.687 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: 0.8341 (ptm) cc_final: 0.8081 (ptt) REVERT: A 1029 MET cc_start: 0.9058 (tpp) cc_final: 0.7941 (tpp) REVERT: B 740 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7451 (tmm) REVERT: B 791 THR cc_start: 0.7186 (t) cc_final: 0.6849 (m) REVERT: B 859 THR cc_start: 0.8618 (p) cc_final: 0.8373 (p) REVERT: B 1017 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7927 (tt0) outliers start: 24 outliers final: 21 residues processed: 189 average time/residue: 0.4510 time to fit residues: 100.3033 Evaluate side-chains 194 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 615 VAL 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 A residue 1096 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR 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 1017 GLU 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 1017 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 223 optimal weight: 3.9990 chunk 280 optimal weight: 0.6980 chunk 249 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 221 optimal weight: 9.9990 chunk 162 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 114 optimal weight: 0.0470 chunk 225 optimal weight: 2.9990 chunk 187 optimal weight: 0.7980 chunk 273 optimal weight: 0.5980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1002 GLN B 394 ASN B 872 GLN B1002 GLN C 388 ASN C 544 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.213549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.200804 restraints weight = 16930.623| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 0.41 r_work: 0.4089 rms_B_bonded: 0.73 restraints_weight: 0.5000 r_work: 0.4047 rms_B_bonded: 1.15 restraints_weight: 0.2500 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3381 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= 0.134 Angle : 0.558 16.750 29889 Z= 0.291 Chirality : 0.047 0.561 3642 Planarity : 0.004 0.042 3783 Dihedral : 4.105 19.286 3000 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.31 % Allowed : 8.84 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.16), residues: 2778 helix: 2.71 (0.21), residues: 606 sheet: 0.83 (0.19), residues: 669 loop : -0.42 (0.15), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 509 TYR 0.019 0.001 TYR B1067 PHE 0.020 0.001 PHE C 898 TRP 0.008 0.001 TRP B 436 HIS 0.005 0.001 HIS C1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (21648) covalent geometry : angle 0.53206 / 0.28 (29655) SS BOND : bond 0.00478 / 0.32 ( 36) SS BOND : angle 1.45966 / 0.91 ( 72) hydrogen bonds : bond 0.05570 / 3.89 ( 1014) hydrogen bonds : angle 5.64335 / 3.99 ( 2925) Misc. bond : bond 0.00032 / 0.01 ( 3) link_BETA1-4 : bond 0.00438 / 0.25 ( 6) link_BETA1-4 : angle 0.97203 / 0.56 ( 18) link_NAG-ASN : bond 0.00341 / 0.23 ( 48) link_NAG-ASN : angle 2.28430 / 1.56 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6727.64 seconds wall clock time: 115 minutes 6.09 seconds (6906.09 seconds total)