Starting phenix.real_space_refine on Thu Mar 5 09:46:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tpi_26056/03_2026/7tpi_26056.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tpi_26056/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tpi_26056/03_2026/7tpi_26056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tpi_26056/03_2026/7tpi_26056.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tpi_26056/03_2026/7tpi_26056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tpi_26056/03_2026/7tpi_26056.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 5.09, per 1000 atoms: 0.24 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: 1.74 Conformation dependent library (CDL) restraints added in 1.0 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: 1.10 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: 4.93 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.23: 233 1.23 - 1.38: 8205 1.38 - 1.54: 12240 1.54 - 1.70: 850 1.70 - 1.86: 120 Bond restraints: 21648 Sorted by residual: bond pdb=" C PRO B 527 " pdb=" N LYS B 528 " ideal model delta sigma weight residual 1.331 1.066 0.265 1.23e-02 6.61e+03 4.63e+02 bond pdb=" C PRO C 527 " pdb=" N LYS C 528 " ideal model delta sigma weight residual 1.331 1.066 0.265 1.23e-02 6.61e+03 4.63e+02 bond pdb=" C PRO A 527 " pdb=" N LYS A 528 " ideal model delta sigma weight residual 1.331 1.067 0.265 1.23e-02 6.61e+03 4.63e+02 bond pdb=" C CYS C1082 " pdb=" O CYS C1082 " ideal model delta sigma weight residual 1.236 1.296 -0.060 1.24e-02 6.50e+03 2.32e+01 bond pdb=" C CYS B1082 " pdb=" O CYS B1082 " ideal model delta sigma weight residual 1.236 1.295 -0.059 1.24e-02 6.50e+03 2.30e+01 ... (remaining 21643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.18: 29514 6.18 - 12.35: 117 12.35 - 18.53: 9 18.53 - 24.71: 9 24.71 - 30.88: 6 Bond angle restraints: 29655 Sorted by residual: angle pdb=" CA PRO C 527 " pdb=" C PRO C 527 " pdb=" N LYS C 528 " ideal model delta sigma weight residual 115.71 146.59 -30.88 1.19e+00 7.06e-01 6.73e+02 angle pdb=" CA PRO B 527 " pdb=" C PRO B 527 " pdb=" N LYS B 528 " ideal model delta sigma weight residual 115.71 146.57 -30.86 1.19e+00 7.06e-01 6.73e+02 angle pdb=" CA PRO A 527 " pdb=" C PRO A 527 " pdb=" N LYS A 528 " ideal model delta sigma weight residual 115.71 146.56 -30.85 1.19e+00 7.06e-01 6.72e+02 angle pdb=" O PRO C 527 " pdb=" C PRO C 527 " pdb=" N LYS C 528 " ideal model delta sigma weight residual 122.98 97.38 25.60 1.09e+00 8.42e-01 5.52e+02 angle pdb=" O PRO A 527 " pdb=" C PRO A 527 " pdb=" N LYS A 528 " ideal model delta sigma weight residual 122.98 97.38 25.60 1.09e+00 8.42e-01 5.51e+02 ... (remaining 29650 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 12816 17.52 - 35.03: 447 35.03 - 52.55: 75 52.55 - 70.06: 45 70.06 - 87.58: 15 Dihedral angle restraints: 13398 sinusoidal: 5064 harmonic: 8334 Sorted by residual: dihedral pdb=" C PRO A 527 " pdb=" N PRO A 527 " pdb=" CA PRO A 527 " pdb=" CB PRO A 527 " ideal model delta harmonic sigma weight residual -120.70 -90.50 -30.20 0 2.50e+00 1.60e-01 1.46e+02 dihedral pdb=" C PRO B 527 " pdb=" N PRO B 527 " pdb=" CA PRO B 527 " pdb=" CB PRO B 527 " ideal model delta harmonic sigma weight residual -120.70 -90.51 -30.19 0 2.50e+00 1.60e-01 1.46e+02 dihedral pdb=" C PRO C 527 " pdb=" N PRO C 527 " pdb=" CA PRO C 527 " pdb=" CB PRO C 527 " ideal model delta harmonic sigma weight residual -120.70 -90.52 -30.18 0 2.50e+00 1.60e-01 1.46e+02 ... (remaining 13395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.175: 3386 0.175 - 0.351: 202 0.351 - 0.526: 48 0.526 - 0.701: 3 0.701 - 0.877: 3 Chirality restraints: 3642 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.99e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.89e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.87e+01 ... (remaining 3639 not shown) Planarity restraints: 3831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " 0.112 2.00e-02 2.50e+03 1.19e-01 1.78e+02 pdb=" CG ASN B 343 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " -0.049 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " -0.175 2.00e-02 2.50e+03 pdb=" C1 NAG B1314 " 0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " 0.112 2.00e-02 2.50e+03 1.19e-01 1.78e+02 pdb=" CG ASN A 343 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.049 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " -0.175 2.00e-02 2.50e+03 pdb=" C1 NAG A1314 " 0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 343 " 0.112 2.00e-02 2.50e+03 1.19e-01 1.77e+02 pdb=" CG ASN C 343 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN C 343 " -0.049 2.00e-02 2.50e+03 pdb=" ND2 ASN C 343 " -0.175 2.00e-02 2.50e+03 pdb=" C1 NAG C1314 " 0.154 2.00e-02 2.50e+03 ... (remaining 3828 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 162 2.66 - 3.22: 18771 3.22 - 3.78: 31638 3.78 - 4.34: 44917 4.34 - 4.90: 71623 Nonbonded interactions: 167111 Sorted by model distance: nonbonded pdb=" O PRO A 527 " pdb=" CB PRO A 527 " model vdw 2.100 2.752 nonbonded pdb=" O PRO B 527 " pdb=" CB PRO B 527 " model vdw 2.100 2.752 nonbonded pdb=" O PRO C 527 " pdb=" CB PRO C 527 " model vdw 2.100 2.752 nonbonded pdb=" O PRO C 527 " pdb=" CA LYS C 528 " model vdw 2.313 2.776 nonbonded pdb=" O PRO A 527 " pdb=" CA LYS A 528 " model vdw 2.313 2.776 ... (remaining 167106 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 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: 12.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.380 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 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:7.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.446 21741 Z= 0.925 Angle : 1.569 30.883 29889 Z= 1.079 Chirality : 0.102 0.877 3642 Planarity : 0.006 0.037 3783 Dihedral : 10.363 87.581 7890 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.49 % Allowed : 1.04 % Favored : 98.47 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 covalent geometry : bond 0.01298 (21648) covalent geometry : angle 1.55026 (29655) SS BOND : bond 0.04032 ( 36) SS BOND : angle 2.24143 ( 72) hydrogen bonds : bond 0.17224 ( 1014) hydrogen bonds : angle 8.88377 ( 2925) Misc. bond : bond 0.44547 ( 3) link_BETA1-4 : bond 0.07381 ( 6) link_BETA1-4 : angle 3.28700 ( 18) link_NAG-ASN : bond 0.06198 ( 48) link_NAG-ASN : angle 3.52241 ( 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 : 0.663 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: 0.6843 time to fit residues: 223.4878 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 : 0.773 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4338 r_free = 0.4338 target = 0.216679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.203423 restraints weight = 17123.009| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 0.42 r_work: 0.4113 rms_B_bonded: 0.79 restraints_weight: 0.5000 r_work: 0.4066 rms_B_bonded: 1.37 restraints_weight: 0.2500 r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.1783 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 : 0.590 5.866 29889 Z= 0.315 Chirality : 0.048 0.214 3642 Planarity : 0.004 0.028 3783 Dihedral : 5.351 39.817 4143 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.36 % Allowed : 5.13 % Favored : 93.51 % 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: 0.88 (0.15), residues: 2778 helix: 1.89 (0.20), residues: 657 sheet: 1.07 (0.19), residues: 675 loop : -0.24 (0.15), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 567 TYR 0.023 0.002 TYR B1067 PHE 0.015 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 covalent geometry : bond 0.00285 (21648) covalent geometry : angle 0.56673 (29655) SS BOND : bond 0.00188 ( 36) SS BOND : angle 0.79174 ( 72) hydrogen bonds : bond 0.06034 ( 1014) hydrogen bonds : angle 6.46917 ( 2925) Misc. bond : bond 0.00602 ( 3) link_BETA1-4 : bond 0.00470 ( 6) link_BETA1-4 : angle 1.82683 ( 18) link_NAG-ASN : bond 0.00347 ( 48) link_NAG-ASN : angle 2.34266 ( 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 256 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 231 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7079 (tt0) REVERT: A 697 MET cc_start: 0.8440 (ptm) cc_final: 0.8126 (ptt) REVERT: A 1029 MET cc_start: 0.9048 (tpp) cc_final: 0.8011 (tpp) REVERT: B 740 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7374 (tmm) REVERT: B 1029 MET cc_start: 0.9070 (tpp) cc_final: 0.8702 (tpp) REVERT: C 356 LYS cc_start: 0.7113 (OUTLIER) cc_final: 0.6891 (tptp) outliers start: 25 outliers final: 6 residues processed: 242 average time/residue: 0.6067 time to fit residues: 168.0147 Evaluate side-chains 204 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 195 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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: 1.9990 chunk 205 optimal weight: 20.0000 chunk 27 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 179 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 195 optimal weight: 4.9990 chunk 277 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 221 optimal weight: 0.2980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 935 GLN A 957 GLN A1002 GLN A1071 GLN A1088 HIS B 388 ASN B 613 GLN B 655 HIS B 872 GLN B 957 GLN B1002 GLN C 388 ASN C 957 GLN C1071 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.213217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.200160 restraints weight = 16892.149| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 0.44 r_work: 0.4073 rms_B_bonded: 0.80 restraints_weight: 0.5000 r_work: 0.4006 rms_B_bonded: 1.67 restraints_weight: 0.2500 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2272 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= 0.191 Angle : 0.637 14.399 29889 Z= 0.336 Chirality : 0.049 0.241 3642 Planarity : 0.004 0.035 3783 Dihedral : 4.876 30.002 4134 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.53 % Allowed : 5.95 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.15), residues: 2778 helix: 2.12 (0.20), residues: 639 sheet: 1.00 (0.19), residues: 681 loop : -0.27 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 577 TYR 0.027 0.002 TYR C1067 PHE 0.023 0.002 PHE A 59 TRP 0.015 0.002 TRP B 886 HIS 0.008 0.002 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00402 (21648) covalent geometry : angle 0.61224 (29655) SS BOND : bond 0.00261 ( 36) SS BOND : angle 1.03130 ( 72) hydrogen bonds : bond 0.06860 ( 1014) hydrogen bonds : angle 6.31760 ( 2925) Misc. bond : bond 0.00070 ( 3) link_BETA1-4 : bond 0.00752 ( 6) link_BETA1-4 : angle 1.96144 ( 18) link_NAG-ASN : bond 0.00366 ( 48) link_NAG-ASN : angle 2.47297 ( 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 225 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7163 (tt0) REVERT: A 697 MET cc_start: 0.8444 (ptm) cc_final: 0.8146 (ptt) REVERT: A 1029 MET cc_start: 0.9129 (tpp) cc_final: 0.8024 (tpp) REVERT: B 740 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7411 (tmm) REVERT: C 740 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7657 (tmm) outliers start: 28 outliers final: 9 residues processed: 211 average time/residue: 0.5771 time to fit residues: 140.6492 Evaluate side-chains 196 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 184 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 C residue 386 LYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 1017 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 182 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 217 optimal weight: 3.9990 chunk 274 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 258 optimal weight: 0.2980 chunk 206 optimal weight: 6.9990 chunk 198 optimal weight: 30.0000 chunk 190 optimal weight: 10.0000 chunk 219 optimal weight: 0.0870 overall best weight: 1.8764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 613 GLN A 644 GLN A 655 HIS A 957 GLN A1002 GLN B 388 ASN B 872 GLN B 957 GLN B1002 GLN C 388 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.210381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.197501 restraints weight = 16907.341| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 0.44 r_work: 0.4046 rms_B_bonded: 0.77 restraints_weight: 0.5000 r_work: 0.4005 rms_B_bonded: 1.15 restraints_weight: 0.2500 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 21741 Z= 0.302 Angle : 0.760 12.019 29889 Z= 0.405 Chirality : 0.055 0.278 3642 Planarity : 0.005 0.052 3783 Dihedral : 5.234 35.034 4134 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.58 % Allowed : 6.11 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.15), residues: 2778 helix: 1.86 (0.20), residues: 621 sheet: 0.86 (0.18), residues: 717 loop : -0.54 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1039 TYR 0.023 0.003 TYR C1067 PHE 0.029 0.003 PHE C 898 TRP 0.017 0.002 TRP C 886 HIS 0.011 0.003 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00662 (21648) covalent geometry : angle 0.73378 (29655) SS BOND : bond 0.00452 ( 36) SS BOND : angle 1.21143 ( 72) hydrogen bonds : bond 0.07919 ( 1014) hydrogen bonds : angle 6.39575 ( 2925) Misc. bond : bond 0.00100 ( 3) link_BETA1-4 : bond 0.00597 ( 6) link_BETA1-4 : angle 2.02217 ( 18) link_NAG-ASN : bond 0.00679 ( 48) link_NAG-ASN : angle 2.76170 ( 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 216 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7127 (tt0) REVERT: A 697 MET cc_start: 0.8412 (ptm) cc_final: 0.8126 (ptt) REVERT: A 1029 MET cc_start: 0.9230 (tpp) cc_final: 0.8072 (tpp) REVERT: B 740 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7366 (tmm) REVERT: B 1017 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: C 740 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7594 (tmm) outliers start: 29 outliers final: 14 residues processed: 199 average time/residue: 0.5307 time to fit residues: 122.4946 Evaluate side-chains 199 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 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: 0.8980 chunk 202 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 152 optimal weight: 0.4980 chunk 187 optimal weight: 0.8980 chunk 51 optimal weight: 0.0980 chunk 189 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 190 optimal weight: 8.9990 chunk 278 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 613 GLN A 658 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** C1088 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.212857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.199839 restraints weight = 16773.685| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 0.44 r_work: 0.4068 rms_B_bonded: 0.80 restraints_weight: 0.5000 r_work: 0.4008 rms_B_bonded: 1.62 restraints_weight: 0.2500 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21741 Z= 0.134 Angle : 0.549 9.722 29889 Z= 0.289 Chirality : 0.047 0.199 3642 Planarity : 0.004 0.040 3783 Dihedral : 4.427 24.627 4134 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.09 % Allowed : 7.47 % Favored : 91.43 % 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: 0.91 (0.15), residues: 2778 helix: 2.48 (0.21), residues: 624 sheet: 0.91 (0.18), residues: 717 loop : -0.40 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1019 TYR 0.021 0.001 TYR A1067 PHE 0.020 0.001 PHE C 898 TRP 0.006 0.001 TRP C 886 HIS 0.005 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00269 (21648) covalent geometry : angle 0.52836 (29655) SS BOND : bond 0.00276 ( 36) SS BOND : angle 1.03718 ( 72) hydrogen bonds : bond 0.05719 ( 1014) hydrogen bonds : angle 5.88583 ( 2925) Misc. bond : bond 0.00041 ( 3) link_BETA1-4 : bond 0.00484 ( 6) link_BETA1-4 : angle 1.52770 ( 18) link_NAG-ASN : bond 0.00327 ( 48) link_NAG-ASN : angle 2.06788 ( 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 207 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8429 (ptm) cc_final: 0.8209 (ptt) REVERT: A 1029 MET cc_start: 0.9098 (tpp) cc_final: 0.8055 (tpp) REVERT: B 740 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7482 (tmm) REVERT: B 791 THR cc_start: 0.7117 (t) cc_final: 0.6794 (m) outliers start: 20 outliers final: 8 residues processed: 197 average time/residue: 0.5331 time to fit residues: 122.1253 Evaluate side-chains 185 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 176 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 615 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 791 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: 0.6980 chunk 31 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 180 optimal weight: 0.6980 chunk 222 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 10 optimal weight: 0.0670 chunk 34 optimal weight: 9.9990 chunk 175 optimal weight: 1.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 957 GLN A1002 GLN B 388 ASN B 872 GLN B 957 GLN B1002 GLN C 388 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.213363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.200270 restraints weight = 16885.919| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 0.42 r_work: 0.4078 rms_B_bonded: 0.78 restraints_weight: 0.5000 r_work: 0.4037 rms_B_bonded: 1.18 restraints_weight: 0.2500 r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21741 Z= 0.146 Angle : 0.556 8.182 29889 Z= 0.293 Chirality : 0.047 0.195 3642 Planarity : 0.004 0.038 3783 Dihedral : 4.335 22.721 4134 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.04 % Allowed : 8.18 % Favored : 90.78 % 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: 0.95 (0.15), residues: 2778 helix: 2.56 (0.21), residues: 624 sheet: 0.95 (0.18), residues: 711 loop : -0.40 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1019 TYR 0.024 0.001 TYR C1067 PHE 0.020 0.002 PHE C 898 TRP 0.006 0.001 TRP B 436 HIS 0.005 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00299 (21648) covalent geometry : angle 0.53676 (29655) SS BOND : bond 0.00287 ( 36) SS BOND : angle 0.93191 ( 72) hydrogen bonds : bond 0.05984 ( 1014) hydrogen bonds : angle 5.83049 ( 2925) Misc. bond : bond 0.00039 ( 3) link_BETA1-4 : bond 0.00546 ( 6) link_BETA1-4 : angle 1.45168 ( 18) link_NAG-ASN : bond 0.00323 ( 48) link_NAG-ASN : angle 2.02270 ( 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 207 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 0.743 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: 0.8306 (ptm) cc_final: 0.8044 (ptt) REVERT: A 1029 MET cc_start: 0.9118 (tpp) cc_final: 0.7950 (tpp) REVERT: B 740 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7426 (tmm) REVERT: B 791 THR cc_start: 0.7063 (t) cc_final: 0.6759 (m) outliers start: 19 outliers final: 10 residues processed: 196 average time/residue: 0.5293 time to fit residues: 121.0731 Evaluate side-chains 192 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 181 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 791 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: 1.9990 chunk 2 optimal weight: 0.7980 chunk 194 optimal weight: 0.0970 chunk 139 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 955 ASN A 957 GLN A1002 GLN B 388 ASN B 872 GLN B1002 GLN B1088 HIS C 388 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.211726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.198865 restraints weight = 16821.684| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 0.45 r_work: 0.4057 rms_B_bonded: 0.80 restraints_weight: 0.5000 r_work: 0.4007 rms_B_bonded: 1.40 restraints_weight: 0.2500 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 21741 Z= 0.235 Angle : 0.664 11.811 29889 Z= 0.353 Chirality : 0.051 0.347 3642 Planarity : 0.005 0.039 3783 Dihedral : 4.770 29.610 4134 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.25 % Allowed : 8.24 % 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: 0.63 (0.15), residues: 2778 helix: 2.16 (0.21), residues: 624 sheet: 0.70 (0.18), residues: 741 loop : -0.52 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 509 TYR 0.022 0.002 TYR B1067 PHE 0.026 0.003 PHE C 898 TRP 0.011 0.002 TRP C 886 HIS 0.007 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00512 (21648) covalent geometry : angle 0.64402 (29655) SS BOND : bond 0.00480 ( 36) SS BOND : angle 1.49061 ( 72) hydrogen bonds : bond 0.07233 ( 1014) hydrogen bonds : angle 6.09907 ( 2925) Misc. bond : bond 0.00073 ( 3) link_BETA1-4 : bond 0.00567 ( 6) link_BETA1-4 : angle 1.64359 ( 18) link_NAG-ASN : bond 0.00371 ( 48) link_NAG-ASN : angle 2.14312 ( 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 203 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 0.765 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: 0.8348 (ptm) cc_final: 0.8052 (ptt) REVERT: A 1029 MET cc_start: 0.9187 (tpp) cc_final: 0.8039 (tpp) REVERT: B 740 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7458 (tmm) REVERT: B 791 THR cc_start: 0.7153 (t) cc_final: 0.6835 (m) outliers start: 23 outliers final: 19 residues processed: 194 average time/residue: 0.5362 time to fit residues: 120.7389 Evaluate side-chains 192 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 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 615 VAL 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 724 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 821 LEU 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: 0.9990 chunk 177 optimal weight: 0.5980 chunk 227 optimal weight: 10.0000 chunk 170 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 129 optimal weight: 10.0000 chunk 144 optimal weight: 0.6980 chunk 190 optimal weight: 10.0000 chunk 202 optimal weight: 5.9990 chunk 18 optimal weight: 0.4980 chunk 172 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1002 GLN B 388 ASN B 872 GLN B1002 GLN C 388 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 = 0.213152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.200050 restraints weight = 16874.490| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 0.41 r_work: 0.4078 rms_B_bonded: 0.76 restraints_weight: 0.5000 r_work: 0.4036 rms_B_bonded: 1.21 restraints_weight: 0.2500 r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 21741 Z= 0.146 Angle : 0.560 11.786 29889 Z= 0.294 Chirality : 0.047 0.300 3642 Planarity : 0.004 0.039 3783 Dihedral : 4.330 23.893 4134 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.04 % Allowed : 8.57 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.82 (0.16), residues: 2778 helix: 2.50 (0.21), residues: 624 sheet: 0.80 (0.19), residues: 699 loop : -0.45 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1019 TYR 0.020 0.001 TYR C1067 PHE 0.020 0.002 PHE C 898 TRP 0.006 0.001 TRP C 886 HIS 0.005 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00304 (21648) covalent geometry : angle 0.53857 (29655) SS BOND : bond 0.00404 ( 36) SS BOND : angle 1.31189 ( 72) hydrogen bonds : bond 0.05896 ( 1014) hydrogen bonds : angle 5.80654 ( 2925) Misc. bond : bond 0.00037 ( 3) link_BETA1-4 : bond 0.00519 ( 6) link_BETA1-4 : angle 1.39963 ( 18) link_NAG-ASN : bond 0.00311 ( 48) link_NAG-ASN : angle 2.06823 ( 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 195 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8292 (ptm) cc_final: 0.8044 (ptt) REVERT: A 1029 MET cc_start: 0.9122 (tpp) cc_final: 0.7938 (tpp) REVERT: B 740 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7454 (tmm) REVERT: B 791 THR cc_start: 0.7203 (t) cc_final: 0.6864 (m) outliers start: 19 outliers final: 15 residues processed: 185 average time/residue: 0.5367 time to fit residues: 115.7460 Evaluate side-chains 192 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain 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 1096 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 791 THR 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: 1.9990 chunk 219 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 266 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 212 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 171 optimal weight: 0.6980 chunk 159 optimal weight: 0.0870 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1002 GLN B 872 GLN B1002 GLN C 388 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.212144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.198945 restraints weight = 16833.947| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 0.43 r_work: 0.4063 rms_B_bonded: 0.79 restraints_weight: 0.5000 r_work: 0.4019 rms_B_bonded: 1.23 restraints_weight: 0.2500 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 21741 Z= 0.207 Angle : 0.631 11.886 29889 Z= 0.334 Chirality : 0.050 0.300 3642 Planarity : 0.004 0.039 3783 Dihedral : 4.602 28.777 4134 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.09 % Allowed : 8.51 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.69 (0.15), residues: 2778 helix: 2.27 (0.21), residues: 624 sheet: 0.80 (0.19), residues: 693 loop : -0.51 (0.15), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 509 TYR 0.023 0.002 TYR C1067 PHE 0.024 0.002 PHE C 898 TRP 0.009 0.001 TRP C 886 HIS 0.007 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00445 (21648) covalent geometry : angle 0.61094 (29655) SS BOND : bond 0.00452 ( 36) SS BOND : angle 1.36792 ( 72) hydrogen bonds : bond 0.06855 ( 1014) hydrogen bonds : angle 5.98662 ( 2925) Misc. bond : bond 0.00063 ( 3) link_BETA1-4 : bond 0.00545 ( 6) link_BETA1-4 : angle 1.50928 ( 18) link_NAG-ASN : bond 0.00339 ( 48) link_NAG-ASN : angle 2.11976 ( 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 200 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8332 (ptm) cc_final: 0.8096 (ptt) REVERT: A 1029 MET cc_start: 0.9188 (tpp) cc_final: 0.8101 (tpp) REVERT: B 587 ILE cc_start: 0.7736 (mt) cc_final: 0.7450 (mt) REVERT: B 740 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7488 (tmm) REVERT: B 791 THR cc_start: 0.7194 (t) cc_final: 0.6867 (m) REVERT: C 740 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7479 (tmm) outliers start: 20 outliers final: 17 residues processed: 190 average time/residue: 0.5473 time to fit residues: 120.9693 Evaluate side-chains 191 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 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 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 724 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 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: 7.9990 chunk 4 optimal weight: 0.5980 chunk 218 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 171 optimal weight: 0.7980 chunk 253 optimal weight: 0.8980 chunk 186 optimal weight: 0.3980 chunk 188 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 228 optimal weight: 5.9990 chunk 162 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1002 GLN A1011 GLN B 872 GLN B1002 GLN C 388 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.213238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.200110 restraints weight = 16960.334| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 0.42 r_work: 0.4079 rms_B_bonded: 0.78 restraints_weight: 0.5000 r_work: 0.4038 rms_B_bonded: 1.16 restraints_weight: 0.2500 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.3291 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= 0.144 Angle : 0.553 11.867 29889 Z= 0.292 Chirality : 0.047 0.283 3642 Planarity : 0.004 0.041 3783 Dihedral : 4.259 23.020 4134 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.09 % Allowed : 8.84 % Favored : 90.07 % 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: 0.86 (0.16), residues: 2778 helix: 2.54 (0.21), residues: 624 sheet: 0.87 (0.19), residues: 693 loop : -0.46 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 509 TYR 0.020 0.001 TYR C1067 PHE 0.020 0.002 PHE C 898 TRP 0.007 0.001 TRP C 436 HIS 0.005 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00299 (21648) covalent geometry : angle 0.53467 (29655) SS BOND : bond 0.00385 ( 36) SS BOND : angle 1.24555 ( 72) hydrogen bonds : bond 0.05828 ( 1014) hydrogen bonds : angle 5.75269 ( 2925) Misc. bond : bond 0.00038 ( 3) link_BETA1-4 : bond 0.00507 ( 6) link_BETA1-4 : angle 1.33820 ( 18) link_NAG-ASN : bond 0.00300 ( 48) link_NAG-ASN : angle 1.91858 ( 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 202 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.749 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: 0.8288 (ptm) cc_final: 0.8034 (ptt) REVERT: A 1029 MET cc_start: 0.9119 (tpp) cc_final: 0.7942 (tpp) REVERT: B 740 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7476 (tmm) REVERT: B 791 THR cc_start: 0.7252 (t) cc_final: 0.6927 (m) REVERT: C 740 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7362 (tmm) outliers start: 20 outliers final: 17 residues processed: 193 average time/residue: 0.5259 time to fit residues: 118.3419 Evaluate side-chains 193 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain 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 1096 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1017 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 223 optimal weight: 2.9990 chunk 280 optimal weight: 0.6980 chunk 249 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 221 optimal weight: 9.9990 chunk 162 optimal weight: 0.2980 chunk 109 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 187 optimal weight: 0.9980 chunk 273 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1002 GLN B 872 GLN B1002 GLN C 388 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.212817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.199649 restraints weight = 16879.411| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 0.41 r_work: 0.4076 rms_B_bonded: 0.76 restraints_weight: 0.5000 r_work: 0.4034 rms_B_bonded: 1.17 restraints_weight: 0.2500 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 21741 Z= 0.164 Angle : 0.585 14.390 29889 Z= 0.309 Chirality : 0.048 0.342 3642 Planarity : 0.004 0.040 3783 Dihedral : 4.316 23.980 4134 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.20 % Allowed : 8.67 % Favored : 90.13 % 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: 2.47 (0.21), residues: 624 sheet: 0.85 (0.19), residues: 693 loop : -0.45 (0.15), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 509 TYR 0.023 0.002 TYR C1067 PHE 0.021 0.002 PHE C 898 TRP 0.007 0.001 TRP C 886 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00349 (21648) covalent geometry : angle 0.56625 (29655) SS BOND : bond 0.00514 ( 36) SS BOND : angle 1.59908 ( 72) hydrogen bonds : bond 0.06188 ( 1014) hydrogen bonds : angle 5.80533 ( 2925) Misc. bond : bond 0.00045 ( 3) link_BETA1-4 : bond 0.00533 ( 6) link_BETA1-4 : angle 1.33882 ( 18) link_NAG-ASN : bond 0.00293 ( 48) link_NAG-ASN : angle 1.90213 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7438.29 seconds wall clock time: 127 minutes 12.69 seconds (7632.69 seconds total)