Starting phenix.real_space_refine on Fri Mar 6 05:40:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cy9_27071/03_2026/8cy9_27071.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cy9_27071/03_2026/8cy9_27071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cy9_27071/03_2026/8cy9_27071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cy9_27071/03_2026/8cy9_27071.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cy9_27071/03_2026/8cy9_27071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cy9_27071/03_2026/8cy9_27071.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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 129 5.16 5 C 18100 2.51 5 N 4787 2.21 5 O 5453 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 28469 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1100, 8581 Classifications: {'peptide': 1100} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1044} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 8585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1100, 8585 Classifications: {'peptide': 1100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1044} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 8585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1100, 8585 Classifications: {'peptide': 1100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1044} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 906 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "E" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 906 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "F" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 906 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Time building chain proxies: 5.87, per 1000 atoms: 0.21 Number of scatterers: 28469 At special positions: 0 Unit cell: (148.73, 165.85, 196.88, 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 129 16.00 O 5453 8.00 N 4787 7.00 C 18100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 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 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 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 291 " - pdb=" SG CYS C 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.2 seconds 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6798 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 65 sheets defined 21.8% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.590A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.703A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.560A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.151A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 619 through 623 removed outlier: 3.525A pdb=" N VAL A 622 " --> pdb=" O GLU A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.626A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.531A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.236A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 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 984 removed outlier: 3.538A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.552A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.954A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 250 No H-bonds generated for 'chain 'B' and resid 248 through 250' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.613A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.606A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.204A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.537A pdb=" N ILE B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 637 removed outlier: 3.937A pdb=" N TRP B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG B 634 " --> pdb=" O THR B 630 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 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 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.635A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.540A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 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 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.468A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.674A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 250 No H-bonds generated for 'chain 'C' and resid 248 through 250' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.595A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.564A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.182A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 623 Processing helix chain 'C' and resid 629 through 634 removed outlier: 4.026A pdb=" N ARG C 634 " --> pdb=" O THR C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.815A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 850 through 854 removed outlier: 3.729A pdb=" N LYS C 854 " --> pdb=" O CYS C 851 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 4.038A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.543A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.939A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 65 removed outlier: 3.581A pdb=" N LYS D 65 " --> pdb=" O HIS D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28 removed outlier: 3.546A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.526A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A 189 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 51 removed outlier: 4.627A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.579A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.073A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 143 through 144 Processing sheet with id=AA7, first strand: chain 'A' and resid 245 through 246 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 317 removed outlier: 5.250A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 327 through 328 removed outlier: 3.578A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.724A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.360A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.861A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.547A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.761A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.005A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.557A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 714 through 728 removed outlier: 6.362A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 735 through 736 removed outlier: 3.916A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR A 859 " --> pdb=" O SER A 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.365A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC3, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC4, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.799A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.799A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC7, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.243A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.741A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 151 through 157 removed outlier: 5.971A pdb=" N TRP B 152 " --> pdb=" O HIS B 146 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N HIS B 146 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG B 246 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR B 145 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.315A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.615A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.114A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 451 through 454 removed outlier: 3.664A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.677A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.752A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP B 578 " --> pdb=" O GLU B 583 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.977A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.715A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 787 through 789 Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.681A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE4, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.263A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.124A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE7, first strand: chain 'C' and resid 153 through 157 removed outlier: 3.894A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER C 155 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 311 through 316 removed outlier: 5.305A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.629A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.982A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 448 through 454 removed outlier: 6.007A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.593A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 538 through 539 Processing sheet with id=AF5, first strand: chain 'C' and resid 542 through 543 removed outlier: 3.506A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.046A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF8, first strand: chain 'C' and resid 718 through 723 Processing sheet with id=AF9, first strand: chain 'C' and resid 718 through 723 removed outlier: 3.501A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.750A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AG3, first strand: chain 'D' and resid 3 through 8 removed outlier: 3.572A pdb=" N LEU D 18 " --> pdb=" O MET D 83 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.669A pdb=" N GLY D 10 " --> pdb=" O GLN D 116 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL D 93 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLN D 39 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.669A pdb=" N GLY D 10 " --> pdb=" O GLN D 116 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR D 110 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N SER D 100 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N VAL D 108 " --> pdb=" O SER D 100 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 2 through 8 Processing sheet with id=AG7, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.595A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL E 117 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASP E 33 " --> pdb=" O GLY E 99 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET E 34 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ARG E 38 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N PHE E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.595A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL E 117 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N SER E 100 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N VAL E 108 " --> pdb=" O SER E 100 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 3 through 8 Processing sheet with id=AH1, first strand: chain 'F' and resid 10 through 12 removed outlier: 5.987A pdb=" N GLY F 10 " --> pdb=" O THR F 118 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA F 97 " --> pdb=" O GLY F 35 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY F 35 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N MET F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 10 through 12 removed outlier: 5.987A pdb=" N GLY F 10 " --> pdb=" O THR F 118 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N SER F 100 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N VAL F 108 " --> pdb=" O SER F 100 " (cutoff:3.500A) 1042 hydrogen bonds defined for protein. 2805 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.70 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9227 1.34 - 1.46: 5684 1.46 - 1.58: 14053 1.58 - 1.70: 0 1.70 - 1.82: 165 Bond restraints: 29129 Sorted by residual: bond pdb=" N VAL A 524 " pdb=" CA VAL A 524 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.14e-02 7.69e+03 1.03e+01 bond pdb=" N LYS A 529 " pdb=" CA LYS A 529 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.19e-02 7.06e+03 8.30e+00 bond pdb=" N VAL C 524 " pdb=" CA VAL C 524 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.24e-02 6.50e+03 7.61e+00 bond pdb=" N LYS B 528 " pdb=" CA LYS B 528 " ideal model delta sigma weight residual 1.454 1.489 -0.034 1.31e-02 5.83e+03 6.86e+00 bond pdb=" N LYS C 528 " pdb=" CA LYS C 528 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.24e-02 6.50e+03 6.85e+00 ... (remaining 29124 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 38935 1.68 - 3.36: 624 3.36 - 5.04: 73 5.04 - 6.72: 11 6.72 - 8.40: 3 Bond angle restraints: 39646 Sorted by residual: angle pdb=" C PHE C 32 " pdb=" CA PHE C 32 " pdb=" CB PHE C 32 " ideal model delta sigma weight residual 116.34 110.35 5.99 1.40e+00 5.10e-01 1.83e+01 angle pdb=" C PHE A 32 " pdb=" CA PHE A 32 " pdb=" CB PHE A 32 " ideal model delta sigma weight residual 115.89 110.49 5.40 1.32e+00 5.74e-01 1.67e+01 angle pdb=" N ILE B 624 " pdb=" CA ILE B 624 " pdb=" C ILE B 624 " ideal model delta sigma weight residual 113.43 109.00 4.43 1.09e+00 8.42e-01 1.65e+01 angle pdb=" N VAL A 729 " pdb=" CA VAL A 729 " pdb=" C VAL A 729 " ideal model delta sigma weight residual 112.96 109.31 3.65 1.00e+00 1.00e+00 1.34e+01 angle pdb=" N ASN A 99 " pdb=" CA ASN A 99 " pdb=" C ASN A 99 " ideal model delta sigma weight residual 111.02 114.89 -3.87 1.25e+00 6.40e-01 9.60e+00 ... (remaining 39641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 15798 17.92 - 35.84: 1227 35.84 - 53.76: 198 53.76 - 71.69: 41 71.69 - 89.61: 31 Dihedral angle restraints: 17295 sinusoidal: 6687 harmonic: 10608 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 173.23 -80.23 1 1.00e+01 1.00e-02 7.97e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 153.53 -60.53 1 1.00e+01 1.00e-02 4.88e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -30.42 -55.58 1 1.00e+01 1.00e-02 4.17e+01 ... (remaining 17292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3082 0.035 - 0.069: 903 0.069 - 0.104: 322 0.104 - 0.139: 156 0.139 - 0.173: 7 Chirality restraints: 4470 Sorted by residual: chirality pdb=" CA THR B 630 " pdb=" N THR B 630 " pdb=" C THR B 630 " pdb=" CB THR B 630 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.52e-01 chirality pdb=" CA GLN A1142 " pdb=" N GLN A1142 " pdb=" C GLN A1142 " pdb=" CB GLN A1142 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA VAL A 524 " pdb=" N VAL A 524 " pdb=" C VAL A 524 " pdb=" CB VAL A 524 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.91e-01 ... (remaining 4467 not shown) Planarity restraints: 5156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 862 " 0.043 5.00e-02 4.00e+02 6.52e-02 6.81e+00 pdb=" N PRO B 863 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 863 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 863 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 862 " -0.042 5.00e-02 4.00e+02 6.34e-02 6.43e+00 pdb=" N PRO C 863 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO C 863 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 863 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 87 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO D 88 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO D 88 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 88 " 0.027 5.00e-02 4.00e+02 ... (remaining 5153 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1830 2.74 - 3.28: 27522 3.28 - 3.82: 47578 3.82 - 4.36: 54102 4.36 - 4.90: 95026 Nonbonded interactions: 226058 Sorted by model distance: nonbonded pdb=" O LEU A 293 " pdb=" OG1 THR A 632 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR C 365 " pdb=" O PRO C 384 " model vdw 2.235 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.236 3.040 nonbonded pdb=" O LEU B 293 " pdb=" OG1 THR B 632 " model vdw 2.238 3.040 nonbonded pdb=" O ALA B 292 " pdb=" NE1 TRP B 633 " model vdw 2.238 3.120 ... (remaining 226053 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 15 through 320 or (resid 321 and (name N or name CA or nam \ e C or name O or name CB )) or resid 322 through 1147)) selection = (chain 'C' and (resid 15 through 320 or (resid 321 and (name N or name CA or nam \ e C or name O or name CB )) or resid 322 through 1147)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.750 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 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 : 0.002 0.061 29167 Z= 0.127 Angle : 0.513 8.401 39722 Z= 0.298 Chirality : 0.042 0.173 4470 Planarity : 0.003 0.065 5156 Dihedral : 13.253 89.607 10383 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.76 % Favored : 96.13 % Rotamer: Outliers : 0.19 % Allowed : 0.16 % Favored : 99.65 % 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: 0.62 (0.14), residues: 3639 helix: 2.00 (0.21), residues: 720 sheet: 1.22 (0.20), residues: 724 loop : -0.42 (0.13), residues: 2195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 905 TYR 0.009 0.000 TYR A 91 PHE 0.022 0.001 PHE A 86 TRP 0.013 0.001 TRP A 633 HIS 0.006 0.000 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00216 (29129) covalent geometry : angle 0.51317 (39646) SS BOND : bond 0.00108 ( 38) SS BOND : angle 0.55556 ( 76) hydrogen bonds : bond 0.22197 ( 1004) hydrogen bonds : angle 8.83160 ( 2805) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 233 time to evaluate : 1.016 Fit side-chains REVERT: A 121 ASN cc_start: 0.7675 (t0) cc_final: 0.7419 (t0) REVERT: A 661 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7691 (tm-30) REVERT: A 904 TYR cc_start: 0.8376 (m-10) cc_final: 0.8072 (m-10) REVERT: A 954 GLN cc_start: 0.8490 (mt0) cc_final: 0.8053 (mt0) REVERT: B 869 MET cc_start: 0.9278 (mtt) cc_final: 0.9056 (mtt) REVERT: B 957 GLN cc_start: 0.8325 (tm-30) cc_final: 0.8020 (tm-30) REVERT: C 140 PHE cc_start: 0.8025 (p90) cc_final: 0.7486 (p90) REVERT: C 203 ILE cc_start: 0.9124 (pt) cc_final: 0.8772 (pp) REVERT: C 528 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.6963 (tmtt) REVERT: C 558 LYS cc_start: 0.8829 (mmpt) cc_final: 0.8511 (mmpt) REVERT: C 585 LEU cc_start: 0.8689 (mt) cc_final: 0.8348 (tp) REVERT: C 740 MET cc_start: 0.8406 (ttp) cc_final: 0.8121 (ttp) REVERT: C 950 ASP cc_start: 0.8144 (m-30) cc_final: 0.7942 (m-30) REVERT: C 1010 GLN cc_start: 0.8789 (mm110) cc_final: 0.8524 (mm110) outliers start: 6 outliers final: 1 residues processed: 239 average time/residue: 0.5296 time to fit residues: 153.1809 Evaluate side-chains 162 residues out of total 3165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain C residue 528 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.3980 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 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 804 GLN A1011 GLN A1119 ASN B 207 HIS ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C 239 GLN C 762 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.183206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.116703 restraints weight = 58234.047| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 3.64 r_work: 0.3380 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29167 Z= 0.126 Angle : 0.514 7.424 39722 Z= 0.272 Chirality : 0.043 0.172 4470 Planarity : 0.004 0.047 5156 Dihedral : 3.410 46.140 3951 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.82 % Favored : 96.07 % Rotamer: Outliers : 0.60 % Allowed : 6.49 % Favored : 92.91 % 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: 0.57 (0.14), residues: 3639 helix: 2.13 (0.21), residues: 714 sheet: 1.18 (0.19), residues: 750 loop : -0.52 (0.13), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 319 TYR 0.020 0.001 TYR C1067 PHE 0.020 0.001 PHE A 823 TRP 0.010 0.001 TRP C 258 HIS 0.005 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00280 (29129) covalent geometry : angle 0.51353 (39646) SS BOND : bond 0.00233 ( 38) SS BOND : angle 0.65936 ( 76) hydrogen bonds : bond 0.04214 ( 1004) hydrogen bonds : angle 6.38592 ( 2805) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.5476 (OUTLIER) cc_final: 0.4999 (t-90) REVERT: A 121 ASN cc_start: 0.7636 (t0) cc_final: 0.7290 (t0) REVERT: A 904 TYR cc_start: 0.8505 (m-10) cc_final: 0.8046 (m-10) REVERT: A 950 ASP cc_start: 0.8660 (t0) cc_final: 0.8415 (t0) REVERT: A 954 GLN cc_start: 0.8625 (mt0) cc_final: 0.8136 (mt0) REVERT: A 957 GLN cc_start: 0.8981 (tt0) cc_final: 0.8777 (pt0) REVERT: B 201 PHE cc_start: 0.6674 (t80) cc_final: 0.6466 (t80) REVERT: B 269 TYR cc_start: 0.6544 (m-80) cc_final: 0.6186 (m-80) REVERT: B 270 LEU cc_start: 0.6889 (mm) cc_final: 0.6500 (mm) REVERT: B 957 GLN cc_start: 0.8462 (tm-30) cc_final: 0.8085 (tm-30) REVERT: C 53 ASP cc_start: 0.7633 (t70) cc_final: 0.7408 (t70) REVERT: C 140 PHE cc_start: 0.8288 (p90) cc_final: 0.7544 (p90) REVERT: C 169 GLU cc_start: 0.8082 (tp30) cc_final: 0.7748 (tp30) REVERT: C 203 ILE cc_start: 0.9085 (pt) cc_final: 0.8670 (pp) REVERT: C 269 TYR cc_start: 0.7600 (m-80) cc_final: 0.7103 (m-80) REVERT: C 528 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7765 (tmtt) outliers start: 19 outliers final: 6 residues processed: 197 average time/residue: 0.5614 time to fit residues: 132.7582 Evaluate side-chains 167 residues out of total 3165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 159 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 137 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 296 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 310 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 242 optimal weight: 4.9990 chunk 259 optimal weight: 30.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN B 207 HIS ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B1002 GLN B1010 GLN C 125 ASN C 134 GLN C 613 GLN C1036 GLN C1119 ASN C1142 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.176477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.107852 restraints weight = 56837.360| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 3.76 r_work: 0.3169 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 29167 Z= 0.244 Angle : 0.587 10.426 39722 Z= 0.310 Chirality : 0.046 0.230 4470 Planarity : 0.004 0.046 5156 Dihedral : 3.988 48.984 3949 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.07 % Favored : 95.82 % Rotamer: Outliers : 1.39 % Allowed : 9.33 % Favored : 89.28 % 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: 0.21 (0.14), residues: 3639 helix: 1.58 (0.20), residues: 724 sheet: 0.81 (0.18), residues: 807 loop : -0.66 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 983 TYR 0.032 0.001 TYR A 91 PHE 0.032 0.002 PHE B 906 TRP 0.019 0.002 TRP C 258 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00567 (29129) covalent geometry : angle 0.58601 (39646) SS BOND : bond 0.00384 ( 38) SS BOND : angle 0.95396 ( 76) hydrogen bonds : bond 0.04653 ( 1004) hydrogen bonds : angle 5.92782 ( 2805) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 163 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6338 (OUTLIER) cc_final: 0.6036 (t-90) REVERT: A 121 ASN cc_start: 0.7545 (t0) cc_final: 0.7144 (t0) REVERT: A 528 LYS cc_start: 0.5972 (OUTLIER) cc_final: 0.5663 (mmpt) REVERT: A 740 MET cc_start: 0.9228 (tpt) cc_final: 0.8962 (tpt) REVERT: A 904 TYR cc_start: 0.8588 (m-10) cc_final: 0.8178 (m-10) REVERT: A 950 ASP cc_start: 0.8904 (t0) cc_final: 0.8681 (t0) REVERT: A 990 GLU cc_start: 0.8530 (tp30) cc_final: 0.7990 (tm-30) REVERT: B 52 GLN cc_start: 0.7714 (tp40) cc_final: 0.7461 (tp40) REVERT: B 53 ASP cc_start: 0.7791 (t0) cc_final: 0.7540 (t0) REVERT: B 201 PHE cc_start: 0.7112 (t80) cc_final: 0.6762 (t80) REVERT: B 957 GLN cc_start: 0.8563 (tm-30) cc_final: 0.8111 (tm-30) REVERT: C 140 PHE cc_start: 0.8621 (p90) cc_final: 0.7780 (p90) REVERT: C 169 GLU cc_start: 0.8321 (tp30) cc_final: 0.8029 (tp30) REVERT: C 177 MET cc_start: -0.0699 (mpt) cc_final: -0.1090 (ptt) REVERT: C 203 ILE cc_start: 0.9030 (pt) cc_final: 0.8620 (pp) REVERT: C 210 ILE cc_start: 0.8166 (pt) cc_final: 0.7936 (pp) REVERT: C 528 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.7885 (tptt) REVERT: C 860 VAL cc_start: 0.8729 (m) cc_final: 0.8528 (m) REVERT: C 868 GLU cc_start: 0.9010 (tt0) cc_final: 0.8410 (tm-30) REVERT: C 985 ASP cc_start: 0.7766 (p0) cc_final: 0.7164 (p0) REVERT: C 994 ASP cc_start: 0.9111 (OUTLIER) cc_final: 0.8716 (t0) outliers start: 44 outliers final: 15 residues processed: 193 average time/residue: 0.5157 time to fit residues: 121.4628 Evaluate side-chains 162 residues out of total 3165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain D residue 47 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 11 optimal weight: 0.9990 chunk 246 optimal weight: 1.9990 chunk 347 optimal weight: 30.0000 chunk 280 optimal weight: 2.9990 chunk 220 optimal weight: 20.0000 chunk 261 optimal weight: 1.9990 chunk 338 optimal weight: 8.9990 chunk 287 optimal weight: 2.9990 chunk 265 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 268 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS A 625 HIS A 913 GLN A 957 GLN A 978 ASN B 207 HIS B 901 GLN B1010 GLN C 580 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.175021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.106862 restraints weight = 56712.251| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.95 r_work: 0.3164 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 29167 Z= 0.215 Angle : 0.555 13.854 39722 Z= 0.289 Chirality : 0.045 0.202 4470 Planarity : 0.004 0.045 5156 Dihedral : 3.967 51.832 3949 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.96 % Favored : 95.96 % Rotamer: Outliers : 1.33 % Allowed : 10.98 % Favored : 87.69 % 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: 0.12 (0.14), residues: 3639 helix: 1.62 (0.20), residues: 723 sheet: 0.60 (0.18), residues: 822 loop : -0.69 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 983 TYR 0.022 0.001 TYR A 91 PHE 0.026 0.001 PHE B 906 TRP 0.021 0.001 TRP C 258 HIS 0.004 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00495 (29129) covalent geometry : angle 0.55418 (39646) SS BOND : bond 0.00338 ( 38) SS BOND : angle 0.96668 ( 76) hydrogen bonds : bond 0.04141 ( 1004) hydrogen bonds : angle 5.64183 ( 2805) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 151 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8543 (tt) cc_final: 0.7783 (mp) REVERT: A 121 ASN cc_start: 0.7561 (t0) cc_final: 0.7186 (t0) REVERT: A 177 MET cc_start: 0.1601 (tpp) cc_final: 0.1374 (tpp) REVERT: A 725 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8436 (tt0) REVERT: A 740 MET cc_start: 0.9262 (tpt) cc_final: 0.8993 (tpt) REVERT: A 990 GLU cc_start: 0.8534 (tp30) cc_final: 0.8068 (tm-30) REVERT: A 1010 GLN cc_start: 0.9103 (tp40) cc_final: 0.8865 (mm-40) REVERT: B 52 GLN cc_start: 0.7694 (tp40) cc_final: 0.7424 (tp40) REVERT: B 53 ASP cc_start: 0.7873 (t0) cc_final: 0.7526 (t0) REVERT: B 201 PHE cc_start: 0.7390 (t80) cc_final: 0.6982 (t80) REVERT: B 269 TYR cc_start: 0.6529 (m-80) cc_final: 0.5848 (m-80) REVERT: B 270 LEU cc_start: 0.6772 (mm) cc_final: 0.6489 (mm) REVERT: B 957 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8174 (tm-30) REVERT: B 1118 ASP cc_start: 0.9046 (t0) cc_final: 0.8817 (t0) REVERT: B 1144 GLU cc_start: 0.8740 (mp0) cc_final: 0.7956 (mp0) REVERT: C 140 PHE cc_start: 0.8717 (p90) cc_final: 0.7707 (p90) REVERT: C 169 GLU cc_start: 0.8368 (tp30) cc_final: 0.8004 (tp30) REVERT: C 177 MET cc_start: -0.0474 (mpt) cc_final: -0.0880 (ptt) REVERT: C 203 ILE cc_start: 0.9063 (pt) cc_final: 0.8608 (pp) REVERT: C 528 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.7821 (tptt) REVERT: C 860 VAL cc_start: 0.8692 (m) cc_final: 0.8435 (t) REVERT: C 990 GLU cc_start: 0.8250 (mm-30) cc_final: 0.8009 (mm-30) REVERT: C 994 ASP cc_start: 0.9121 (OUTLIER) cc_final: 0.8694 (t0) outliers start: 42 outliers final: 14 residues processed: 181 average time/residue: 0.5239 time to fit residues: 115.4598 Evaluate side-chains 159 residues out of total 3165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain D residue 47 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 285 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 186 optimal weight: 0.9980 chunk 328 optimal weight: 0.9980 chunk 146 optimal weight: 0.0870 chunk 307 optimal weight: 0.5980 chunk 98 optimal weight: 0.3980 chunk 64 optimal weight: 0.6980 chunk 35 optimal weight: 30.0000 chunk 265 optimal weight: 30.0000 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 957 GLN B 207 HIS B 907 ASN B1010 GLN C 564 GLN C 762 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.175531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.109223 restraints weight = 57443.747| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 3.66 r_work: 0.3212 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 29167 Z= 0.108 Angle : 0.499 10.476 39722 Z= 0.259 Chirality : 0.043 0.182 4470 Planarity : 0.004 0.044 5156 Dihedral : 3.835 55.373 3949 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.79 % Favored : 96.13 % Rotamer: Outliers : 1.17 % Allowed : 11.71 % Favored : 87.12 % 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: 0.21 (0.14), residues: 3639 helix: 1.80 (0.20), residues: 722 sheet: 0.60 (0.18), residues: 837 loop : -0.66 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 983 TYR 0.023 0.001 TYR A 170 PHE 0.019 0.001 PHE B 192 TRP 0.020 0.001 TRP C 258 HIS 0.003 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00245 (29129) covalent geometry : angle 0.49880 (39646) SS BOND : bond 0.00201 ( 38) SS BOND : angle 0.73493 ( 76) hydrogen bonds : bond 0.03704 ( 1004) hydrogen bonds : angle 5.37285 ( 2805) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8936 (t70) cc_final: 0.8696 (t70) REVERT: A 117 LEU cc_start: 0.8439 (tt) cc_final: 0.7653 (mp) REVERT: A 121 ASN cc_start: 0.7483 (t0) cc_final: 0.7020 (t0) REVERT: A 740 MET cc_start: 0.9268 (tpt) cc_final: 0.8998 (tpt) REVERT: A 950 ASP cc_start: 0.8891 (t0) cc_final: 0.8632 (m-30) REVERT: A 990 GLU cc_start: 0.8500 (tp30) cc_final: 0.7960 (tm-30) REVERT: A 1010 GLN cc_start: 0.9067 (tp40) cc_final: 0.8820 (mm-40) REVERT: B 52 GLN cc_start: 0.7726 (tp40) cc_final: 0.7475 (tp40) REVERT: B 53 ASP cc_start: 0.7935 (t0) cc_final: 0.7681 (t0) REVERT: B 201 PHE cc_start: 0.7234 (t80) cc_final: 0.6944 (t80) REVERT: B 269 TYR cc_start: 0.6519 (m-80) cc_final: 0.5881 (m-80) REVERT: B 270 LEU cc_start: 0.6784 (mm) cc_final: 0.6468 (mm) REVERT: B 957 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8106 (tm-30) REVERT: B 1144 GLU cc_start: 0.8721 (mp0) cc_final: 0.7934 (mp0) REVERT: C 140 PHE cc_start: 0.8678 (p90) cc_final: 0.7680 (p90) REVERT: C 169 GLU cc_start: 0.8211 (tp30) cc_final: 0.7897 (tp30) REVERT: C 177 MET cc_start: -0.0436 (mpt) cc_final: -0.0876 (ptt) REVERT: C 203 ILE cc_start: 0.9018 (pt) cc_final: 0.8545 (pp) REVERT: C 269 TYR cc_start: 0.7734 (m-10) cc_final: 0.7308 (m-80) REVERT: C 528 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.7869 (tptt) REVERT: C 565 PHE cc_start: 0.6483 (OUTLIER) cc_final: 0.5990 (t80) REVERT: C 868 GLU cc_start: 0.8907 (tt0) cc_final: 0.8299 (tm-30) REVERT: C 990 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8048 (mm-30) REVERT: C 994 ASP cc_start: 0.9023 (OUTLIER) cc_final: 0.8664 (t0) outliers start: 37 outliers final: 14 residues processed: 178 average time/residue: 0.5057 time to fit residues: 110.4262 Evaluate side-chains 159 residues out of total 3165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain D residue 47 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 19 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 348 optimal weight: 30.0000 chunk 212 optimal weight: 0.0770 chunk 130 optimal weight: 0.8980 chunk 246 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 957 GLN B 207 HIS B 907 ASN B1010 GLN C 762 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.175740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.106843 restraints weight = 57840.017| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 3.87 r_work: 0.3221 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 29167 Z= 0.127 Angle : 0.503 9.810 39722 Z= 0.261 Chirality : 0.043 0.177 4470 Planarity : 0.004 0.046 5156 Dihedral : 3.811 58.807 3949 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.93 % Favored : 95.99 % Rotamer: Outliers : 1.30 % Allowed : 12.21 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.14), residues: 3639 helix: 1.89 (0.20), residues: 716 sheet: 0.58 (0.18), residues: 819 loop : -0.62 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 983 TYR 0.018 0.001 TYR A 91 PHE 0.018 0.001 PHE A 565 TRP 0.016 0.001 TRP B 633 HIS 0.003 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00292 (29129) covalent geometry : angle 0.50253 (39646) SS BOND : bond 0.00216 ( 38) SS BOND : angle 0.73707 ( 76) hydrogen bonds : bond 0.03663 ( 1004) hydrogen bonds : angle 5.26283 ( 2805) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8431 (tt) cc_final: 0.7699 (mp) REVERT: A 121 ASN cc_start: 0.7462 (t0) cc_final: 0.7038 (t0) REVERT: A 740 MET cc_start: 0.9263 (tpt) cc_final: 0.8974 (tpt) REVERT: A 990 GLU cc_start: 0.8499 (tp30) cc_final: 0.7983 (tm-30) REVERT: B 52 GLN cc_start: 0.7682 (tp40) cc_final: 0.7429 (tp40) REVERT: B 53 ASP cc_start: 0.7954 (t0) cc_final: 0.7651 (t0) REVERT: B 117 LEU cc_start: 0.7532 (mm) cc_final: 0.6667 (tm) REVERT: B 201 PHE cc_start: 0.7507 (t80) cc_final: 0.7114 (t80) REVERT: B 269 TYR cc_start: 0.6483 (m-80) cc_final: 0.5900 (m-80) REVERT: B 270 LEU cc_start: 0.6821 (mm) cc_final: 0.6488 (mm) REVERT: B 957 GLN cc_start: 0.8636 (tm-30) cc_final: 0.8154 (tm-30) REVERT: C 140 PHE cc_start: 0.8683 (p90) cc_final: 0.7737 (p90) REVERT: C 169 GLU cc_start: 0.8247 (tp30) cc_final: 0.7928 (tp30) REVERT: C 177 MET cc_start: -0.0228 (mpt) cc_final: -0.0757 (ptt) REVERT: C 203 ILE cc_start: 0.9050 (pt) cc_final: 0.8574 (pp) REVERT: C 269 TYR cc_start: 0.7681 (m-10) cc_final: 0.7272 (m-80) REVERT: C 528 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.7955 (tmtt) REVERT: C 868 GLU cc_start: 0.8901 (tt0) cc_final: 0.8321 (tm-30) REVERT: C 994 ASP cc_start: 0.9025 (OUTLIER) cc_final: 0.8675 (t0) outliers start: 41 outliers final: 22 residues processed: 178 average time/residue: 0.4724 time to fit residues: 104.0736 Evaluate side-chains 165 residues out of total 3165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain D residue 47 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 247 optimal weight: 4.9990 chunk 176 optimal weight: 0.6980 chunk 151 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 33 optimal weight: 20.0000 chunk 250 optimal weight: 0.9980 chunk 220 optimal weight: 9.9990 chunk 312 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 143 optimal weight: 50.0000 chunk 264 optimal weight: 40.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN B 207 HIS B1010 GLN C 66 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.172968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.105607 restraints weight = 57627.873| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.67 r_work: 0.3182 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 29167 Z= 0.215 Angle : 0.542 8.810 39722 Z= 0.284 Chirality : 0.044 0.169 4470 Planarity : 0.004 0.045 5156 Dihedral : 3.938 58.886 3949 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.12 % Favored : 95.80 % Rotamer: Outliers : 1.55 % Allowed : 12.27 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.15 (0.14), residues: 3639 helix: 1.81 (0.20), residues: 709 sheet: 0.49 (0.17), residues: 846 loop : -0.68 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 983 TYR 0.023 0.001 TYR A 91 PHE 0.018 0.001 PHE B 906 TRP 0.025 0.001 TRP B 633 HIS 0.004 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00502 (29129) covalent geometry : angle 0.54117 (39646) SS BOND : bond 0.00285 ( 38) SS BOND : angle 0.87869 ( 76) hydrogen bonds : bond 0.04012 ( 1004) hydrogen bonds : angle 5.32810 ( 2805) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 146 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8437 (tt) cc_final: 0.7797 (mp) REVERT: A 121 ASN cc_start: 0.7423 (t0) cc_final: 0.7003 (t0) REVERT: A 740 MET cc_start: 0.9268 (tpt) cc_final: 0.9006 (tpt) REVERT: A 990 GLU cc_start: 0.8521 (tp30) cc_final: 0.8075 (tm-30) REVERT: A 1072 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8596 (pm20) REVERT: B 53 ASP cc_start: 0.7987 (t0) cc_final: 0.7732 (t0) REVERT: B 117 LEU cc_start: 0.7636 (mm) cc_final: 0.6787 (tm) REVERT: B 190 ARG cc_start: 0.7848 (mtm110) cc_final: 0.7192 (mtt90) REVERT: B 201 PHE cc_start: 0.7622 (t80) cc_final: 0.7216 (t80) REVERT: B 269 TYR cc_start: 0.6442 (m-80) cc_final: 0.5822 (m-80) REVERT: B 270 LEU cc_start: 0.6876 (mm) cc_final: 0.6585 (mm) REVERT: B 855 PHE cc_start: 0.8316 (m-80) cc_final: 0.8051 (m-80) REVERT: B 957 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8236 (tm-30) REVERT: C 125 ASN cc_start: 0.6483 (OUTLIER) cc_final: 0.5640 (p0) REVERT: C 140 PHE cc_start: 0.8750 (p90) cc_final: 0.7788 (p90) REVERT: C 169 GLU cc_start: 0.8275 (tp30) cc_final: 0.7915 (tp30) REVERT: C 177 MET cc_start: -0.0283 (mpt) cc_final: -0.0809 (ptt) REVERT: C 203 ILE cc_start: 0.9078 (pt) cc_final: 0.8614 (pp) REVERT: C 269 TYR cc_start: 0.7643 (m-10) cc_final: 0.7279 (m-80) REVERT: C 528 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.7959 (tmtt) REVERT: C 860 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8350 (t) REVERT: C 868 GLU cc_start: 0.8941 (tt0) cc_final: 0.8366 (tm-30) REVERT: C 994 ASP cc_start: 0.9085 (OUTLIER) cc_final: 0.8724 (t0) outliers start: 49 outliers final: 22 residues processed: 181 average time/residue: 0.4837 time to fit residues: 108.2064 Evaluate side-chains 169 residues out of total 3165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain D residue 47 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 6 optimal weight: 1.9990 chunk 334 optimal weight: 7.9990 chunk 327 optimal weight: 1.9990 chunk 24 optimal weight: 30.0000 chunk 100 optimal weight: 0.5980 chunk 182 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 340 optimal weight: 6.9990 chunk 251 optimal weight: 7.9990 chunk 169 optimal weight: 0.8980 chunk 302 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 957 GLN B 207 HIS B1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.175608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.106524 restraints weight = 57740.957| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.99 r_work: 0.3174 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 29167 Z= 0.171 Angle : 0.529 8.994 39722 Z= 0.276 Chirality : 0.043 0.173 4470 Planarity : 0.004 0.047 5156 Dihedral : 3.944 56.356 3949 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.12 % Favored : 95.80 % Rotamer: Outliers : 1.36 % Allowed : 12.56 % Favored : 86.08 % 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: 0.13 (0.14), residues: 3639 helix: 1.78 (0.20), residues: 709 sheet: 0.45 (0.18), residues: 846 loop : -0.67 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 983 TYR 0.020 0.001 TYR A 91 PHE 0.013 0.001 PHE A1121 TRP 0.030 0.001 TRP C 258 HIS 0.003 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00397 (29129) covalent geometry : angle 0.52858 (39646) SS BOND : bond 0.00283 ( 38) SS BOND : angle 0.79848 ( 76) hydrogen bonds : bond 0.03870 ( 1004) hydrogen bonds : angle 5.23154 ( 2805) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 146 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8506 (tt) cc_final: 0.7866 (mp) REVERT: A 121 ASN cc_start: 0.7498 (t0) cc_final: 0.7114 (t0) REVERT: A 207 HIS cc_start: 0.8190 (OUTLIER) cc_final: 0.7745 (t-90) REVERT: A 740 MET cc_start: 0.9218 (tpt) cc_final: 0.8939 (tpt) REVERT: A 990 GLU cc_start: 0.8488 (tp30) cc_final: 0.7996 (tm-30) REVERT: A 1010 GLN cc_start: 0.9072 (tp40) cc_final: 0.8763 (mm-40) REVERT: A 1072 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8613 (pm20) REVERT: B 117 LEU cc_start: 0.7586 (mm) cc_final: 0.6771 (tm) REVERT: B 201 PHE cc_start: 0.7670 (t80) cc_final: 0.7197 (t80) REVERT: B 269 TYR cc_start: 0.6352 (m-80) cc_final: 0.5761 (m-80) REVERT: B 270 LEU cc_start: 0.6848 (mm) cc_final: 0.6567 (mm) REVERT: B 855 PHE cc_start: 0.8402 (m-80) cc_final: 0.8109 (m-80) REVERT: B 957 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8226 (tm-30) REVERT: C 140 PHE cc_start: 0.8744 (p90) cc_final: 0.7746 (p90) REVERT: C 169 GLU cc_start: 0.8216 (tp30) cc_final: 0.7864 (tp30) REVERT: C 177 MET cc_start: -0.0330 (mpt) cc_final: -0.0823 (ptt) REVERT: C 203 ILE cc_start: 0.9111 (pt) cc_final: 0.8641 (pp) REVERT: C 211 ASN cc_start: 0.8668 (t0) cc_final: 0.8410 (m-40) REVERT: C 269 TYR cc_start: 0.7685 (m-80) cc_final: 0.7298 (m-80) REVERT: C 528 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.7987 (tmtt) REVERT: C 994 ASP cc_start: 0.9068 (OUTLIER) cc_final: 0.8720 (t0) outliers start: 43 outliers final: 26 residues processed: 178 average time/residue: 0.5055 time to fit residues: 110.7314 Evaluate side-chains 174 residues out of total 3165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain D residue 47 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 95 optimal weight: 0.8980 chunk 358 optimal weight: 0.0980 chunk 185 optimal weight: 0.8980 chunk 299 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 264 optimal weight: 30.0000 chunk 82 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 124 optimal weight: 20.0000 chunk 316 optimal weight: 0.5980 chunk 330 optimal weight: 20.0000 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 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 957 GLN B 207 HIS B1010 GLN C 762 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.175359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.105955 restraints weight = 58175.168| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.81 r_work: 0.3211 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 29167 Z= 0.117 Angle : 0.516 8.673 39722 Z= 0.269 Chirality : 0.043 0.214 4470 Planarity : 0.004 0.049 5156 Dihedral : 3.874 54.335 3949 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.09 % Favored : 95.82 % Rotamer: Outliers : 1.17 % Allowed : 12.97 % Favored : 85.86 % 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: 0.20 (0.14), residues: 3639 helix: 1.93 (0.20), residues: 697 sheet: 0.52 (0.18), residues: 831 loop : -0.66 (0.13), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 983 TYR 0.024 0.001 TYR A 170 PHE 0.013 0.001 PHE B 92 TRP 0.033 0.001 TRP B 633 HIS 0.004 0.001 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00271 (29129) covalent geometry : angle 0.51583 (39646) SS BOND : bond 0.00206 ( 38) SS BOND : angle 0.70626 ( 76) hydrogen bonds : bond 0.03674 ( 1004) hydrogen bonds : angle 5.13584 ( 2805) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8950 (t70) cc_final: 0.8703 (t70) REVERT: A 117 LEU cc_start: 0.8559 (tt) cc_final: 0.7935 (mp) REVERT: A 121 ASN cc_start: 0.7443 (t0) cc_final: 0.7028 (t0) REVERT: A 207 HIS cc_start: 0.8173 (OUTLIER) cc_final: 0.7663 (t-90) REVERT: A 740 MET cc_start: 0.9204 (tpt) cc_final: 0.8916 (tpt) REVERT: A 990 GLU cc_start: 0.8445 (tp30) cc_final: 0.7959 (tm-30) REVERT: A 1010 GLN cc_start: 0.9036 (tp40) cc_final: 0.8722 (mm-40) REVERT: B 117 LEU cc_start: 0.7596 (mm) cc_final: 0.6762 (tm) REVERT: B 201 PHE cc_start: 0.7710 (t80) cc_final: 0.7236 (t80) REVERT: B 269 TYR cc_start: 0.6324 (m-80) cc_final: 0.5902 (m-80) REVERT: B 855 PHE cc_start: 0.8393 (m-80) cc_final: 0.8064 (m-80) REVERT: B 934 ILE cc_start: 0.8898 (tp) cc_final: 0.8696 (pp) REVERT: B 957 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8177 (tm-30) REVERT: C 140 PHE cc_start: 0.8747 (p90) cc_final: 0.7725 (p90) REVERT: C 169 GLU cc_start: 0.8319 (tp30) cc_final: 0.8002 (tp30) REVERT: C 177 MET cc_start: -0.0411 (mpt) cc_final: -0.0873 (ptt) REVERT: C 203 ILE cc_start: 0.9050 (pt) cc_final: 0.8579 (pp) REVERT: C 211 ASN cc_start: 0.8641 (t0) cc_final: 0.8376 (m-40) REVERT: C 269 TYR cc_start: 0.7677 (m-80) cc_final: 0.7271 (m-80) REVERT: C 528 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8017 (tmtt) REVERT: C 994 ASP cc_start: 0.9020 (OUTLIER) cc_final: 0.8709 (t0) outliers start: 37 outliers final: 24 residues processed: 176 average time/residue: 0.4681 time to fit residues: 102.0655 Evaluate side-chains 170 residues out of total 3165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain D residue 47 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 101 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 145 optimal weight: 20.0000 chunk 359 optimal weight: 8.9990 chunk 275 optimal weight: 3.9990 chunk 260 optimal weight: 40.0000 chunk 178 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 266 optimal weight: 8.9990 chunk 274 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1002 GLN B 207 HIS B 321 GLN B1010 GLN C 762 GLN E 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.165616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.091448 restraints weight = 57332.124| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.80 r_work: 0.3146 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 29167 Z= 0.354 Angle : 0.655 10.462 39722 Z= 0.346 Chirality : 0.048 0.213 4470 Planarity : 0.004 0.055 5156 Dihedral : 4.324 53.231 3949 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.36 % Favored : 94.56 % Rotamer: Outliers : 1.27 % Allowed : 13.13 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.13 (0.14), residues: 3639 helix: 1.53 (0.20), residues: 702 sheet: 0.19 (0.17), residues: 882 loop : -0.78 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 983 TYR 0.030 0.002 TYR A 904 PHE 0.024 0.002 PHE A1121 TRP 0.042 0.002 TRP B 633 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00827 (29129) covalent geometry : angle 0.65371 (39646) SS BOND : bond 0.00451 ( 38) SS BOND : angle 1.14939 ( 76) hydrogen bonds : bond 0.04709 ( 1004) hydrogen bonds : angle 5.51863 ( 2805) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8608 (tt) cc_final: 0.7958 (mp) REVERT: A 121 ASN cc_start: 0.7609 (t0) cc_final: 0.7235 (t0) REVERT: A 207 HIS cc_start: 0.8301 (OUTLIER) cc_final: 0.7815 (t-90) REVERT: A 740 MET cc_start: 0.9341 (tpt) cc_final: 0.9101 (tpt) REVERT: A 990 GLU cc_start: 0.8563 (tp30) cc_final: 0.8240 (tm-30) REVERT: A 1010 GLN cc_start: 0.9141 (tp40) cc_final: 0.8860 (mm-40) REVERT: B 117 LEU cc_start: 0.7604 (mm) cc_final: 0.6810 (tm) REVERT: B 201 PHE cc_start: 0.7696 (t80) cc_final: 0.7225 (t80) REVERT: B 270 LEU cc_start: 0.7171 (mm) cc_final: 0.6887 (mm) REVERT: B 855 PHE cc_start: 0.8484 (m-80) cc_final: 0.8167 (m-80) REVERT: B 957 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8382 (tm-30) REVERT: C 79 PHE cc_start: 0.4849 (m-80) cc_final: 0.4237 (m-80) REVERT: C 125 ASN cc_start: 0.6729 (OUTLIER) cc_final: 0.5890 (p0) REVERT: C 140 PHE cc_start: 0.8794 (p90) cc_final: 0.7663 (p90) REVERT: C 177 MET cc_start: -0.0483 (mpt) cc_final: -0.1021 (ptt) REVERT: C 203 ILE cc_start: 0.9182 (pt) cc_final: 0.8753 (pp) REVERT: C 211 ASN cc_start: 0.8605 (t0) cc_final: 0.8306 (p0) REVERT: C 242 LEU cc_start: 0.8499 (mm) cc_final: 0.8253 (mm) REVERT: C 528 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.7987 (tmtt) REVERT: C 614 ASP cc_start: 0.9270 (t0) cc_final: 0.8609 (t0) REVERT: C 949 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8566 (mm-40) REVERT: C 994 ASP cc_start: 0.9257 (OUTLIER) cc_final: 0.8877 (t0) outliers start: 40 outliers final: 23 residues processed: 172 average time/residue: 0.4794 time to fit residues: 101.7541 Evaluate side-chains 165 residues out of total 3165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain D residue 47 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 120 optimal weight: 10.0000 chunk 282 optimal weight: 0.9990 chunk 339 optimal weight: 20.0000 chunk 260 optimal weight: 9.9990 chunk 332 optimal weight: 8.9990 chunk 223 optimal weight: 3.9990 chunk 274 optimal weight: 1.9990 chunk 364 optimal weight: 30.0000 chunk 177 optimal weight: 1.9990 chunk 158 optimal weight: 40.0000 chunk 249 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1002 GLN B 207 HIS B 777 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.166697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.094664 restraints weight = 58606.793| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.75 r_work: 0.3138 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 29167 Z= 0.238 Angle : 0.584 9.211 39722 Z= 0.307 Chirality : 0.045 0.302 4470 Planarity : 0.004 0.048 5156 Dihedral : 4.266 51.954 3949 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.23 % Favored : 95.69 % Rotamer: Outliers : 0.98 % Allowed : 13.67 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.13 (0.14), residues: 3639 helix: 1.59 (0.20), residues: 702 sheet: 0.19 (0.17), residues: 876 loop : -0.81 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 983 TYR 0.023 0.001 TYR A 91 PHE 0.019 0.002 PHE B 592 TRP 0.046 0.002 TRP B 633 HIS 0.004 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00557 (29129) covalent geometry : angle 0.58344 (39646) SS BOND : bond 0.00334 ( 38) SS BOND : angle 0.94613 ( 76) hydrogen bonds : bond 0.04236 ( 1004) hydrogen bonds : angle 5.38954 ( 2805) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12567.92 seconds wall clock time: 213 minutes 37.57 seconds (12817.57 seconds total)