Starting phenix.real_space_refine on Sun Jul 5 14:42:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yvn_34133/07_2026/7yvn_34133.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvn_34133/07_2026/7yvn_34133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yvn_34133/07_2026/7yvn_34133.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvn_34133/07_2026/7yvn_34133.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7yvn_34133/07_2026/7yvn_34133.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yvn_34133/07_2026/7yvn_34133.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yvn_34133/07_2026/7yvn_34133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvn_34133/07_2026/7yvn_34133.map" } resolution = 3.4 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= -0.001 sd= 0.033 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 18210 2.51 5 N 4695 2.21 5 O 5469 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 177 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28503 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 7649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7649 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 364 Unresolved non-hydrogen angles: 450 Unresolved non-hydrogen dihedrals: 296 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASP:plan': 13, 'GLN:plan1': 9, 'ASN:plan1': 9, 'GLU:plan': 11, 'PHE:plan': 3, 'ARG:plan': 9, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 237 Chain: "B" Number of atoms: 7643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7643 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASP:plan': 13, 'GLN:plan1': 9, 'ASN:plan1': 9, 'GLU:plan': 11, 'PHE:plan': 3, 'ARG:plan': 10, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 242 Chain: "A" Number of atoms: 7634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7634 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 470 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 13, 'GLN:plan1': 9, 'ASN:plan1': 9, 'GLU:plan': 11, 'PHE:plan': 4, 'ARG:plan': 10, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 248 Chain: "H" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 821 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 870 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "K" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 821 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 870 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "N" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 821 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "O" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 870 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.96, per 1000 atoms: 0.21 Number of scatterers: 28503 At special positions: 0 Unit cell: (145.14, 149.24, 225.5, 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 5469 8.00 N 4695 7.00 C 18210 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 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=2.04 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=2.04 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=2.02 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 A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.05 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.01 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 95 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 95 " distance=2.04 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: 2.33 Conformation dependent library (CDL) restraints added in 1.2 seconds 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6972 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 52 sheets defined 21.3% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 344 Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.876A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.686A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.532A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.634A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.682A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.967A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.097A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.934A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 403 through 410 removed outlier: 4.852A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.585A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.626A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.867A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.956A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.078A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.845A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 344 Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.888A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.650A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.647A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.782A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.015A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.139A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.791A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.134A pdb=" N SER H 83 " --> pdb=" O SER H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 75 Processing helix chain 'I' and resid 86 through 90 removed outlier: 4.050A pdb=" N THR I 90 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 4.060A pdb=" N SER K 83 " --> pdb=" O SER K 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 75 Processing helix chain 'L' and resid 86 through 90 removed outlier: 3.982A pdb=" N THR L 90 " --> pdb=" O ALA L 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.026A pdb=" N SER N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 72 through 75 Processing helix chain 'O' and resid 86 through 90 removed outlier: 3.952A pdb=" N THR O 90 " --> pdb=" O ALA O 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.814A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 3.611A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.471A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.169A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.320A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.933A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.949A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.125A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 702 through 703 Processing sheet with id=AB2, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.100A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C1052 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.100A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.465A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 788 through 789 removed outlier: 6.150A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.455A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.568A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.210A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.550A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.877A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.144A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.646A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 3.852A pdb=" N CYS B 525 " --> pdb=" O CYS B 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.940A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.133A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.133A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.441A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 788 through 789 removed outlier: 6.221A pdb=" N ILE B 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.440A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.527A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.609A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.830A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.157A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.854A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AD9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.988A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.091A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.091A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.565A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.505A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.815A pdb=" N GLU H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.772A pdb=" N LEU H 11 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL H 85 " --> pdb=" O GLN H 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 3 through 7 removed outlier: 4.075A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL I 5 " --> pdb=" O ALA I 23 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 10 through 12 removed outlier: 5.808A pdb=" N GLY I 10 " --> pdb=" O THR I 115 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR I 112 " --> pdb=" O TYR I 93 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 5 through 7 removed outlier: 3.782A pdb=" N GLU K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.408A pdb=" N LEU K 11 " --> pdb=" O GLU K 107 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 3 through 7 removed outlier: 4.029A pdb=" N GLN L 3 " --> pdb=" O SER L 25 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER L 25 " --> pdb=" O GLN L 3 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 11 through 12 removed outlier: 3.593A pdb=" N VAL L 12 " --> pdb=" O THR L 115 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N MET L 34 " --> pdb=" O VAL L 50 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL L 50 " --> pdb=" O MET L 34 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.587A pdb=" N PHE N 71 " --> pdb=" O CYS N 23 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.334A pdb=" N LEU N 11 " --> pdb=" O GLU N 107 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AF7, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.450A pdb=" N GLY O 10 " --> pdb=" O THR O 115 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) 1145 hydrogen bonds defined for protein. 3075 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: 7.49 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9150 1.35 - 1.49: 8156 1.49 - 1.62: 11688 1.62 - 1.76: 14 1.76 - 1.90: 151 Bond restraints: 29159 Sorted by residual: bond pdb=" C PHE B 329 " pdb=" N PRO B 330 " ideal model delta sigma weight residual 1.334 1.416 -0.082 2.34e-02 1.83e+03 1.22e+01 bond pdb=" CB CYS B 749 " pdb=" SG CYS B 749 " ideal model delta sigma weight residual 1.808 1.711 0.097 3.30e-02 9.18e+02 8.64e+00 bond pdb=" C PHE A 329 " pdb=" N PRO A 330 " ideal model delta sigma weight residual 1.334 1.401 -0.067 2.34e-02 1.83e+03 8.15e+00 bond pdb=" CB CYS B 743 " pdb=" SG CYS B 743 " ideal model delta sigma weight residual 1.808 1.716 0.092 3.30e-02 9.18e+02 7.79e+00 bond pdb=" CB CYS B 649 " pdb=" SG CYS B 649 " ideal model delta sigma weight residual 1.808 1.718 0.090 3.30e-02 9.18e+02 7.50e+00 ... (remaining 29154 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 39239 3.19 - 6.38: 507 6.38 - 9.57: 56 9.57 - 12.76: 18 12.76 - 15.95: 8 Bond angle restraints: 39828 Sorted by residual: angle pdb=" CA CYS A 432 " pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 114.40 130.35 -15.95 2.30e+00 1.89e-01 4.81e+01 angle pdb=" CA CYS C 432 " pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 114.40 130.27 -15.87 2.30e+00 1.89e-01 4.76e+01 angle pdb=" N GLY C 526 " pdb=" CA GLY C 526 " pdb=" C GLY C 526 " ideal model delta sigma weight residual 112.34 125.56 -13.22 2.04e+00 2.40e-01 4.20e+01 angle pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " ideal model delta sigma weight residual 114.40 128.20 -13.80 2.30e+00 1.89e-01 3.60e+01 angle pdb=" CA TYR H 49 " pdb=" CB TYR H 49 " pdb=" CG TYR H 49 " ideal model delta sigma weight residual 113.90 124.41 -10.51 1.80e+00 3.09e-01 3.41e+01 ... (remaining 39823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 15479 17.53 - 35.06: 1153 35.06 - 52.59: 184 52.59 - 70.12: 60 70.12 - 87.65: 27 Dihedral angle restraints: 16903 sinusoidal: 6043 harmonic: 10860 Sorted by residual: dihedral pdb=" CA PRO N 95 " pdb=" C PRO N 95 " pdb=" N PRO N 96 " pdb=" CA PRO N 96 " ideal model delta harmonic sigma weight residual -180.00 -126.72 -53.28 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA PRO H 95 " pdb=" C PRO H 95 " pdb=" N PRO H 96 " pdb=" CA PRO H 96 " ideal model delta harmonic sigma weight residual -180.00 -130.73 -49.27 0 5.00e+00 4.00e-02 9.71e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 5.62 87.38 1 1.00e+01 1.00e-02 9.16e+01 ... (remaining 16900 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3904 0.077 - 0.154: 713 0.154 - 0.231: 46 0.231 - 0.308: 7 0.308 - 0.385: 6 Chirality restraints: 4676 Sorted by residual: chirality pdb=" CA CYS A 432 " pdb=" N CYS A 432 " pdb=" C CYS A 432 " pdb=" CB CYS A 432 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CA PRO A 330 " pdb=" N PRO A 330 " pdb=" C PRO A 330 " pdb=" CB PRO A 330 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA CYS B 432 " pdb=" N CYS B 432 " pdb=" C CYS B 432 " pdb=" CB CYS B 432 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.35e+00 ... (remaining 4673 not shown) Planarity restraints: 5100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP H 94 " -0.062 5.00e-02 4.00e+02 9.38e-02 1.41e+01 pdb=" N PRO H 95 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO H 95 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO H 95 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP K 94 " 0.062 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO K 95 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO K 95 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO K 95 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO K 95 " 0.051 5.00e-02 4.00e+02 7.86e-02 9.88e+00 pdb=" N PRO K 96 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO K 96 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO K 96 " 0.043 5.00e-02 4.00e+02 ... (remaining 5097 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 2080 2.72 - 3.27: 28529 3.27 - 3.81: 43994 3.81 - 4.36: 51979 4.36 - 4.90: 91411 Nonbonded interactions: 217993 Sorted by model distance: nonbonded pdb=" O LEU B 455 " pdb=" OH TYR I 107 " model vdw 2.179 3.040 nonbonded pdb=" NH2 ARG C 454 " pdb=" O ASP C 467 " model vdw 2.192 3.120 nonbonded pdb=" OH TYR H 49 " pdb=" O VAL I 5 " model vdw 2.203 3.040 nonbonded pdb=" OG SER H 83 " pdb=" OE1 GLU H 107 " model vdw 2.205 3.040 nonbonded pdb=" NH1 ARG C 34 " pdb=" O GLY C 219 " model vdw 2.211 3.120 ... (remaining 217988 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 27 through 328 or (resid 329 and (name N or name CA or nam \ e C or name O or name CB )) or resid 330 through 532 or (resid 533 and (name N o \ r name CA or name C or name O or name CB )) or resid 534 through 1311)) selection = (chain 'C' and (resid 27 through 327 or (resid 328 through 329 and (name N or na \ me CA or name C or name O or name CB )) or resid 330 through 532 or (resid 533 a \ nd (name N or name CA or name C or name O or name CB )) or resid 534 through 131 \ 1)) } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'O' } 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: 10.570 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 27.340 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 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 : 0.007 0.097 29204 Z= 0.297 Angle : 1.006 15.951 39918 Z= 0.542 Chirality : 0.058 0.385 4676 Planarity : 0.005 0.094 5100 Dihedral : 12.984 87.648 9796 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.62 % Allowed : 5.28 % Favored : 94.10 % Rotamer: Outliers : 1.06 % Allowed : 7.27 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -2.39 (0.12), residues: 3693 helix: 0.20 (0.20), residues: 649 sheet: -1.20 (0.14), residues: 997 loop : -2.48 (0.12), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 61 TYR 0.051 0.002 TYR H 49 PHE 0.029 0.003 PHE B 456 TRP 0.036 0.003 TRP N 94 HIS 0.011 0.001 HIS B 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00705 / 0.30 (29159) covalent geometry : angle 0.98566 / 0.53 (39828) SS BOND : bond 0.00881 / 0.59 ( 45) SS BOND : angle 4.38168 / 2.89 ( 90) hydrogen bonds : bond 0.21089 / 13.56 ( 1130) hydrogen bonds : angle 7.96083 / 5.50 ( 3075) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 306 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 200 TYR cc_start: 0.8625 (m-80) cc_final: 0.8375 (m-80) REVERT: C 241 LEU cc_start: 0.7744 (pp) cc_final: 0.6926 (mp) REVERT: C 776 LYS cc_start: 0.8763 (ttpp) cc_final: 0.8434 (ttpp) REVERT: C 950 ASP cc_start: 0.7986 (m-30) cc_final: 0.7784 (m-30) REVERT: B 258 TRP cc_start: 0.5537 (t-100) cc_final: 0.4423 (m-90) REVERT: B 497 PHE cc_start: 0.4025 (m-80) cc_final: 0.3478 (m-80) REVERT: I 78 LEU cc_start: 0.4378 (mm) cc_final: 0.3953 (mt) REVERT: K 32 ASP cc_start: 0.7633 (m-30) cc_final: 0.7194 (p0) REVERT: K 38 GLN cc_start: 0.6756 (tt0) cc_final: 0.6454 (tt0) REVERT: K 92 ASN cc_start: 0.5695 (p0) cc_final: 0.5441 (t0) REVERT: L 85 LEU cc_start: 0.2907 (OUTLIER) cc_final: 0.1988 (tp) REVERT: N 37 GLN cc_start: 0.8258 (tt0) cc_final: 0.7988 (tm-30) REVERT: N 99 THR cc_start: 0.7704 (m) cc_final: 0.7487 (m) REVERT: O 3 GLN cc_start: 0.7408 (tp-100) cc_final: 0.7126 (pp30) REVERT: O 36 TRP cc_start: 0.4306 (m100) cc_final: 0.3656 (m100) REVERT: O 45 LEU cc_start: 0.7651 (tp) cc_final: 0.7424 (tp) REVERT: O 108 TRP cc_start: 0.6578 (m100) cc_final: 0.5882 (m100) outliers start: 31 outliers final: 6 residues processed: 333 average time/residue: 0.2056 time to fit residues: 106.7346 Evaluate side-chains 193 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 186 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 85 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 50.0000 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 239 GLN C 417 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN C 540 ASN C 657 ASN C1074 ASN C1134 ASN B 360 ASN B 493 GLN B 505 HIS B 506 GLN B 657 ASN B 762 GLN B 965 GLN A 354 ASN A 417 ASN A 493 GLN A 506 GLN A 657 ASN A 762 GLN A 953 ASN A 955 ASN A1005 GLN A1074 ASN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN N 92 ASN N 102 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.146980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.090887 restraints weight = 68030.349| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 5.07 r_work: 0.3091 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 29204 Z= 0.179 Angle : 0.696 10.570 39918 Z= 0.361 Chirality : 0.047 0.232 4676 Planarity : 0.005 0.070 5100 Dihedral : 4.937 47.570 4002 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.28 % Favored : 95.61 % Rotamer: Outliers : 2.30 % Allowed : 11.18 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -1.31 (0.13), residues: 3693 helix: 1.52 (0.21), residues: 660 sheet: -0.67 (0.15), residues: 948 loop : -1.84 (0.13), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 61 TYR 0.019 0.002 TYR C 449 PHE 0.027 0.002 PHE A 970 TRP 0.022 0.002 TRP K 94 HIS 0.005 0.001 HIS B 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (29159) covalent geometry : angle 0.68663 / 0.36 (39828) SS BOND : bond 0.00676 / 0.44 ( 45) SS BOND : angle 2.45588 / 1.67 ( 90) hydrogen bonds : bond 0.05467 / 3.56 ( 1130) hydrogen bonds : angle 6.07264 / 4.19 ( 3075) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 209 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 200 TYR cc_start: 0.8930 (m-80) cc_final: 0.8608 (m-80) REVERT: C 241 LEU cc_start: 0.8321 (pp) cc_final: 0.7662 (mp) REVERT: C 712 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8871 (tt) REVERT: C 755 GLN cc_start: 0.8621 (mp10) cc_final: 0.8284 (pm20) REVERT: C 1002 GLN cc_start: 0.8391 (tm-30) cc_final: 0.8189 (tm-30) REVERT: B 237 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.6673 (ptm-80) REVERT: B 258 TRP cc_start: 0.6030 (t-100) cc_final: 0.4670 (m-90) REVERT: B 497 PHE cc_start: 0.4533 (m-80) cc_final: 0.4018 (m-80) REVERT: B 740 MET cc_start: 0.8235 (tpp) cc_final: 0.8001 (tpp) REVERT: A 135 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7056 (m-80) REVERT: A 578 ASP cc_start: 0.4595 (m-30) cc_final: 0.3871 (t0) REVERT: A 856 ASN cc_start: 0.8843 (m-40) cc_final: 0.8122 (t0) REVERT: A 868 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8221 (tp30) REVERT: K 92 ASN cc_start: 0.6943 (p0) cc_final: 0.6651 (t0) REVERT: L 82 MET cc_start: 0.5755 (mtm) cc_final: 0.5501 (ptm) REVERT: L 85 LEU cc_start: 0.4220 (OUTLIER) cc_final: 0.3063 (tp) REVERT: N 37 GLN cc_start: 0.8210 (tt0) cc_final: 0.8007 (tm-30) REVERT: O 51 MET cc_start: 0.5834 (ppp) cc_final: 0.5462 (ptm) outliers start: 67 outliers final: 32 residues processed: 262 average time/residue: 0.1710 time to fit residues: 73.5952 Evaluate side-chains 214 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 178 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain K residue 71 PHE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain O residue 4 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 47 optimal weight: 1.9990 chunk 265 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 351 optimal weight: 20.0000 chunk 331 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 339 optimal weight: 6.9990 chunk 330 optimal weight: 6.9990 chunk 229 optimal weight: 5.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 801 ASN C 856 ASN B 334 ASN B 422 ASN ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 417 ASN A 762 GLN A 801 ASN A1134 ASN N 92 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.143826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.085650 restraints weight = 68000.489| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 4.39 r_work: 0.3039 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 29204 Z= 0.257 Angle : 0.712 16.720 39918 Z= 0.369 Chirality : 0.048 0.299 4676 Planarity : 0.005 0.066 5100 Dihedral : 4.868 40.125 3994 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.20 % Favored : 94.77 % Rotamer: Outliers : 3.22 % Allowed : 12.86 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -1.08 (0.13), residues: 3693 helix: 1.65 (0.20), residues: 666 sheet: -0.59 (0.15), residues: 971 loop : -1.63 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 346 TYR 0.021 0.002 TYR C 265 PHE 0.027 0.002 PHE B 392 TRP 0.020 0.002 TRP H 94 HIS 0.006 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.26 (29159) covalent geometry : angle 0.70180 / 0.36 (39828) SS BOND : bond 0.00552 / 0.37 ( 45) SS BOND : angle 2.64167 / 1.83 ( 90) hydrogen bonds : bond 0.05742 / 3.79 ( 1130) hydrogen bonds : angle 5.92694 / 4.09 ( 3075) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 188 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 200 TYR cc_start: 0.8899 (m-80) cc_final: 0.8614 (m-80) REVERT: C 238 PHE cc_start: 0.6928 (OUTLIER) cc_final: 0.6333 (p90) REVERT: C 712 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8919 (tt) REVERT: C 756 TYR cc_start: 0.8438 (m-10) cc_final: 0.8147 (m-80) REVERT: C 856 ASN cc_start: 0.9178 (OUTLIER) cc_final: 0.8131 (t0) REVERT: C 1002 GLN cc_start: 0.8486 (tm-30) cc_final: 0.8236 (tm-30) REVERT: B 237 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.6682 (ptm-80) REVERT: B 365 TYR cc_start: 0.7861 (m-80) cc_final: 0.7057 (t80) REVERT: B 432 CYS cc_start: 0.7493 (OUTLIER) cc_final: 0.7214 (p) REVERT: B 497 PHE cc_start: 0.4895 (m-80) cc_final: 0.4269 (m-80) REVERT: B 534 VAL cc_start: 0.8446 (t) cc_final: 0.8229 (p) REVERT: A 118 LEU cc_start: 0.7227 (mp) cc_final: 0.7021 (tp) REVERT: A 135 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.6852 (m-80) REVERT: A 377 PHE cc_start: 0.7621 (t80) cc_final: 0.7357 (t80) REVERT: A 417 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8089 (p0) REVERT: A 525 CYS cc_start: 0.7146 (OUTLIER) cc_final: 0.6852 (m) REVERT: A 762 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8329 (mp10) REVERT: A 950 ASP cc_start: 0.8739 (m-30) cc_final: 0.8507 (m-30) REVERT: A 1096 VAL cc_start: 0.9297 (OUTLIER) cc_final: 0.9060 (p) REVERT: I 82 MET cc_start: -0.1417 (ptp) cc_final: -0.1658 (ppp) REVERT: K 47 LEU cc_start: 0.5227 (OUTLIER) cc_final: 0.4933 (pp) REVERT: K 86 TYR cc_start: 0.6201 (m-80) cc_final: 0.5763 (m-10) REVERT: K 92 ASN cc_start: 0.7441 (p0) cc_final: 0.6846 (t0) REVERT: L 82 MET cc_start: 0.5868 (mtm) cc_final: 0.5596 (ptm) REVERT: L 85 LEU cc_start: 0.3899 (OUTLIER) cc_final: 0.3001 (tp) REVERT: O 38 ARG cc_start: 0.4861 (ptt180) cc_final: 0.4524 (ptt180) REVERT: O 45 LEU cc_start: 0.7742 (tp) cc_final: 0.7346 (mt) REVERT: O 51 MET cc_start: 0.5776 (ppp) cc_final: 0.5398 (ptm) outliers start: 94 outliers final: 49 residues processed: 267 average time/residue: 0.1579 time to fit residues: 69.9881 Evaluate side-chains 227 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 166 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 417 ASN Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 236 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 322 optimal weight: 40.0000 chunk 194 optimal weight: 0.9980 chunk 148 optimal weight: 10.0000 chunk 309 optimal weight: 9.9990 chunk 262 optimal weight: 1.9990 chunk 36 optimal weight: 40.0000 chunk 132 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 422 ASN A 417 ASN A 762 GLN A 953 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.145482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.088281 restraints weight = 67271.070| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 4.92 r_work: 0.3051 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 29204 Z= 0.171 Angle : 0.637 12.363 39918 Z= 0.330 Chirality : 0.045 0.246 4676 Planarity : 0.004 0.067 5100 Dihedral : 4.745 38.021 3994 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.85 % Favored : 95.13 % Rotamer: Outliers : 2.98 % Allowed : 14.48 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -0.80 (0.14), residues: 3693 helix: 1.84 (0.21), residues: 671 sheet: -0.37 (0.16), residues: 963 loop : -1.47 (0.13), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 983 TYR 0.026 0.001 TYR I 79 PHE 0.026 0.002 PHE C 238 TRP 0.020 0.001 TRP A 104 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (29159) covalent geometry : angle 0.62830 / 0.33 (39828) SS BOND : bond 0.00497 / 0.31 ( 45) SS BOND : angle 2.27782 / 1.56 ( 90) hydrogen bonds : bond 0.05019 / 3.32 ( 1130) hydrogen bonds : angle 5.63719 / 3.90 ( 3075) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 184 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ASP cc_start: 0.8433 (m-30) cc_final: 0.8047 (p0) REVERT: C 200 TYR cc_start: 0.8930 (m-80) cc_final: 0.8629 (m-80) REVERT: C 238 PHE cc_start: 0.6793 (OUTLIER) cc_final: 0.6311 (p90) REVERT: C 1002 GLN cc_start: 0.8433 (tm-30) cc_final: 0.8193 (tm-30) REVERT: B 237 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.6679 (ptm-80) REVERT: B 365 TYR cc_start: 0.7781 (m-80) cc_final: 0.6880 (t80) REVERT: B 497 PHE cc_start: 0.5091 (m-80) cc_final: 0.4387 (m-80) REVERT: B 534 VAL cc_start: 0.8515 (t) cc_final: 0.8286 (p) REVERT: B 918 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8256 (mp0) REVERT: A 135 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.6849 (m-80) REVERT: A 762 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8360 (mp10) REVERT: A 868 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8351 (mp0) REVERT: A 902 MET cc_start: 0.9368 (tpt) cc_final: 0.9152 (tpt) REVERT: A 950 ASP cc_start: 0.8784 (m-30) cc_final: 0.8543 (m-30) REVERT: A 1096 VAL cc_start: 0.9259 (OUTLIER) cc_final: 0.9015 (p) REVERT: K 47 LEU cc_start: 0.5391 (OUTLIER) cc_final: 0.5185 (pp) REVERT: K 86 TYR cc_start: 0.6154 (m-80) cc_final: 0.5797 (m-10) REVERT: K 92 ASN cc_start: 0.7400 (p0) cc_final: 0.6800 (t0) REVERT: O 45 LEU cc_start: 0.7631 (tp) cc_final: 0.7216 (mt) outliers start: 87 outliers final: 53 residues processed: 252 average time/residue: 0.1719 time to fit residues: 72.5063 Evaluate side-chains 228 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 168 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 417 ASN Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 99 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 319 optimal weight: 5.9990 chunk 167 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 293 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 345 optimal weight: 30.0000 chunk 174 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 332 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.145807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.085650 restraints weight = 67741.519| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.65 r_work: 0.3110 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 : 0.003 0.048 29204 Z= 0.140 Angle : 0.611 14.256 39918 Z= 0.315 Chirality : 0.045 0.243 4676 Planarity : 0.004 0.052 5100 Dihedral : 4.573 35.271 3991 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.98 % Favored : 94.99 % Rotamer: Outliers : 3.26 % Allowed : 15.33 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -0.60 (0.14), residues: 3693 helix: 1.99 (0.21), residues: 671 sheet: -0.20 (0.16), residues: 972 loop : -1.36 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 983 TYR 0.025 0.001 TYR I 79 PHE 0.026 0.001 PHE C 238 TRP 0.016 0.001 TRP A 104 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (29159) covalent geometry : angle 0.60268 / 0.31 (39828) SS BOND : bond 0.00633 / 0.39 ( 45) SS BOND : angle 2.22810 / 1.47 ( 90) hydrogen bonds : bond 0.04588 / 3.04 ( 1130) hydrogen bonds : angle 5.42522 / 3.75 ( 3075) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 178 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 200 TYR cc_start: 0.8897 (m-80) cc_final: 0.8585 (m-80) REVERT: C 238 PHE cc_start: 0.6851 (OUTLIER) cc_final: 0.6370 (p90) REVERT: C 1002 GLN cc_start: 0.8384 (tm-30) cc_final: 0.8155 (tm-30) REVERT: B 237 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.6750 (ptm-80) REVERT: B 365 TYR cc_start: 0.7739 (m-80) cc_final: 0.6975 (t80) REVERT: B 497 PHE cc_start: 0.5198 (m-80) cc_final: 0.4554 (m-80) REVERT: B 534 VAL cc_start: 0.8507 (t) cc_final: 0.8274 (p) REVERT: B 918 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8244 (mp0) REVERT: A 762 GLN cc_start: 0.8690 (mt0) cc_final: 0.8292 (mp10) REVERT: A 856 ASN cc_start: 0.8864 (m-40) cc_final: 0.8225 (t0) REVERT: A 902 MET cc_start: 0.9316 (tpt) cc_final: 0.9074 (tpt) REVERT: A 950 ASP cc_start: 0.8755 (m-30) cc_final: 0.8484 (m-30) REVERT: A 1096 VAL cc_start: 0.9248 (OUTLIER) cc_final: 0.9017 (p) REVERT: K 86 TYR cc_start: 0.6152 (m-80) cc_final: 0.5798 (m-10) REVERT: K 100 PHE cc_start: 0.5965 (m-80) cc_final: 0.5744 (t80) REVERT: L 85 LEU cc_start: 0.4446 (OUTLIER) cc_final: 0.3321 (tp) outliers start: 95 outliers final: 58 residues processed: 258 average time/residue: 0.1700 time to fit residues: 73.6417 Evaluate side-chains 227 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 164 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 277 optimal weight: 8.9990 chunk 317 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 344 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 313 optimal weight: 50.0000 chunk 1 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 30 ASN C 519 HIS ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1134 ASN K 38 GLN N 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.138163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.081439 restraints weight = 69737.307| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 4.94 r_work: 0.2964 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.102 29204 Z= 0.353 Angle : 0.777 20.683 39918 Z= 0.402 Chirality : 0.050 0.349 4676 Planarity : 0.005 0.077 5100 Dihedral : 5.111 33.957 3991 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.93 % Favored : 94.04 % Rotamer: Outliers : 4.01 % Allowed : 15.81 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.13), residues: 3693 helix: 1.66 (0.20), residues: 662 sheet: -0.40 (0.16), residues: 989 loop : -1.52 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 346 TYR 0.025 0.002 TYR I 79 PHE 0.032 0.002 PHE C 238 TRP 0.017 0.002 TRP A 886 HIS 0.006 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00849 / 0.35 (29159) covalent geometry : angle 0.76200 / 0.40 (39828) SS BOND : bond 0.00607 / 0.43 ( 45) SS BOND : angle 3.27152 / 2.37 ( 90) hydrogen bonds : bond 0.06168 / 4.12 ( 1130) hydrogen bonds : angle 5.85128 / 4.03 ( 3075) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 166 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 200 TYR cc_start: 0.8966 (m-80) cc_final: 0.8635 (m-80) REVERT: C 238 PHE cc_start: 0.6935 (OUTLIER) cc_final: 0.6143 (p90) REVERT: C 258 TRP cc_start: 0.3611 (OUTLIER) cc_final: 0.2846 (m100) REVERT: C 791 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8742 (p) REVERT: C 983 ARG cc_start: 0.8786 (ttp80) cc_final: 0.8361 (ttp80) REVERT: C 1002 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8343 (tm-30) REVERT: B 237 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.6896 (ptm-80) REVERT: B 318 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.7917 (p90) REVERT: B 365 TYR cc_start: 0.7803 (m-80) cc_final: 0.6934 (t80) REVERT: B 455 LEU cc_start: 0.6381 (OUTLIER) cc_final: 0.6114 (tt) REVERT: B 497 PHE cc_start: 0.5381 (m-80) cc_final: 0.4804 (m-80) REVERT: B 534 VAL cc_start: 0.8764 (t) cc_final: 0.8525 (p) REVERT: B 918 GLU cc_start: 0.9212 (OUTLIER) cc_final: 0.8426 (mp0) REVERT: A 318 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8875 (p90) REVERT: A 762 GLN cc_start: 0.8877 (mt0) cc_final: 0.8405 (mp10) REVERT: K 86 TYR cc_start: 0.6021 (m-80) cc_final: 0.5817 (m-10) REVERT: L 85 LEU cc_start: 0.3097 (OUTLIER) cc_final: 0.1726 (tp) REVERT: O 38 ARG cc_start: 0.3732 (ptm-80) cc_final: 0.3357 (ptm160) REVERT: O 45 LEU cc_start: 0.7734 (tp) cc_final: 0.7382 (mp) outliers start: 117 outliers final: 80 residues processed: 267 average time/residue: 0.1729 time to fit residues: 77.6043 Evaluate side-chains 244 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 155 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 99 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 69 optimal weight: 0.9980 chunk 268 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 147 optimal weight: 20.0000 chunk 357 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 chunk 337 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 953 ASN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.152769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.093285 restraints weight = 69102.662| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.50 r_work: 0.3078 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 29204 Z= 0.154 Angle : 0.637 14.172 39918 Z= 0.328 Chirality : 0.045 0.242 4676 Planarity : 0.005 0.115 5100 Dihedral : 4.763 34.970 3991 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.93 % Favored : 95.04 % Rotamer: Outliers : 3.29 % Allowed : 17.22 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.14), residues: 3693 helix: 2.04 (0.21), residues: 664 sheet: -0.25 (0.16), residues: 980 loop : -1.38 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG N 24 TYR 0.021 0.001 TYR O 79 PHE 0.027 0.001 PHE C 238 TRP 0.022 0.001 TRP L 36 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (29159) covalent geometry : angle 0.62431 / 0.32 (39828) SS BOND : bond 0.00489 / 0.34 ( 45) SS BOND : angle 2.69158 / 1.98 ( 90) hydrogen bonds : bond 0.04865 / 3.21 ( 1130) hydrogen bonds : angle 5.43442 / 3.73 ( 3075) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 171 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 200 TYR cc_start: 0.8997 (m-80) cc_final: 0.8722 (m-80) REVERT: C 238 PHE cc_start: 0.7014 (OUTLIER) cc_final: 0.6384 (p90) REVERT: C 258 TRP cc_start: 0.3459 (OUTLIER) cc_final: 0.2741 (m100) REVERT: C 351 TYR cc_start: 0.8135 (t80) cc_final: 0.7838 (t80) REVERT: C 791 THR cc_start: 0.8894 (OUTLIER) cc_final: 0.8667 (p) REVERT: C 983 ARG cc_start: 0.8716 (ttp80) cc_final: 0.8274 (ttp80) REVERT: C 1002 GLN cc_start: 0.8459 (tm-30) cc_final: 0.8206 (tm-30) REVERT: B 237 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.6843 (ptm-80) REVERT: B 365 TYR cc_start: 0.7943 (m-80) cc_final: 0.7110 (t80) REVERT: B 455 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.6195 (tt) REVERT: B 497 PHE cc_start: 0.5313 (m-80) cc_final: 0.4778 (m-80) REVERT: B 534 VAL cc_start: 0.8774 (t) cc_final: 0.8533 (p) REVERT: B 740 MET cc_start: 0.8403 (tpp) cc_final: 0.8165 (tpp) REVERT: B 918 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8302 (mp0) REVERT: A 762 GLN cc_start: 0.8733 (mt0) cc_final: 0.8333 (mp10) REVERT: A 868 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8289 (mp0) REVERT: A 950 ASP cc_start: 0.8728 (m-30) cc_final: 0.8511 (m-30) REVERT: K 92 ASN cc_start: 0.7807 (p0) cc_final: 0.7580 (m-40) REVERT: K 100 PHE cc_start: 0.6232 (m-80) cc_final: 0.5992 (t80) REVERT: L 85 LEU cc_start: 0.4155 (OUTLIER) cc_final: 0.2886 (tp) REVERT: O 38 ARG cc_start: 0.3941 (ptm-80) cc_final: 0.3625 (ptm160) REVERT: O 45 LEU cc_start: 0.7693 (tp) cc_final: 0.7365 (mp) outliers start: 96 outliers final: 68 residues processed: 251 average time/residue: 0.1569 time to fit residues: 66.2986 Evaluate side-chains 239 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 164 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 51 MET Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 51 MET Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 99 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 148 optimal weight: 10.0000 chunk 238 optimal weight: 30.0000 chunk 155 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 265 optimal weight: 0.7980 chunk 262 optimal weight: 0.6980 chunk 198 optimal weight: 3.9990 chunk 171 optimal weight: 0.6980 chunk 293 optimal weight: 2.9990 chunk 233 optimal weight: 9.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 334 ASN A 751 ASN A 953 ASN K 38 GLN K 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.152413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.093088 restraints weight = 69325.865| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.50 r_work: 0.3073 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29204 Z= 0.171 Angle : 0.633 10.862 39918 Z= 0.327 Chirality : 0.045 0.227 4676 Planarity : 0.004 0.063 5100 Dihedral : 4.684 35.674 3991 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.31 % Favored : 94.67 % Rotamer: Outliers : 3.12 % Allowed : 17.70 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.03 % 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: -0.55 (0.14), residues: 3693 helix: 2.10 (0.21), residues: 666 sheet: -0.21 (0.16), residues: 1019 loop : -1.34 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 346 TYR 0.029 0.001 TYR I 79 PHE 0.027 0.001 PHE C 238 TRP 0.020 0.001 TRP L 36 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (29159) covalent geometry : angle 0.62202 / 0.32 (39828) SS BOND : bond 0.00519 / 0.37 ( 45) SS BOND : angle 2.49460 / 1.82 ( 90) hydrogen bonds : bond 0.04817 / 3.19 ( 1130) hydrogen bonds : angle 5.33832 / 3.66 ( 3075) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 170 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ASP cc_start: 0.8335 (m-30) cc_final: 0.8079 (p0) REVERT: C 200 TYR cc_start: 0.8984 (m-80) cc_final: 0.8707 (m-80) REVERT: C 238 PHE cc_start: 0.7005 (OUTLIER) cc_final: 0.6356 (p90) REVERT: C 258 TRP cc_start: 0.3244 (OUTLIER) cc_final: 0.2634 (m100) REVERT: C 351 TYR cc_start: 0.8249 (t80) cc_final: 0.7955 (t80) REVERT: C 791 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8682 (p) REVERT: C 983 ARG cc_start: 0.8724 (ttp80) cc_final: 0.8266 (ttp80) REVERT: C 1002 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8195 (tm-30) REVERT: B 237 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.6816 (ptm-80) REVERT: B 318 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.7768 (p90) REVERT: B 365 TYR cc_start: 0.7894 (m-80) cc_final: 0.7041 (t80) REVERT: B 497 PHE cc_start: 0.5346 (m-80) cc_final: 0.4794 (m-80) REVERT: B 534 VAL cc_start: 0.8794 (t) cc_final: 0.8568 (p) REVERT: B 740 MET cc_start: 0.8420 (tpp) cc_final: 0.8189 (tpp) REVERT: B 918 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8347 (mp0) REVERT: A 368 LEU cc_start: 0.8861 (mm) cc_final: 0.8501 (tp) REVERT: A 762 GLN cc_start: 0.8710 (mt0) cc_final: 0.8329 (mp10) REVERT: A 950 ASP cc_start: 0.8723 (m-30) cc_final: 0.8498 (m-30) REVERT: K 100 PHE cc_start: 0.6299 (m-80) cc_final: 0.6027 (t80) REVERT: L 82 MET cc_start: 0.6045 (mtm) cc_final: 0.5740 (mtm) REVERT: L 85 LEU cc_start: 0.4287 (OUTLIER) cc_final: 0.2676 (tp) REVERT: O 38 ARG cc_start: 0.4025 (ptm-80) cc_final: 0.3701 (ptm160) REVERT: O 45 LEU cc_start: 0.7674 (tp) cc_final: 0.7266 (mp) outliers start: 91 outliers final: 68 residues processed: 247 average time/residue: 0.1562 time to fit residues: 65.3677 Evaluate side-chains 238 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 163 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 51 MET Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 53 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 261 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 309 optimal weight: 8.9990 chunk 125 optimal weight: 0.8980 chunk 50 optimal weight: 0.0270 chunk 138 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 266 optimal weight: 0.9980 chunk 181 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 281 optimal weight: 0.7980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 422 ASN A 801 ASN A 953 ASN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.145569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.086272 restraints weight = 67878.536| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.60 r_work: 0.3127 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 29204 Z= 0.110 Angle : 0.599 10.064 39918 Z= 0.309 Chirality : 0.044 0.220 4676 Planarity : 0.004 0.043 5100 Dihedral : 4.481 35.119 3991 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.60 % Favored : 95.37 % Rotamer: Outliers : 2.09 % Allowed : 18.70 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.14), residues: 3693 helix: 2.26 (0.21), residues: 667 sheet: -0.07 (0.16), residues: 1014 loop : -1.22 (0.14), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG O 19 TYR 0.025 0.001 TYR I 79 PHE 0.024 0.001 PHE C 238 TRP 0.036 0.001 TRP L 36 HIS 0.004 0.001 HIS A 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (29159) covalent geometry : angle 0.58989 / 0.31 (39828) SS BOND : bond 0.00415 / 0.28 ( 45) SS BOND : angle 2.22638 / 1.63 ( 90) hydrogen bonds : bond 0.04085 / 2.68 ( 1130) hydrogen bonds : angle 5.06592 / 3.47 ( 3075) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 181 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 200 TYR cc_start: 0.8971 (m-80) cc_final: 0.8728 (m-80) REVERT: C 258 TRP cc_start: 0.3048 (OUTLIER) cc_final: 0.2566 (m100) REVERT: C 351 TYR cc_start: 0.8251 (t80) cc_final: 0.7943 (t80) REVERT: C 759 PHE cc_start: 0.8050 (m-80) cc_final: 0.7800 (m-80) REVERT: B 237 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.6852 (ptm-80) REVERT: B 365 TYR cc_start: 0.7799 (m-80) cc_final: 0.6979 (t80) REVERT: B 497 PHE cc_start: 0.5291 (m-80) cc_final: 0.4740 (m-80) REVERT: B 534 VAL cc_start: 0.8872 (t) cc_final: 0.8644 (p) REVERT: B 740 MET cc_start: 0.8369 (tpp) cc_final: 0.8149 (tpp) REVERT: B 918 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8351 (mp0) REVERT: A 317 ASN cc_start: 0.8639 (p0) cc_final: 0.8184 (t0) REVERT: A 368 LEU cc_start: 0.8856 (mm) cc_final: 0.8503 (tp) REVERT: A 762 GLN cc_start: 0.8606 (mt0) cc_final: 0.8363 (mp10) REVERT: A 856 ASN cc_start: 0.8821 (m-40) cc_final: 0.8234 (t0) REVERT: A 950 ASP cc_start: 0.8688 (m-30) cc_final: 0.8459 (m-30) REVERT: I 82 MET cc_start: 0.0130 (ppp) cc_final: -0.0096 (ppp) REVERT: L 85 LEU cc_start: 0.4630 (OUTLIER) cc_final: 0.3260 (tp) REVERT: O 45 LEU cc_start: 0.7632 (tp) cc_final: 0.7280 (mp) outliers start: 61 outliers final: 45 residues processed: 232 average time/residue: 0.1692 time to fit residues: 65.7084 Evaluate side-chains 218 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 169 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 294 optimal weight: 0.6980 chunk 119 optimal weight: 8.9990 chunk 280 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 52 optimal weight: 0.4980 chunk 205 optimal weight: 2.9990 chunk 214 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 213 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 269 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 901 GLN B 30 ASN B1005 GLN A 953 ASN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.153603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.094473 restraints weight = 68923.290| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.52 r_work: 0.3094 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 29204 Z= 0.153 Angle : 0.620 11.773 39918 Z= 0.319 Chirality : 0.045 0.219 4676 Planarity : 0.004 0.043 5100 Dihedral : 4.510 34.554 3991 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.85 % Favored : 95.13 % Rotamer: Outliers : 2.06 % Allowed : 18.90 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.33 (0.14), residues: 3693 helix: 2.24 (0.21), residues: 666 sheet: -0.00 (0.16), residues: 1018 loop : -1.23 (0.14), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG O 19 TYR 0.026 0.001 TYR I 79 PHE 0.034 0.001 PHE C 238 TRP 0.048 0.001 TRP L 36 HIS 0.003 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (29159) covalent geometry : angle 0.61059 / 0.31 (39828) SS BOND : bond 0.00456 / 0.31 ( 45) SS BOND : angle 2.31124 / 1.69 ( 90) hydrogen bonds : bond 0.04488 / 2.97 ( 1130) hydrogen bonds : angle 5.12304 / 3.52 ( 3075) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 171 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ASP cc_start: 0.8308 (m-30) cc_final: 0.8055 (p0) REVERT: C 200 TYR cc_start: 0.8973 (m-80) cc_final: 0.8719 (m-80) REVERT: C 258 TRP cc_start: 0.2952 (OUTLIER) cc_final: 0.2492 (m100) REVERT: C 351 TYR cc_start: 0.8267 (t80) cc_final: 0.7993 (t80) REVERT: C 791 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8671 (p) REVERT: C 983 ARG cc_start: 0.8718 (ttp80) cc_final: 0.8250 (ttp80) REVERT: B 237 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.6808 (ptm-80) REVERT: B 365 TYR cc_start: 0.7843 (m-80) cc_final: 0.7014 (t80) REVERT: B 497 PHE cc_start: 0.5326 (m-80) cc_final: 0.4773 (m-80) REVERT: B 534 VAL cc_start: 0.8864 (t) cc_final: 0.8629 (p) REVERT: B 740 MET cc_start: 0.8448 (tpp) cc_final: 0.8237 (tpp) REVERT: B 918 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8351 (mp0) REVERT: A 175 PHE cc_start: 0.7689 (m-80) cc_final: 0.7131 (p90) REVERT: A 317 ASN cc_start: 0.8643 (p0) cc_final: 0.8171 (t0) REVERT: A 368 LEU cc_start: 0.8857 (mm) cc_final: 0.8521 (tp) REVERT: A 762 GLN cc_start: 0.8635 (mt0) cc_final: 0.8363 (mp10) REVERT: A 950 ASP cc_start: 0.8712 (m-30) cc_final: 0.8481 (m-30) REVERT: K 94 TRP cc_start: 0.6755 (t60) cc_final: 0.5963 (t-100) REVERT: K 100 PHE cc_start: 0.6002 (t80) cc_final: 0.5431 (t80) REVERT: L 85 LEU cc_start: 0.3841 (OUTLIER) cc_final: 0.2468 (tp) REVERT: O 45 LEU cc_start: 0.7631 (tp) cc_final: 0.7237 (mp) outliers start: 60 outliers final: 49 residues processed: 221 average time/residue: 0.1712 time to fit residues: 64.3069 Evaluate side-chains 221 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 167 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 13 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 115 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 137 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 278 optimal weight: 0.6980 chunk 292 optimal weight: 3.9990 chunk 214 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 184 optimal weight: 0.6980 chunk 215 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 901 GLN B1005 GLN A 953 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.152815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.093555 restraints weight = 69188.684| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.52 r_work: 0.3085 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29204 Z= 0.155 Angle : 0.614 9.690 39918 Z= 0.317 Chirality : 0.045 0.214 4676 Planarity : 0.004 0.046 5100 Dihedral : 4.513 35.097 3991 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.77 % Favored : 95.21 % Rotamer: Outliers : 2.13 % Allowed : 19.01 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.34 (0.14), residues: 3693 helix: 2.22 (0.21), residues: 667 sheet: -0.00 (0.16), residues: 1028 loop : -1.25 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG O 19 TYR 0.027 0.001 TYR I 79 PHE 0.034 0.001 PHE C 238 TRP 0.055 0.001 TRP L 36 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 (29159) covalent geometry : angle 0.60586 / 0.31 (39828) SS BOND : bond 0.00456 / 0.30 ( 45) SS BOND : angle 2.22949 / 1.62 ( 90) hydrogen bonds : bond 0.04537 / 2.99 ( 1130) hydrogen bonds : angle 5.12976 / 3.52 ( 3075) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9176.99 seconds wall clock time: 157 minutes 14.11 seconds (9434.11 seconds total)