Starting phenix.real_space_refine on Sun Jul 5 21:17:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yvp_34135/07_2026/7yvp_34135.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvp_34135/07_2026/7yvp_34135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yvp_34135/07_2026/7yvp_34135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvp_34135/07_2026/7yvp_34135.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7yvp_34135/07_2026/7yvp_34135.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yvp_34135/07_2026/7yvp_34135.cif" model { file = "/net/cci-nas-00/data/ceres_data/7yvp_34135/07_2026/7yvp_34135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvp_34135/07_2026/7yvp_34135.cif" } resolution = 3.8 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= 0.029 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 131 5.16 5 C 19286 2.51 5 N 4950 2.21 5 O 5810 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 176 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: 30177 Number of models: 1 Model: "" Number of chains: 14 Chain: "I" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 914 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 796 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "L" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 914 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 796 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "O" 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: "P" 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: "A" Number of atoms: 7725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7725 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 10, 'GLN:plan1': 10, 'ASN:plan1': 7, 'GLU:plan': 8, 'PHE:plan': 2, 'ARG:plan': 5, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 174 Chain: "B" Number of atoms: 7413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7413 Classifications: {'peptide': 987} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 54, 'TRANS': 932} Chain breaks: 10 Unresolved non-hydrogen bonds: 316 Unresolved non-hydrogen angles: 388 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 11, 'GLN:plan1': 9, 'ASN:plan1': 7, 'GLU:plan': 10, 'PHE:plan': 2, 'ARG:plan': 7, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 198 Chain: "C" Number of atoms: 7719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7719 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 359 Unresolved non-hydrogen dihedrals: 237 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 10, 'GLN:plan1': 10, 'ASN:plan1': 7, 'GLU:plan': 8, 'PHE:plan': 3, 'ARG:plan': 5, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 180 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: "K" 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: "A" 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: "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: "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 Time building chain proxies: 5.02, per 1000 atoms: 0.17 Number of scatterers: 30177 At special positions: 0 Unit cell: (178.76, 148.42, 227.14, 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 131 16.00 O 5810 8.00 N 4950 7.00 C 19286 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 97 " distance=2.02 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 90 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 97 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 90 " distance=2.02 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 95 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=1.99 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.05 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=2.02 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=2.01 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 B 131 " - pdb=" SG CYS B 166 " distance=2.06 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.01 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.1 seconds 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7332 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 63 sheets defined 20.3% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'I' and resid 88 through 92 removed outlier: 3.661A pdb=" N THR I 92 " --> pdb=" O PRO I 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 85 removed outlier: 3.678A pdb=" N ASP J 85 " --> pdb=" O ALA J 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 92 removed outlier: 3.846A pdb=" N THR L 92 " --> pdb=" O PRO L 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 85 removed outlier: 3.714A pdb=" N ASP M 85 " --> pdb=" O ALA M 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 83 removed outlier: 4.024A pdb=" N SER O 83 " --> pdb=" O SER O 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 73 through 75 No H-bonds generated for 'chain 'P' and resid 73 through 75' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.576A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.885A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.594A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) 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 801 through 805 removed outlier: 4.494A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.828A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.784A 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: 3.909A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.871A 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 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.554A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.073A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.118A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1140 through 1145' 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 407 removed outlier: 3.542A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 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 801 through 805 removed outlier: 4.533A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.761A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.622A 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: 3.843A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.835A 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 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.563A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.955A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.072A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1140 through 1145' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.098A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.557A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.579A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.642A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) 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 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: 3.638A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.721A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 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: 3.850A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.830A 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 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.716A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.891A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.774A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.162A pdb=" N SER H 83 " --> pdb=" O SER H 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 75 Processing sheet with id=AA1, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'I' and resid 59 through 61 removed outlier: 5.676A pdb=" N TRP I 49 " --> pdb=" O ARG I 40 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ARG I 40 " --> pdb=" O TRP I 49 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA I 51 " --> pdb=" O TRP I 38 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR I 108 " --> pdb=" O HIS I 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 59 through 61 removed outlier: 5.676A pdb=" N TRP I 49 " --> pdb=" O ARG I 40 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ARG I 40 " --> pdb=" O TRP I 49 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA I 51 " --> pdb=" O TRP I 38 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR I 95 " --> pdb=" O THR I 113 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 18 through 21 Processing sheet with id=AA6, first strand: chain 'J' and resid 47 through 50 removed outlier: 6.294A pdb=" N LEU J 48 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN J 39 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE J 50 " --> pdb=" O TRP J 37 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 47 through 50 removed outlier: 6.294A pdb=" N LEU J 48 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN J 39 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE J 50 " --> pdb=" O TRP J 37 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'L' and resid 11 through 12 Processing sheet with id=AB1, first strand: chain 'L' and resid 59 through 61 removed outlier: 5.461A pdb=" N TRP L 49 " --> pdb=" O ARG L 40 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ARG L 40 " --> pdb=" O TRP L 49 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA L 51 " --> pdb=" O TRP L 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 9 through 10 removed outlier: 3.731A pdb=" N VAL M 10 " --> pdb=" O LYS M 105 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLN M 39 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU M 48 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 9 through 10 removed outlier: 3.731A pdb=" N VAL M 10 " --> pdb=" O LYS M 105 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 18 through 20 Processing sheet with id=AB5, first strand: chain 'O' and resid 5 through 7 removed outlier: 3.739A pdb=" N GLU O 70 " --> pdb=" O SER O 67 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.102A pdb=" N LEU O 11 " --> pdb=" O GLU O 107 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL O 85 " --> pdb=" O GLN O 38 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 3 through 7 removed outlier: 3.768A pdb=" N GLN P 3 " --> pdb=" O SER P 25 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.245A pdb=" N GLY P 10 " --> pdb=" O THR P 115 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.506A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.712A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.144A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.502A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.240A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.526A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.114A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.114A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.299A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.216A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AD3, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.206A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.206A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AD6, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.059A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.621A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 30 through 31 Processing sheet with id=AD9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.942A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 63 through 66 removed outlier: 4.439A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.823A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.557A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 324 through 328 removed outlier: 5.514A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.649A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.617A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.267A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AF1, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.139A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.139A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 735 through 736 removed outlier: 3.637A pdb=" N SER B 735 " --> pdb=" O THR B 859 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.533A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 29 through 31 removed outlier: 8.585A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.641A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.714A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.079A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.980A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.079A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.060A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.060A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.396A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.486A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.958A pdb=" N GLU H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.385A pdb=" N LEU H 11 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL H 85 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.973A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.428A pdb=" N GLY K 10 " --> pdb=" O THR K 115 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N MET K 34 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) 1173 hydrogen bonds defined for protein. 3117 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.18 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8697 1.33 - 1.46: 8369 1.46 - 1.59: 13642 1.59 - 1.72: 1 1.72 - 1.84: 167 Bond restraints: 30876 Sorted by residual: bond pdb=" C PRO B 862 " pdb=" O PRO B 862 " ideal model delta sigma weight residual 1.240 1.204 0.037 1.12e-02 7.97e+03 1.08e+01 bond pdb=" C PRO A 862 " pdb=" O PRO A 862 " ideal model delta sigma weight residual 1.240 1.204 0.037 1.12e-02 7.97e+03 1.07e+01 bond pdb=" N THR A 333 " pdb=" CA THR A 333 " ideal model delta sigma weight residual 1.459 1.486 -0.027 9.10e-03 1.21e+04 8.90e+00 bond pdb=" N LYS A 528 " pdb=" CA LYS A 528 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.53e+00 bond pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 7.14e+00 ... (remaining 30871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.03: 41825 4.03 - 8.06: 296 8.06 - 12.09: 30 12.09 - 16.12: 5 16.12 - 20.15: 2 Bond angle restraints: 42158 Sorted by residual: angle pdb=" C ILE C 326 " pdb=" N VAL C 327 " pdb=" CA VAL C 327 " ideal model delta sigma weight residual 121.97 133.53 -11.56 1.80e+00 3.09e-01 4.12e+01 angle pdb=" C HIS A 519 " pdb=" N ALA A 520 " pdb=" CA ALA A 520 " ideal model delta sigma weight residual 121.59 101.44 20.15 3.54e+00 7.98e-02 3.24e+01 angle pdb=" N TYR J 51 " pdb=" CA TYR J 51 " pdb=" C TYR J 51 " ideal model delta sigma weight residual 109.52 101.20 8.32 1.55e+00 4.16e-01 2.88e+01 angle pdb=" CA CYS B 432 " pdb=" CB CYS B 432 " pdb=" SG CYS B 432 " ideal model delta sigma weight residual 114.40 126.37 -11.97 2.30e+00 1.89e-01 2.71e+01 angle pdb=" C CYS A 336 " pdb=" CA CYS A 336 " pdb=" CB CYS A 336 " ideal model delta sigma weight residual 110.17 100.05 10.12 1.97e+00 2.58e-01 2.64e+01 ... (remaining 42153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.31: 17059 23.31 - 46.62: 745 46.62 - 69.94: 95 69.94 - 93.25: 24 93.25 - 116.56: 1 Dihedral angle restraints: 17924 sinusoidal: 6504 harmonic: 11420 Sorted by residual: 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 -63.44 -116.56 0 5.00e+00 4.00e-02 5.43e+02 dihedral pdb=" CA PRO O 95 " pdb=" C PRO O 95 " pdb=" N PRO O 96 " pdb=" CA PRO O 96 " ideal model delta harmonic sigma weight residual 180.00 -122.32 -57.68 0 5.00e+00 4.00e-02 1.33e+02 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -5.33 -80.67 1 1.00e+01 1.00e-02 8.04e+01 ... (remaining 17921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4516 0.098 - 0.196: 411 0.196 - 0.294: 18 0.294 - 0.391: 2 0.391 - 0.489: 1 Chirality restraints: 4948 Sorted by residual: chirality pdb=" CG LEU B 518 " pdb=" CB LEU B 518 " pdb=" CD1 LEU B 518 " pdb=" CD2 LEU B 518 " both_signs ideal model delta sigma weight residual False -2.59 -2.10 -0.49 2.00e-01 2.50e+01 5.98e+00 chirality pdb=" CA TRP H 94 " pdb=" N TRP H 94 " pdb=" C TRP H 94 " pdb=" CB TRP H 94 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA CYS A 617 " pdb=" N CYS A 617 " pdb=" C CYS A 617 " pdb=" CB CYS A 617 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.36 2.00e-01 2.50e+01 3.15e+00 ... (remaining 4945 not shown) Planarity restraints: 5371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 526 " -0.062 5.00e-02 4.00e+02 9.51e-02 1.45e+01 pdb=" N PRO C 527 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO C 527 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 527 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE L 102 " -0.062 5.00e-02 4.00e+02 9.44e-02 1.43e+01 pdb=" N PRO L 103 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO L 103 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO L 103 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP H 94 " -0.060 5.00e-02 4.00e+02 8.91e-02 1.27e+01 pdb=" N PRO H 95 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO H 95 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO H 95 " -0.049 5.00e-02 4.00e+02 ... (remaining 5368 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 934 2.67 - 3.23: 30348 3.23 - 3.78: 45783 3.78 - 4.34: 59739 4.34 - 4.90: 99329 Nonbonded interactions: 236133 Sorted by model distance: nonbonded pdb=" O ILE L 105 " pdb=" OH TYR M 38 " model vdw 2.111 3.040 nonbonded pdb=" ND2 ASN A1098 " pdb=" O7 NAG A1309 " model vdw 2.139 3.120 nonbonded pdb=" NE2 GLN H 42 " pdb=" O ALA H 43 " model vdw 2.141 3.120 nonbonded pdb=" O THR B1076 " pdb=" OG SER B1097 " model vdw 2.149 3.040 nonbonded pdb=" O CYS P 22 " pdb=" OG1 THR P 77 " model vdw 2.150 3.040 ... (remaining 236128 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' 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 368 or (resid 369 and (name N o \ r name CA or name C or name O or name CB )) or resid 370 through 402 or (resid 4 \ 03 and (name N or name CA or name C or name O or name CB )) or resid 404 through \ 405 or (resid 406 and (name N or name CA or name C or name O or name CB )) or r \ esid 407 through 423 or (resid 424 and (name N or name CA or name C or name O or \ name CB )) or resid 425 through 438 or (resid 439 and (name N or name CA or nam \ e C or name O or name CB )) or resid 440 through 441 or (resid 442 and (name N o \ r name CA or name C or name O or name CB )) or resid 443 or resid 451 through 46 \ 4 or (resid 465 and (name N or name CA or name C or name O or name CB )) or resi \ d 491 through 497 or resid 503 through 508 or (resid 509 and (name N or name CA \ or name C or name O or name CB )) or resid 510 through 1312)) 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 1312)) selection = (chain 'C' and (resid 27 through 368 or (resid 369 and (name N or name CA or nam \ e C or name O or name CB )) or resid 370 through 402 or (resid 403 and (name N o \ r name CA or name C or name O or name CB )) or resid 404 through 405 or (resid 4 \ 06 and (name N or name CA or name C or name O or name CB )) or resid 407 through \ 423 or (resid 424 and (name N or name CA or name C or name O or name CB )) or r \ esid 425 through 438 or (resid 439 and (name N or name CA or name C or name O or \ name CB )) or resid 440 through 441 or (resid 442 and (name N or name CA or nam \ e C or name O or name CB )) or resid 443 or resid 451 through 464 or (resid 465 \ and (name N or name CA or name C or name O or name CB )) or resid 491 through 49 \ 7 or resid 503 through 508 or (resid 509 and (name N or name CA or name C or nam \ e O or name CB )) or resid 510 through 1312)) } ncs_group { reference = chain 'H' selection = chain 'O' } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'K' selection = chain 'P' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.040 Process input model: 23.650 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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 : 0.009 0.117 30922 Z= 0.379 Angle : 1.042 20.146 42250 Z= 0.559 Chirality : 0.057 0.489 4948 Planarity : 0.006 0.095 5371 Dihedral : 12.927 116.559 10454 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.48 % Favored : 94.03 % Rotamer: Outliers : 1.21 % Allowed : 8.08 % Favored : 90.71 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -2.70 (0.12), residues: 3871 helix: -0.02 (0.19), residues: 657 sheet: -1.71 (0.14), residues: 1030 loop : -2.47 (0.12), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1000 TYR 0.031 0.003 TYR A 873 PHE 0.031 0.003 PHE B 194 TRP 0.058 0.004 TRP H 94 HIS 0.008 0.002 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00851 / 0.38 (30876) covalent geometry : angle 1.03165 / 0.56 (42158) SS BOND : bond 0.01210 / 0.83 ( 46) SS BOND : angle 3.24066 / 2.06 ( 92) hydrogen bonds : bond 0.21785 / 14.51 ( 1136) hydrogen bonds : angle 8.61520 / 5.84 ( 3117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 225 time to evaluate : 1.023 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 77 LYS cc_start: 0.4591 (tttm) cc_final: 0.4160 (mttt) REVERT: I 96 TYR cc_start: 0.7344 (m-80) cc_final: 0.6710 (m-80) REVERT: L 54 TYR cc_start: 0.4346 (m-80) cc_final: 0.4146 (m-80) REVERT: M 52 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8749 (mm-30) REVERT: B 200 TYR cc_start: 0.8994 (m-80) cc_final: 0.8640 (m-10) REVERT: B 773 GLU cc_start: 0.8865 (tp30) cc_final: 0.8532 (tp30) REVERT: B 780 GLU cc_start: 0.7960 (pt0) cc_final: 0.7517 (pt0) REVERT: C 129 LYS cc_start: 0.8555 (mtpt) cc_final: 0.8355 (mtpp) REVERT: C 229 LEU cc_start: 0.9121 (mt) cc_final: 0.8770 (pp) REVERT: C 365 TYR cc_start: 0.8584 (m-80) cc_final: 0.8172 (m-80) REVERT: C 960 ASN cc_start: 0.9388 (t0) cc_final: 0.9041 (t0) REVERT: C 1138 TYR cc_start: 0.8057 (m-80) cc_final: 0.7519 (m-10) REVERT: H 4 MET cc_start: 0.3606 (mmm) cc_final: 0.3326 (mtt) outliers start: 38 outliers final: 14 residues processed: 262 average time/residue: 0.1954 time to fit residues: 80.4470 Evaluate side-chains 146 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 538 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 50.0000 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 8.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 16 GLN M 6 GLN ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 450 ASN A 460 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 ASN A 762 GLN A 955 ASN A1134 ASN B 334 ASN B 388 ASN B 506 GLN B 657 ASN B 709 ASN B 762 GLN C 417 ASN ** C 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1134 ASN ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.107974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.069575 restraints weight = 140916.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.068711 restraints weight = 79417.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.069583 restraints weight = 54290.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.069505 restraints weight = 35177.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.069644 restraints weight = 34422.039| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 30922 Z= 0.173 Angle : 0.698 10.589 42250 Z= 0.363 Chirality : 0.047 0.362 4948 Planarity : 0.005 0.107 5371 Dihedral : 5.318 53.070 4220 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.58 % Favored : 94.29 % Rotamer: Outliers : 1.97 % Allowed : 11.20 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -1.65 (0.13), residues: 3871 helix: 1.15 (0.21), residues: 652 sheet: -0.93 (0.14), residues: 1125 loop : -1.98 (0.12), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 765 TYR 0.037 0.002 TYR P 107 PHE 0.023 0.002 PHE B 429 TRP 0.017 0.001 TRP O 94 HIS 0.004 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (30876) covalent geometry : angle 0.69305 / 0.36 (42158) SS BOND : bond 0.00693 / 0.47 ( 46) SS BOND : angle 1.90317 / 1.17 ( 92) hydrogen bonds : bond 0.05295 / 3.48 ( 1136) hydrogen bonds : angle 6.48844 / 4.40 ( 3117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 165 time to evaluate : 1.019 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 77 LYS cc_start: 0.5408 (tttm) cc_final: 0.4234 (mttt) REVERT: L 38 TRP cc_start: 0.4417 (m100) cc_final: 0.4170 (m100) REVERT: M 52 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8621 (mm-30) REVERT: P 82 MET cc_start: 0.5618 (mtm) cc_final: 0.5338 (mtm) REVERT: A 902 MET cc_start: 0.9113 (tpp) cc_final: 0.8900 (tpt) REVERT: A 1135 ASN cc_start: 0.8874 (t0) cc_final: 0.8540 (t0) REVERT: B 200 TYR cc_start: 0.9212 (m-80) cc_final: 0.8836 (m-10) REVERT: B 380 TYR cc_start: 0.7283 (m-80) cc_final: 0.7043 (m-10) REVERT: B 773 GLU cc_start: 0.8814 (tp30) cc_final: 0.8405 (tp30) REVERT: C 229 LEU cc_start: 0.9344 (mt) cc_final: 0.8937 (pp) REVERT: C 365 TYR cc_start: 0.8255 (m-80) cc_final: 0.7867 (m-80) REVERT: C 524 VAL cc_start: 0.7100 (OUTLIER) cc_final: 0.6662 (p) REVERT: C 902 MET cc_start: 0.9363 (tpp) cc_final: 0.8846 (tpt) REVERT: C 960 ASN cc_start: 0.9213 (t0) cc_final: 0.8853 (t0) REVERT: C 1138 TYR cc_start: 0.7970 (m-80) cc_final: 0.7464 (m-10) REVERT: H 36 TYR cc_start: 0.2962 (m-80) cc_final: 0.2618 (m-80) REVERT: K 36 TRP cc_start: 0.4836 (m100) cc_final: 0.4541 (m100) REVERT: K 94 TYR cc_start: 0.6792 (m-80) cc_final: 0.6580 (m-10) REVERT: K 110 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.8124 (pm20) outliers start: 62 outliers final: 23 residues processed: 221 average time/residue: 0.1642 time to fit residues: 59.2942 Evaluate side-chains 162 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain P residue 38 ARG Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain K residue 110 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 56 optimal weight: 9.9990 chunk 193 optimal weight: 40.0000 chunk 103 optimal weight: 3.9990 chunk 290 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 230 optimal weight: 0.5980 chunk 228 optimal weight: 4.9990 chunk 359 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 250 optimal weight: 0.7980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 GLN M 39 GLN ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 110 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN H 38 GLN H 90 GLN ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.107466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.068164 restraints weight = 141112.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.068624 restraints weight = 79531.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.068754 restraints weight = 44769.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.068789 restraints weight = 44354.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.068870 restraints weight = 38902.567| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30922 Z= 0.159 Angle : 0.640 12.639 42250 Z= 0.332 Chirality : 0.045 0.355 4948 Planarity : 0.004 0.063 5371 Dihedral : 5.018 54.421 4209 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.40 % Favored : 94.52 % Rotamer: Outliers : 2.42 % Allowed : 12.50 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % 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: 3871 helix: 1.38 (0.21), residues: 659 sheet: -0.73 (0.15), residues: 1124 loop : -1.74 (0.12), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 40 TYR 0.020 0.001 TYR L 96 PHE 0.019 0.001 PHE B 201 TRP 0.022 0.001 TRP L 109 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (30876) covalent geometry : angle 0.63417 / 0.33 (42158) SS BOND : bond 0.00776 / 0.55 ( 46) SS BOND : angle 2.01118 / 1.20 ( 92) hydrogen bonds : bond 0.04767 / 3.12 ( 1136) hydrogen bonds : angle 6.07255 / 4.10 ( 3117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 152 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 77 LYS cc_start: 0.5202 (tttm) cc_final: 0.4150 (mttt) REVERT: L 48 GLU cc_start: 0.3920 (mp0) cc_final: 0.3692 (mp0) REVERT: L 73 LYS cc_start: 0.7471 (pptt) cc_final: 0.6909 (tptm) REVERT: M 52 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8653 (mm-30) REVERT: P 1 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7388 (pp20) REVERT: P 66 ARG cc_start: 0.5258 (ptm160) cc_final: 0.4998 (ttp-170) REVERT: B 191 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8334 (mt-10) REVERT: B 200 TYR cc_start: 0.9257 (m-80) cc_final: 0.8877 (m-10) REVERT: B 773 GLU cc_start: 0.8854 (tp30) cc_final: 0.8393 (tp30) REVERT: B 902 MET cc_start: 0.9316 (tpp) cc_final: 0.9024 (tpt) REVERT: C 229 LEU cc_start: 0.9356 (mt) cc_final: 0.8889 (pp) REVERT: C 365 TYR cc_start: 0.8233 (m-80) cc_final: 0.7870 (m-80) REVERT: C 904 TYR cc_start: 0.8523 (OUTLIER) cc_final: 0.8297 (m-10) REVERT: C 960 ASN cc_start: 0.9174 (t0) cc_final: 0.8797 (t0) REVERT: C 1002 GLN cc_start: 0.8971 (tp40) cc_final: 0.8757 (tp40) REVERT: C 1138 TYR cc_start: 0.7988 (m-80) cc_final: 0.7463 (m-10) REVERT: K 36 TRP cc_start: 0.4680 (m100) cc_final: 0.4397 (m100) REVERT: K 110 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8256 (pm20) outliers start: 76 outliers final: 36 residues processed: 213 average time/residue: 0.1804 time to fit residues: 62.4037 Evaluate side-chains 171 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 132 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain P residue 1 GLU Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain K residue 110 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 131 optimal weight: 0.8980 chunk 342 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 305 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 210 optimal weight: 0.9990 chunk 165 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 chunk 201 optimal weight: 0.0980 chunk 55 optimal weight: 20.0000 chunk 373 optimal weight: 50.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 78 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 ASN ** 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 = 0.4179 r_free = 0.4179 target = 0.107089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.068244 restraints weight = 139781.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.067301 restraints weight = 76420.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.068628 restraints weight = 54734.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.068401 restraints weight = 34867.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.068586 restraints weight = 33994.825| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30922 Z= 0.164 Angle : 0.630 12.241 42250 Z= 0.325 Chirality : 0.045 0.339 4948 Planarity : 0.004 0.061 5371 Dihedral : 4.933 51.448 4207 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.42 % Favored : 94.52 % Rotamer: Outliers : 2.42 % Allowed : 14.25 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % 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: -1.13 (0.13), residues: 3871 helix: 1.43 (0.21), residues: 660 sheet: -0.65 (0.15), residues: 1111 loop : -1.55 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 38 TYR 0.018 0.001 TYR K 79 PHE 0.024 0.001 PHE B 429 TRP 0.015 0.001 TRP L 109 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (30876) covalent geometry : angle 0.62409 / 0.32 (42158) SS BOND : bond 0.00453 / 0.31 ( 46) SS BOND : angle 1.95632 / 1.25 ( 92) hydrogen bonds : bond 0.04496 / 2.94 ( 1136) hydrogen bonds : angle 5.85846 / 3.95 ( 3117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 145 time to evaluate : 0.788 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 77 LYS cc_start: 0.5280 (tttm) cc_final: 0.4067 (mttt) REVERT: I 78 ASN cc_start: 0.1137 (OUTLIER) cc_final: 0.0821 (p0) REVERT: L 39 ILE cc_start: 0.7495 (mm) cc_final: 0.7262 (mm) REVERT: M 52 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8651 (mm-30) REVERT: P 34 MET cc_start: 0.5563 (ptp) cc_final: 0.5263 (ptp) REVERT: P 51 MET cc_start: 0.7021 (tpp) cc_final: 0.6718 (tpp) REVERT: P 79 TYR cc_start: 0.8883 (m-80) cc_final: 0.8592 (m-80) REVERT: A 900 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8836 (mtm) REVERT: A 904 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.8307 (m-80) REVERT: A 1017 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8619 (tp30) REVERT: B 191 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8298 (mt-10) REVERT: B 200 TYR cc_start: 0.9259 (m-80) cc_final: 0.8862 (m-10) REVERT: B 437 ASN cc_start: 0.9088 (m110) cc_final: 0.8719 (m-40) REVERT: B 773 GLU cc_start: 0.9107 (tp30) cc_final: 0.8535 (tp30) REVERT: B 902 MET cc_start: 0.9384 (tpp) cc_final: 0.9067 (tpt) REVERT: B 904 TYR cc_start: 0.8080 (OUTLIER) cc_final: 0.7745 (m-10) REVERT: C 229 LEU cc_start: 0.9330 (mt) cc_final: 0.8779 (pp) REVERT: C 365 TYR cc_start: 0.8260 (m-80) cc_final: 0.7872 (m-80) REVERT: C 904 TYR cc_start: 0.8544 (OUTLIER) cc_final: 0.8289 (m-10) REVERT: C 960 ASN cc_start: 0.9417 (t0) cc_final: 0.8999 (t0) REVERT: C 1138 TYR cc_start: 0.8261 (m-80) cc_final: 0.7732 (m-10) outliers start: 76 outliers final: 42 residues processed: 211 average time/residue: 0.1816 time to fit residues: 62.4087 Evaluate side-chains 173 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 126 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 78 ASN Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain O residue 98 TYR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain K residue 68 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 114 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 367 optimal weight: 50.0000 chunk 317 optimal weight: 1.9990 chunk 334 optimal weight: 0.9980 chunk 42 optimal weight: 40.0000 chunk 338 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 315 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 264 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 ASN ** 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 = 0.4184 r_free = 0.4184 target = 0.107655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.069238 restraints weight = 139988.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.068609 restraints weight = 79439.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.069273 restraints weight = 54724.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.068983 restraints weight = 41178.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.069008 restraints weight = 40527.005| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30922 Z= 0.119 Angle : 0.588 12.874 42250 Z= 0.303 Chirality : 0.044 0.349 4948 Planarity : 0.004 0.103 5371 Dihedral : 4.756 49.125 4207 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.19 % Favored : 94.76 % Rotamer: Outliers : 2.51 % Allowed : 14.60 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.08 % 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: -0.89 (0.13), residues: 3871 helix: 1.68 (0.21), residues: 653 sheet: -0.43 (0.15), residues: 1112 loop : -1.45 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 328 TYR 0.018 0.001 TYR K 79 PHE 0.019 0.001 PHE B 201 TRP 0.030 0.001 TRP K 36 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (30876) covalent geometry : angle 0.58363 / 0.30 (42158) SS BOND : bond 0.00538 / 0.36 ( 46) SS BOND : angle 1.57295 / 0.94 ( 92) hydrogen bonds : bond 0.04114 / 2.70 ( 1136) hydrogen bonds : angle 5.59652 / 3.79 ( 3117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 153 time to evaluate : 0.960 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 77 LYS cc_start: 0.5153 (tttm) cc_final: 0.4075 (mttt) REVERT: L 38 TRP cc_start: 0.4529 (m100) cc_final: 0.4232 (m100) REVERT: L 39 ILE cc_start: 0.7501 (mm) cc_final: 0.7149 (mm) REVERT: M 52 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8630 (mm-30) REVERT: P 34 MET cc_start: 0.6006 (ptp) cc_final: 0.5533 (ptp) REVERT: P 51 MET cc_start: 0.6870 (tpp) cc_final: 0.6638 (tpp) REVERT: A 791 THR cc_start: 0.8950 (OUTLIER) cc_final: 0.8643 (t) REVERT: A 900 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8682 (mtm) REVERT: A 979 ASP cc_start: 0.9497 (m-30) cc_final: 0.9124 (p0) REVERT: B 191 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8240 (mt-10) REVERT: B 200 TYR cc_start: 0.9277 (m-80) cc_final: 0.8827 (m-80) REVERT: B 773 GLU cc_start: 0.9067 (tp30) cc_final: 0.8468 (tp30) REVERT: B 902 MET cc_start: 0.9361 (tpp) cc_final: 0.9086 (tpt) REVERT: B 904 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.7819 (m-10) REVERT: C 229 LEU cc_start: 0.9248 (mt) cc_final: 0.8801 (pp) REVERT: C 242 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8710 (mm) REVERT: C 365 TYR cc_start: 0.8252 (m-80) cc_final: 0.7947 (m-80) REVERT: C 501 TYR cc_start: 0.8322 (OUTLIER) cc_final: 0.8107 (m-10) REVERT: C 546 LEU cc_start: 0.8789 (tp) cc_final: 0.8427 (pp) REVERT: C 904 TYR cc_start: 0.8489 (OUTLIER) cc_final: 0.8121 (m-10) REVERT: C 960 ASN cc_start: 0.9429 (t0) cc_final: 0.9001 (t0) REVERT: C 1002 GLN cc_start: 0.9223 (tp40) cc_final: 0.8978 (tp40) REVERT: C 1138 TYR cc_start: 0.8385 (m-80) cc_final: 0.7829 (m-10) REVERT: K 36 TRP cc_start: 0.4728 (m100) cc_final: 0.4471 (m100) outliers start: 79 outliers final: 43 residues processed: 223 average time/residue: 0.1723 time to fit residues: 63.6611 Evaluate side-chains 181 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 132 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain O residue 98 TYR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain K residue 68 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 327 optimal weight: 5.9990 chunk 287 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 245 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 214 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 104 optimal weight: 0.0980 chunk 49 optimal weight: 0.9980 chunk 88 optimal weight: 8.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1010 GLN B 751 ASN C 450 ASN C 751 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.106934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.069506 restraints weight = 140116.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.067374 restraints weight = 87700.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.067509 restraints weight = 67312.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.067575 restraints weight = 56295.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.067607 restraints weight = 49134.795| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 30922 Z= 0.115 Angle : 0.568 10.426 42250 Z= 0.294 Chirality : 0.043 0.288 4948 Planarity : 0.004 0.090 5371 Dihedral : 4.578 46.671 4206 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.30 % Favored : 94.68 % Rotamer: Outliers : 2.48 % Allowed : 15.34 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.08 % 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: -0.76 (0.13), residues: 3871 helix: 1.71 (0.21), residues: 659 sheet: -0.32 (0.15), residues: 1120 loop : -1.37 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 995 TYR 0.017 0.001 TYR K 79 PHE 0.034 0.001 PHE B 429 TRP 0.016 0.001 TRP K 36 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (30876) covalent geometry : angle 0.56416 / 0.29 (42158) SS BOND : bond 0.00508 / 0.34 ( 46) SS BOND : angle 1.48589 / 0.90 ( 92) hydrogen bonds : bond 0.03921 / 2.58 ( 1136) hydrogen bonds : angle 5.39172 / 3.66 ( 3117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 145 time to evaluate : 1.070 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 77 LYS cc_start: 0.5091 (tttm) cc_final: 0.4033 (mttt) REVERT: P 51 MET cc_start: 0.6874 (tpp) cc_final: 0.6633 (tpp) REVERT: P 79 TYR cc_start: 0.8800 (m-80) cc_final: 0.8596 (m-80) REVERT: A 791 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8700 (t) REVERT: A 900 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8663 (mtm) REVERT: A 979 ASP cc_start: 0.9516 (m-30) cc_final: 0.9132 (p0) REVERT: B 191 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8211 (mt-10) REVERT: B 200 TYR cc_start: 0.9303 (m-80) cc_final: 0.8863 (m-80) REVERT: B 229 LEU cc_start: 0.9315 (mm) cc_final: 0.9014 (tp) REVERT: B 902 MET cc_start: 0.9271 (tpp) cc_final: 0.9039 (tpt) REVERT: B 904 TYR cc_start: 0.7884 (OUTLIER) cc_final: 0.7526 (m-10) REVERT: C 229 LEU cc_start: 0.9221 (mt) cc_final: 0.8770 (pp) REVERT: C 242 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8768 (mm) REVERT: C 365 TYR cc_start: 0.8311 (m-80) cc_final: 0.8001 (m-80) REVERT: C 501 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.8143 (m-10) REVERT: C 546 LEU cc_start: 0.8742 (tp) cc_final: 0.8470 (pp) REVERT: C 904 TYR cc_start: 0.8274 (OUTLIER) cc_final: 0.7794 (m-10) REVERT: C 960 ASN cc_start: 0.9403 (t0) cc_final: 0.8980 (t0) REVERT: C 1138 TYR cc_start: 0.8412 (m-80) cc_final: 0.7846 (m-10) REVERT: K 51 MET cc_start: 0.3967 (OUTLIER) cc_final: 0.3672 (mpp) outliers start: 78 outliers final: 44 residues processed: 213 average time/residue: 0.1570 time to fit residues: 55.6362 Evaluate side-chains 180 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 129 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain O residue 98 TYR Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain K residue 51 MET Chi-restraints excluded: chain K residue 68 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 366 optimal weight: 40.0000 chunk 341 optimal weight: 3.9990 chunk 246 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 113 optimal weight: 7.9990 chunk 359 optimal weight: 1.9990 chunk 374 optimal weight: 0.5980 chunk 131 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 ASN A 239 GLN A 417 ASN A 755 GLN B 960 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1125 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.106306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.068726 restraints weight = 139851.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.066435 restraints weight = 99212.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.066643 restraints weight = 71648.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.066760 restraints weight = 59161.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.067001 restraints weight = 48584.250| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30922 Z= 0.138 Angle : 0.586 14.389 42250 Z= 0.301 Chirality : 0.043 0.262 4948 Planarity : 0.004 0.062 5371 Dihedral : 4.494 44.400 4204 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.48 % Allowed : 16.13 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % 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: -0.65 (0.13), residues: 3871 helix: 1.69 (0.21), residues: 653 sheet: -0.21 (0.15), residues: 1142 loop : -1.28 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 346 TYR 0.016 0.001 TYR C1067 PHE 0.017 0.001 PHE B 515 TRP 0.023 0.001 TRP K 36 HIS 0.007 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (30876) covalent geometry : angle 0.58226 / 0.30 (42158) SS BOND : bond 0.00493 / 0.35 ( 46) SS BOND : angle 1.45383 / 0.87 ( 92) hydrogen bonds : bond 0.03997 / 2.62 ( 1136) hydrogen bonds : angle 5.36638 / 3.65 ( 3117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 134 time to evaluate : 1.005 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: symmetry clash REVERT: I 77 LYS cc_start: 0.4988 (tttm) cc_final: 0.4037 (mttt) REVERT: P 34 MET cc_start: 0.6119 (ptp) cc_final: 0.5818 (ptp) REVERT: P 79 TYR cc_start: 0.8790 (m-80) cc_final: 0.8548 (m-80) REVERT: A 239 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7361 (tp40) REVERT: A 791 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8749 (t) REVERT: A 979 ASP cc_start: 0.9525 (m-30) cc_final: 0.9138 (p0) REVERT: B 191 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8222 (mt-10) REVERT: B 200 TYR cc_start: 0.9262 (m-80) cc_final: 0.8803 (m-80) REVERT: B 773 GLU cc_start: 0.8824 (tp30) cc_final: 0.8606 (tp30) REVERT: B 902 MET cc_start: 0.9306 (tpp) cc_final: 0.9038 (tpt) REVERT: B 904 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7657 (m-10) REVERT: B 960 ASN cc_start: 0.9326 (OUTLIER) cc_final: 0.8780 (t0) REVERT: C 242 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8643 (mm) REVERT: C 473 TYR cc_start: 0.6362 (t80) cc_final: 0.5771 (t80) REVERT: C 501 TYR cc_start: 0.8447 (OUTLIER) cc_final: 0.8156 (m-10) REVERT: C 904 TYR cc_start: 0.8447 (OUTLIER) cc_final: 0.7928 (m-10) REVERT: C 960 ASN cc_start: 0.9312 (t0) cc_final: 0.8904 (t0) REVERT: C 1002 GLN cc_start: 0.9087 (tp40) cc_final: 0.8855 (tp40) REVERT: C 1138 TYR cc_start: 0.8254 (m-80) cc_final: 0.7731 (m-10) outliers start: 78 outliers final: 51 residues processed: 200 average time/residue: 0.1675 time to fit residues: 56.0416 Evaluate side-chains 182 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 124 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain O residue 98 TYR Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 98 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 328 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 288 optimal weight: 6.9990 chunk 52 optimal weight: 40.0000 chunk 110 optimal weight: 0.2980 chunk 67 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 225 optimal weight: 1.9990 chunk 259 optimal weight: 2.9990 chunk 242 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 ASN ** P 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 ASN A 239 GLN A 914 ASN B 239 GLN B 960 ASN B1134 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.103006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.064672 restraints weight = 136812.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.065944 restraints weight = 68646.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.065534 restraints weight = 40898.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.065807 restraints weight = 42720.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.065953 restraints weight = 39924.532| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 30922 Z= 0.221 Angle : 0.647 13.017 42250 Z= 0.332 Chirality : 0.045 0.246 4948 Planarity : 0.004 0.064 5371 Dihedral : 4.764 49.340 4204 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.48 % Allowed : 16.51 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % 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: -0.77 (0.13), residues: 3871 helix: 1.38 (0.21), residues: 658 sheet: -0.33 (0.15), residues: 1135 loop : -1.25 (0.13), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 40 TYR 0.019 0.002 TYR C1067 PHE 0.020 0.002 PHE P 67 TRP 0.023 0.001 TRP M 37 HIS 0.007 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.22 (30876) covalent geometry : angle 0.64234 / 0.33 (42158) SS BOND : bond 0.00607 / 0.41 ( 46) SS BOND : angle 1.77242 / 1.09 ( 92) hydrogen bonds : bond 0.04531 / 2.94 ( 1136) hydrogen bonds : angle 5.62682 / 3.81 ( 3117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 124 time to evaluate : 1.081 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: symmetry clash revert: symmetry clash REVERT: P 79 TYR cc_start: 0.8773 (m-80) cc_final: 0.8472 (m-80) REVERT: A 239 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7534 (tp40) REVERT: A 740 MET cc_start: 0.9290 (tpp) cc_final: 0.8678 (tpp) REVERT: A 791 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8808 (t) REVERT: B 200 TYR cc_start: 0.9193 (m-80) cc_final: 0.8745 (m-80) REVERT: B 773 GLU cc_start: 0.8831 (tp30) cc_final: 0.8388 (tp30) REVERT: C 242 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8530 (mm) REVERT: C 473 TYR cc_start: 0.6322 (t80) cc_final: 0.5643 (t80) REVERT: C 501 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.8071 (m-10) REVERT: C 524 VAL cc_start: 0.5430 (OUTLIER) cc_final: 0.5203 (p) REVERT: C 904 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.7941 (m-10) REVERT: C 960 ASN cc_start: 0.9310 (t0) cc_final: 0.8902 (t0) REVERT: C 1138 TYR cc_start: 0.8248 (m-80) cc_final: 0.7764 (m-10) outliers start: 78 outliers final: 56 residues processed: 191 average time/residue: 0.1711 time to fit residues: 54.8481 Evaluate side-chains 179 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 117 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain M residue 51 TYR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain O residue 98 TYR Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 1 GLU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain K residue 68 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 99 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 230 optimal weight: 1.9990 chunk 378 optimal weight: 8.9990 chunk 255 optimal weight: 0.9990 chunk 227 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 329 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 91 optimal weight: 30.0000 chunk 182 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 ASN ** P 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN H 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.103164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.066004 restraints weight = 135858.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.066378 restraints weight = 70279.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.066235 restraints weight = 45636.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.066464 restraints weight = 45868.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.066619 restraints weight = 38045.219| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30922 Z= 0.179 Angle : 0.624 12.813 42250 Z= 0.320 Chirality : 0.044 0.266 4948 Planarity : 0.004 0.064 5371 Dihedral : 4.749 47.603 4204 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.32 % Allowed : 16.80 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % 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: -0.74 (0.13), residues: 3871 helix: 1.44 (0.21), residues: 655 sheet: -0.32 (0.15), residues: 1154 loop : -1.23 (0.13), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 40 TYR 0.017 0.001 TYR H 36 PHE 0.016 0.001 PHE B 515 TRP 0.026 0.001 TRP M 37 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (30876) covalent geometry : angle 0.61789 / 0.32 (42158) SS BOND : bond 0.00492 / 0.33 ( 46) SS BOND : angle 1.94775 / 1.30 ( 92) hydrogen bonds : bond 0.04343 / 2.83 ( 1136) hydrogen bonds : angle 5.52457 / 3.74 ( 3117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 122 time to evaluate : 0.889 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 41 GLN cc_start: 0.8283 (mp10) cc_final: 0.8078 (mp10) REVERT: L 55 TRP cc_start: 0.8341 (p-90) cc_final: 0.7800 (p90) REVERT: P 79 TYR cc_start: 0.8793 (m-80) cc_final: 0.8504 (m-80) REVERT: A 239 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7622 (tp40) REVERT: A 740 MET cc_start: 0.9326 (tpp) cc_final: 0.8700 (tpp) REVERT: A 791 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8808 (t) REVERT: A 979 ASP cc_start: 0.9537 (m-30) cc_final: 0.9119 (p0) REVERT: B 200 TYR cc_start: 0.9179 (m-80) cc_final: 0.8704 (m-10) REVERT: B 904 TYR cc_start: 0.8412 (OUTLIER) cc_final: 0.8093 (m-10) REVERT: C 242 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8505 (mm) REVERT: C 473 TYR cc_start: 0.6331 (t80) cc_final: 0.5692 (t80) REVERT: C 501 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.8061 (m-10) REVERT: C 524 VAL cc_start: 0.5459 (OUTLIER) cc_final: 0.5228 (p) REVERT: C 904 TYR cc_start: 0.8291 (OUTLIER) cc_final: 0.7855 (m-10) REVERT: C 960 ASN cc_start: 0.9327 (t0) cc_final: 0.8923 (t0) REVERT: C 1002 GLN cc_start: 0.9197 (tp40) cc_final: 0.8974 (tp40) REVERT: C 1138 TYR cc_start: 0.8263 (m-80) cc_final: 0.7765 (m-10) REVERT: K 51 MET cc_start: 0.4754 (mpp) cc_final: 0.4393 (mpp) outliers start: 73 outliers final: 58 residues processed: 180 average time/residue: 0.1693 time to fit residues: 50.6769 Evaluate side-chains 183 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 118 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain L residue 78 ASN Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain M residue 49 MET Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 98 TYR Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 1 GLU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain K residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 24 optimal weight: 50.0000 chunk 375 optimal weight: 30.0000 chunk 19 optimal weight: 10.0000 chunk 310 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 364 optimal weight: 0.9980 chunk 306 optimal weight: 20.0000 chunk 292 optimal weight: 9.9990 chunk 291 optimal weight: 20.0000 chunk 194 optimal weight: 8.9990 chunk 38 optimal weight: 40.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN A 239 GLN A 901 GLN A1011 GLN B 49 HIS B 234 ASN B 282 ASN B 901 GLN ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS C 370 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.101555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.063296 restraints weight = 137983.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.063842 restraints weight = 72517.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.063954 restraints weight = 46153.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.064117 restraints weight = 46339.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.064093 restraints weight = 41254.297| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.113 30922 Z= 0.377 Angle : 0.809 12.449 42250 Z= 0.411 Chirality : 0.048 0.241 4948 Planarity : 0.005 0.067 5371 Dihedral : 5.283 48.096 4204 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.42 % Allowed : 16.99 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % 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: -1.21 (0.13), residues: 3871 helix: 0.74 (0.20), residues: 654 sheet: -0.55 (0.15), residues: 1123 loop : -1.46 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 40 TYR 0.026 0.002 TYR A1067 PHE 0.029 0.003 PHE C 92 TRP 0.029 0.002 TRP M 37 HIS 0.009 0.002 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00856 / 0.38 (30876) covalent geometry : angle 0.80289 / 0.41 (42158) SS BOND : bond 0.00629 / 0.42 ( 46) SS BOND : angle 2.21206 / 1.45 ( 92) hydrogen bonds : bond 0.05405 / 3.50 ( 1136) hydrogen bonds : angle 6.16667 / 4.17 ( 3117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 116 time to evaluate : 0.923 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: P 51 MET cc_start: 0.6927 (tpp) cc_final: 0.6698 (tpp) REVERT: A 740 MET cc_start: 0.9387 (tpp) cc_final: 0.8804 (tpp) REVERT: A 791 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8924 (t) REVERT: B 200 TYR cc_start: 0.9304 (m-80) cc_final: 0.8796 (m-10) REVERT: B 773 GLU cc_start: 0.8888 (tp30) cc_final: 0.8555 (tp30) REVERT: C 229 LEU cc_start: 0.9246 (mt) cc_final: 0.8982 (mt) REVERT: C 501 TYR cc_start: 0.8316 (OUTLIER) cc_final: 0.7989 (m-10) REVERT: C 524 VAL cc_start: 0.5586 (OUTLIER) cc_final: 0.5332 (p) REVERT: C 904 TYR cc_start: 0.8388 (OUTLIER) cc_final: 0.8083 (m-10) REVERT: C 960 ASN cc_start: 0.9367 (t0) cc_final: 0.8978 (t0) REVERT: C 1002 GLN cc_start: 0.9337 (tp40) cc_final: 0.9099 (tp40) REVERT: C 1138 TYR cc_start: 0.8341 (m-80) cc_final: 0.7823 (m-10) REVERT: K 51 MET cc_start: 0.4587 (mpp) cc_final: 0.4314 (mpp) outliers start: 76 outliers final: 61 residues processed: 180 average time/residue: 0.1659 time to fit residues: 50.2198 Evaluate side-chains 180 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 115 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain L residue 78 ASN Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain M residue 49 MET Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain O residue 89 GLN Chi-restraints excluded: chain O residue 98 TYR Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 1 GLU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain K residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 176 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 chunk 332 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 32 optimal weight: 0.0370 chunk 90 optimal weight: 0.7980 chunk 180 optimal weight: 0.0070 chunk 257 optimal weight: 1.9990 chunk 363 optimal weight: 0.9980 chunk 242 optimal weight: 4.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 83 ASN A 239 GLN A 901 GLN B 282 ASN B 901 GLN C 901 GLN C 965 GLN H 6 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.106067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.067526 restraints weight = 140647.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.066369 restraints weight = 86563.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.066923 restraints weight = 61392.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.066777 restraints weight = 48577.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.066790 restraints weight = 44989.299| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 30922 Z= 0.113 Angle : 0.620 12.698 42250 Z= 0.316 Chirality : 0.045 0.266 4948 Planarity : 0.004 0.063 5371 Dihedral : 4.789 46.200 4204 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.81 % Allowed : 17.66 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % 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: -0.71 (0.13), residues: 3871 helix: 1.47 (0.21), residues: 655 sheet: -0.27 (0.15), residues: 1141 loop : -1.23 (0.13), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 40 TYR 0.018 0.001 TYR A 453 PHE 0.030 0.001 PHE A 238 TRP 0.030 0.002 TRP M 37 HIS 0.003 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (30876) covalent geometry : angle 0.61627 / 0.31 (42158) SS BOND : bond 0.00477 / 0.29 ( 46) SS BOND : angle 1.65639 / 1.08 ( 92) hydrogen bonds : bond 0.04218 / 2.79 ( 1136) hydrogen bonds : angle 5.42289 / 3.67 ( 3117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6020.58 seconds wall clock time: 104 minutes 20.11 seconds (6260.11 seconds total)