Starting phenix.real_space_refine on Mon Aug 25 20:09:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvp_34135/08_2025/7yvp_34135.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvp_34135/08_2025/7yvp_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_34135/08_2025/7yvp_34135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvp_34135/08_2025/7yvp_34135.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvp_34135/08_2025/7yvp_34135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvp_34135/08_2025/7yvp_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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 dihedrals: 36 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 dihedrals: 36 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 dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 5.52, per 1000 atoms: 0.18 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: 2.24 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 1.2 microseconds 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: 1.30 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: 7.80 Time building geometry restraints manager: 2.97 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: 17737 23.31 - 46.62: 802 46.62 - 69.94: 137 69.94 - 93.25: 24 93.25 - 116.56: 1 Dihedral angle restraints: 18701 sinusoidal: 7281 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 18698 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.680 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: 0.570 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 26.740 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 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 : 13.186 116.559 11231 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 aren 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 covalent geometry : bond 0.00851 (30876) covalent geometry : angle 1.03165 (42158) SS BOND : bond 0.01210 ( 46) SS BOND : angle 3.24066 ( 92) hydrogen bonds : bond 0.21785 ( 1136) hydrogen bonds : angle 8.61520 ( 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 : 1.065 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: 0.9097 (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: 0.1918 time to fit residues: 78.3444 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 : 0.721 ------------------------------------------------------------------------------- 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: 4.9990 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... Flipped N/Q/H residues before XYZ refinement: ** 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 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.107945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.068931 restraints weight = 140924.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.068759 restraints weight = 72819.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.069050 restraints weight = 50609.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.069373 restraints weight = 35011.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.069318 restraints weight = 33091.491| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30922 Z= 0.176 Angle : 0.697 10.631 42250 Z= 0.363 Chirality : 0.047 0.297 4948 Planarity : 0.005 0.107 5371 Dihedral : 7.130 57.605 4997 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.71 % Favored : 94.16 % Rotamer: Outliers : 1.91 % Allowed : 11.07 % Favored : 87.02 % 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 aren not related in a simple way. whole: -1.65 (0.13), residues: 3871 helix: 1.17 (0.21), residues: 652 sheet: -0.94 (0.14), residues: 1127 loop : -1.98 (0.12), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 765 TYR 0.032 0.002 TYR P 107 PHE 0.022 0.002 PHE B 429 TRP 0.016 0.001 TRP O 94 HIS 0.004 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00389 (30876) covalent geometry : angle 0.69137 (42158) SS BOND : bond 0.00993 ( 46) SS BOND : angle 1.99940 ( 92) hydrogen bonds : bond 0.05324 ( 1136) hydrogen bonds : angle 6.46224 ( 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 226 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 166 time to evaluate : 1.125 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: I 77 LYS cc_start: 0.5486 (tttm) cc_final: 0.4287 (mttt) REVERT: M 52 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8610 (mm-30) REVERT: P 82 MET cc_start: 0.5732 (mtm) cc_final: 0.5455 (mtm) REVERT: A 902 MET cc_start: 0.9109 (tpp) cc_final: 0.8881 (tpt) REVERT: A 1135 ASN cc_start: 0.8920 (t0) cc_final: 0.8572 (t0) REVERT: B 200 TYR cc_start: 0.9204 (m-80) cc_final: 0.8824 (m-10) REVERT: B 773 GLU cc_start: 0.8950 (tp30) cc_final: 0.8487 (tp30) REVERT: C 229 LEU cc_start: 0.9346 (mt) cc_final: 0.8935 (pp) REVERT: C 365 TYR cc_start: 0.8255 (m-80) cc_final: 0.7856 (m-80) REVERT: C 524 VAL cc_start: 0.7096 (OUTLIER) cc_final: 0.6631 (p) REVERT: C 902 MET cc_start: 0.9375 (tpp) cc_final: 0.8845 (tpt) REVERT: C 960 ASN cc_start: 0.9323 (t0) cc_final: 0.8932 (t0) REVERT: C 1138 TYR cc_start: 0.8041 (m-80) cc_final: 0.7526 (m-10) REVERT: H 36 TYR cc_start: 0.2953 (m-80) cc_final: 0.2588 (m-80) REVERT: H 38 GLN cc_start: 0.4030 (tp-100) cc_final: 0.3804 (mt0) REVERT: K 36 TRP cc_start: 0.4851 (m100) cc_final: 0.4588 (m100) REVERT: K 94 TYR cc_start: 0.6797 (m-80) cc_final: 0.6583 (m-10) outliers start: 60 outliers final: 22 residues processed: 220 average time/residue: 0.1971 time to fit residues: 70.6830 Evaluate side-chains 158 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 56 optimal weight: 10.0000 chunk 193 optimal weight: 40.0000 chunk 103 optimal weight: 0.9980 chunk 290 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 228 optimal weight: 4.9990 chunk 359 optimal weight: 0.6980 chunk 24 optimal weight: 30.0000 chunk 250 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 78 ASN ** 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 37 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 = 0.4188 r_free = 0.4188 target = 0.107630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.068741 restraints weight = 141300.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.068595 restraints weight = 79833.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.069505 restraints weight = 52521.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.069144 restraints weight = 40423.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.069135 restraints weight = 35732.547| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30922 Z= 0.151 Angle : 0.629 12.629 42250 Z= 0.326 Chirality : 0.045 0.364 4948 Planarity : 0.004 0.057 5371 Dihedral : 6.432 56.623 4984 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.27 % Favored : 94.65 % Rotamer: Outliers : 2.58 % Allowed : 12.38 % Favored : 85.05 % 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 aren not related in a simple way. whole: -1.25 (0.13), residues: 3871 helix: 1.46 (0.21), residues: 659 sheet: -0.73 (0.14), residues: 1137 loop : -1.69 (0.13), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 40 TYR 0.022 0.001 TYR L 96 PHE 0.018 0.001 PHE B 201 TRP 0.027 0.002 TRP L 109 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00341 (30876) covalent geometry : angle 0.62392 (42158) SS BOND : bond 0.00699 ( 46) SS BOND : angle 1.85406 ( 92) hydrogen bonds : bond 0.04595 ( 1136) hydrogen bonds : angle 5.92645 ( 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 242 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 161 time to evaluate : 1.209 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: symmetry clash revert: symmetry clash REVERT: I 77 LYS cc_start: 0.5346 (tttm) cc_final: 0.4214 (mttt) REVERT: I 78 ASN cc_start: 0.1044 (OUTLIER) cc_final: 0.0841 (p0) REVERT: L 38 TRP cc_start: 0.4835 (m100) cc_final: 0.4366 (m100) REVERT: M 52 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8684 (mm-30) REVERT: O 86 TYR cc_start: 0.5502 (m-10) cc_final: 0.4650 (m-80) REVERT: P 1 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7372 (pp20) REVERT: P 79 TYR cc_start: 0.8849 (m-80) cc_final: 0.8552 (m-80) REVERT: A 902 MET cc_start: 0.9137 (tpp) cc_final: 0.8869 (tpt) REVERT: B 191 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8298 (mt-10) REVERT: B 200 TYR cc_start: 0.9270 (m-80) cc_final: 0.8882 (m-10) REVERT: B 773 GLU cc_start: 0.9089 (tp30) cc_final: 0.8523 (tp30) REVERT: C 229 LEU cc_start: 0.9374 (mt) cc_final: 0.8924 (pp) REVERT: C 365 TYR cc_start: 0.8214 (m-80) cc_final: 0.7807 (m-80) REVERT: C 904 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.8263 (m-10) REVERT: C 960 ASN cc_start: 0.9397 (t0) cc_final: 0.8982 (t0) REVERT: C 1002 GLN cc_start: 0.9160 (tp40) cc_final: 0.8932 (tp40) REVERT: C 1138 TYR cc_start: 0.8269 (m-80) cc_final: 0.7697 (m-10) REVERT: H 36 TYR cc_start: 0.3025 (m-80) cc_final: 0.2713 (m-80) REVERT: H 38 GLN cc_start: 0.4120 (tp-100) cc_final: 0.3812 (mt0) REVERT: K 36 TRP cc_start: 0.4636 (m100) cc_final: 0.4422 (m100) outliers start: 81 outliers final: 40 residues processed: 228 average time/residue: 0.1982 time to fit residues: 73.5154 Evaluate side-chains 179 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 50 ILE Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 98 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 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 334 ASN 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 740 MET 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 C residue 131 CYS 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 131 optimal weight: 0.9980 chunk 342 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 305 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 210 optimal weight: 0.9980 chunk 165 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 chunk 201 optimal weight: 0.5980 chunk 55 optimal weight: 7.9990 chunk 373 optimal weight: 20.0000 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 = 0.4178 r_free = 0.4178 target = 0.107005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.067949 restraints weight = 139820.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.068124 restraints weight = 77899.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.068795 restraints weight = 49553.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.068719 restraints weight = 36404.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.068759 restraints weight = 34938.369| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2496 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= 0.168 Angle : 0.630 11.984 42250 Z= 0.325 Chirality : 0.045 0.329 4948 Planarity : 0.004 0.108 5371 Dihedral : 6.255 58.153 4984 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.63 % Favored : 94.32 % Rotamer: Outliers : 2.51 % Allowed : 14.54 % Favored : 82.95 % 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 aren not related in a simple way. whole: -1.08 (0.13), residues: 3871 helix: 1.47 (0.21), residues: 660 sheet: -0.60 (0.15), residues: 1111 loop : -1.53 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 40 TYR 0.021 0.001 TYR M 93 PHE 0.021 0.001 PHE L 24 TRP 0.023 0.001 TRP M 37 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00378 (30876) covalent geometry : angle 0.62470 (42158) SS BOND : bond 0.00649 ( 46) SS BOND : angle 1.88816 ( 92) hydrogen bonds : bond 0.04476 ( 1136) hydrogen bonds : angle 5.84588 ( 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 225 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 146 time to evaluate : 0.968 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: symmetry clash REVERT: I 77 LYS cc_start: 0.5152 (tttm) cc_final: 0.4037 (mttt) REVERT: I 78 ASN cc_start: 0.1832 (OUTLIER) cc_final: 0.1305 (p0) REVERT: J 49 MET cc_start: -0.3442 (tmm) cc_final: -0.4234 (tmm) REVERT: M 52 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8642 (mm-30) REVERT: P 51 MET cc_start: 0.6930 (tpp) cc_final: 0.6676 (tpp) REVERT: A 900 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8709 (mtm) REVERT: A 1017 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8367 (tp30) REVERT: B 191 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8318 (mt-10) REVERT: B 200 TYR cc_start: 0.9171 (m-80) cc_final: 0.8797 (m-10) REVERT: B 437 ASN cc_start: 0.9106 (m110) cc_final: 0.8736 (m-40) REVERT: B 773 GLU cc_start: 0.8876 (tp30) cc_final: 0.8405 (tp30) REVERT: B 904 TYR cc_start: 0.8167 (OUTLIER) cc_final: 0.7848 (m-10) REVERT: C 229 LEU cc_start: 0.9327 (mt) cc_final: 0.8915 (pp) REVERT: C 365 TYR cc_start: 0.8315 (m-80) cc_final: 0.7970 (m-80) REVERT: C 904 TYR cc_start: 0.8509 (OUTLIER) cc_final: 0.8168 (m-10) REVERT: C 909 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.9106 (tp) REVERT: C 960 ASN cc_start: 0.9219 (t0) cc_final: 0.8830 (t0) REVERT: C 1138 TYR cc_start: 0.7977 (m-80) cc_final: 0.7520 (m-10) REVERT: H 38 GLN cc_start: 0.4144 (tp-100) cc_final: 0.3850 (mt0) outliers start: 79 outliers final: 44 residues processed: 213 average time/residue: 0.1766 time to fit residues: 62.0431 Evaluate side-chains 178 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 129 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 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 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 453 TYR 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 869 MET Chi-restraints excluded: chain B residue 904 TYR 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 378 LYS Chi-restraints excluded: chain C residue 445 VAL 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 909 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 98 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 114 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 367 optimal weight: 30.0000 chunk 317 optimal weight: 4.9990 chunk 334 optimal weight: 0.8980 chunk 42 optimal weight: 40.0000 chunk 338 optimal weight: 3.9990 chunk 36 optimal weight: 30.0000 chunk 315 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 264 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 ASN A 239 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN B 960 ASN B1134 ASN C 450 ASN C 751 ASN ** C 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1125 ASN ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.104334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.066592 restraints weight = 136284.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.066929 restraints weight = 74696.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.066599 restraints weight = 48456.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.067091 restraints weight = 49228.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.067375 restraints weight = 40077.026| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 30922 Z= 0.229 Angle : 0.658 11.918 42250 Z= 0.339 Chirality : 0.045 0.305 4948 Planarity : 0.004 0.062 5371 Dihedral : 6.277 56.623 4984 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.81 % Favored : 94.14 % Rotamer: Outliers : 2.99 % Allowed : 15.37 % Favored : 81.64 % 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 aren not related in a simple way. whole: -1.10 (0.13), residues: 3871 helix: 1.40 (0.20), residues: 646 sheet: -0.59 (0.15), residues: 1129 loop : -1.52 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 328 TYR 0.020 0.002 TYR C1067 PHE 0.028 0.002 PHE B 429 TRP 0.032 0.002 TRP K 36 HIS 0.007 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00520 (30876) covalent geometry : angle 0.65347 (42158) SS BOND : bond 0.00670 ( 46) SS BOND : angle 1.75372 ( 92) hydrogen bonds : bond 0.04733 ( 1136) hydrogen bonds : angle 5.93346 ( 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 228 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 134 time to evaluate : 1.184 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: 0.4576 (tttm) cc_final: 0.3688 (mttt) REVERT: M 52 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8715 (mm-30) REVERT: P 51 MET cc_start: 0.6846 (tpp) cc_final: 0.6549 (tpp) REVERT: A 791 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8809 (t) REVERT: B 191 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8320 (mt-10) REVERT: B 200 TYR cc_start: 0.9117 (m-80) cc_final: 0.8727 (m-10) REVERT: B 773 GLU cc_start: 0.8851 (tp30) cc_final: 0.8486 (tp30) REVERT: B 960 ASN cc_start: 0.9305 (OUTLIER) cc_final: 0.8749 (t0) REVERT: C 229 LEU cc_start: 0.9286 (mt) cc_final: 0.8903 (pp) REVERT: C 365 TYR cc_start: 0.8411 (m-80) cc_final: 0.8201 (m-80) REVERT: C 501 TYR cc_start: 0.8391 (OUTLIER) cc_final: 0.8089 (m-10) REVERT: C 546 LEU cc_start: 0.8853 (tp) cc_final: 0.8466 (pp) REVERT: C 904 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.8054 (m-10) REVERT: C 960 ASN cc_start: 0.9227 (t0) cc_final: 0.8833 (t0) REVERT: C 1002 GLN cc_start: 0.9122 (tp40) cc_final: 0.8884 (tp40) REVERT: C 1138 TYR cc_start: 0.8083 (m-80) cc_final: 0.7624 (m-10) REVERT: K 36 TRP cc_start: 0.4473 (m100) cc_final: 0.4223 (m100) outliers start: 94 outliers final: 56 residues processed: 217 average time/residue: 0.1756 time to fit residues: 62.9483 Evaluate side-chains 187 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 127 time to evaluate : 1.217 ------------------------------------------------------------------------------- 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 50 ILE 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 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 761 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 886 TRP 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 387 LEU 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 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 960 ASN 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 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 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 1094 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 327 optimal weight: 5.9990 chunk 287 optimal weight: 1.9990 chunk 120 optimal weight: 0.0870 chunk 245 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 214 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 104 optimal weight: 0.9990 chunk 49 optimal weight: 20.0000 chunk 88 optimal weight: 0.7980 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 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 ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.105827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.066781 restraints weight = 134701.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.068638 restraints weight = 65439.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.068638 restraints weight = 36504.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.068922 restraints weight = 33430.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.068920 restraints weight = 30624.200| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30922 Z= 0.113 Angle : 0.576 13.439 42250 Z= 0.297 Chirality : 0.044 0.269 4948 Planarity : 0.004 0.063 5371 Dihedral : 5.738 57.112 4984 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.06 % Favored : 94.89 % Rotamer: Outliers : 2.74 % Allowed : 15.65 % Favored : 81.61 % 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 aren not related in a simple way. whole: -0.82 (0.13), residues: 3871 helix: 1.65 (0.21), residues: 660 sheet: -0.39 (0.15), residues: 1102 loop : -1.37 (0.13), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 346 TYR 0.016 0.001 TYR K 79 PHE 0.024 0.001 PHE B 429 TRP 0.021 0.001 TRP M 37 HIS 0.006 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00247 (30876) covalent geometry : angle 0.57258 (42158) SS BOND : bond 0.00482 ( 46) SS BOND : angle 1.49128 ( 92) hydrogen bonds : bond 0.04036 ( 1136) hydrogen bonds : angle 5.46318 ( 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 237 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 151 time to evaluate : 1.072 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: symmetry clash revert: symmetry clash REVERT: I 77 LYS cc_start: 0.4554 (tttm) cc_final: 0.3711 (mttt) REVERT: L 73 LYS cc_start: 0.7695 (pptt) cc_final: 0.7257 (tmtt) REVERT: M 52 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8632 (mm-30) REVERT: P 34 MET cc_start: 0.6125 (ptp) cc_final: 0.5911 (ptp) REVERT: A 791 THR cc_start: 0.9043 (OUTLIER) cc_final: 0.8772 (t) REVERT: A 979 ASP cc_start: 0.9477 (m-30) cc_final: 0.9124 (p0) REVERT: B 191 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8147 (mt-10) REVERT: B 200 TYR cc_start: 0.8977 (m-80) cc_final: 0.8634 (m-80) REVERT: B 229 LEU cc_start: 0.9235 (mm) cc_final: 0.8941 (tp) REVERT: B 773 GLU cc_start: 0.8814 (tp30) cc_final: 0.8333 (tp30) REVERT: B 904 TYR cc_start: 0.8319 (OUTLIER) cc_final: 0.8004 (m-10) REVERT: C 229 LEU cc_start: 0.9261 (mt) cc_final: 0.8854 (pp) REVERT: C 242 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8551 (mm) REVERT: C 501 TYR cc_start: 0.8404 (OUTLIER) cc_final: 0.8094 (m-10) REVERT: C 546 LEU cc_start: 0.8757 (tp) cc_final: 0.8474 (pp) REVERT: C 904 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.8032 (m-10) REVERT: C 960 ASN cc_start: 0.9279 (t0) cc_final: 0.8871 (t0) REVERT: C 1002 GLN cc_start: 0.9136 (tp40) cc_final: 0.8889 (tp40) REVERT: C 1138 TYR cc_start: 0.8125 (m-80) cc_final: 0.7635 (m-10) outliers start: 86 outliers final: 51 residues processed: 226 average time/residue: 0.1908 time to fit residues: 70.5558 Evaluate side-chains 187 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 131 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 50 ILE 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 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 501 TYR 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 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 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 869 MET Chi-restraints excluded: chain B residue 904 TYR 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 501 TYR Chi-restraints excluded: chain C residue 599 THR 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 H residue 1 GLU Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 98 TYR 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: 50.0000 chunk 341 optimal weight: 0.9980 chunk 246 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 113 optimal weight: 7.9990 chunk 359 optimal weight: 3.9990 chunk 374 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 86 optimal weight: 0.0770 chunk 93 optimal weight: 3.9990 chunk 23 optimal weight: 30.0000 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 ASN O 42 GLN A 239 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1010 GLN B 239 GLN B 960 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.105455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.067499 restraints weight = 140031.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.065200 restraints weight = 92174.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.066394 restraints weight = 63875.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.065899 restraints weight = 47276.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.065953 restraints weight = 46098.912| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30922 Z= 0.170 Angle : 0.604 13.174 42250 Z= 0.311 Chirality : 0.044 0.239 4948 Planarity : 0.004 0.065 5371 Dihedral : 5.714 59.885 4983 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.58 % Allowed : 16.86 % Favored : 80.56 % 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 aren not related in a simple way. whole: -0.77 (0.13), residues: 3871 helix: 1.59 (0.21), residues: 653 sheet: -0.39 (0.15), residues: 1161 loop : -1.30 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 346 TYR 0.018 0.001 TYR C1067 PHE 0.029 0.001 PHE B 429 TRP 0.024 0.001 TRP M 37 HIS 0.008 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00387 (30876) covalent geometry : angle 0.60075 (42158) SS BOND : bond 0.00517 ( 46) SS BOND : angle 1.52093 ( 92) hydrogen bonds : bond 0.04243 ( 1136) hydrogen bonds : angle 5.52478 ( 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 217 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 136 time to evaluate : 1.155 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: symmetry clash REVERT: I 77 LYS cc_start: 0.4937 (tttm) cc_final: 0.3958 (mttt) REVERT: J 50 ILE cc_start: 0.0343 (OUTLIER) cc_final: -0.0860 (mt) REVERT: L 55 TRP cc_start: 0.8415 (p-90) cc_final: 0.7821 (p90) REVERT: M 52 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8637 (mm-30) REVERT: P 79 TYR cc_start: 0.8784 (m-80) cc_final: 0.8555 (m-80) REVERT: A 239 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7480 (tp40) REVERT: A 740 MET cc_start: 0.9288 (tpp) cc_final: 0.8643 (tpp) REVERT: A 791 THR cc_start: 0.9043 (OUTLIER) cc_final: 0.8767 (t) REVERT: A 979 ASP cc_start: 0.9527 (m-30) cc_final: 0.9128 (p0) REVERT: B 191 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8204 (mt-10) REVERT: B 200 TYR cc_start: 0.9242 (m-80) cc_final: 0.8809 (m-80) REVERT: B 773 GLU cc_start: 0.9027 (tp30) cc_final: 0.8505 (tp30) REVERT: B 960 ASN cc_start: 0.9330 (OUTLIER) cc_final: 0.9040 (t0) REVERT: C 229 LEU cc_start: 0.9316 (mt) cc_final: 0.9047 (tp) REVERT: C 242 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8634 (mm) REVERT: C 501 TYR cc_start: 0.8340 (OUTLIER) cc_final: 0.8067 (m-10) REVERT: C 524 VAL cc_start: 0.5554 (OUTLIER) cc_final: 0.5335 (p) REVERT: C 904 TYR cc_start: 0.8505 (OUTLIER) cc_final: 0.8053 (m-10) REVERT: C 960 ASN cc_start: 0.9336 (t0) cc_final: 0.8920 (t0) REVERT: C 1002 GLN cc_start: 0.9204 (tp40) cc_final: 0.8938 (tp40) REVERT: C 1138 TYR cc_start: 0.8339 (m-80) cc_final: 0.7819 (m-10) outliers start: 81 outliers final: 54 residues processed: 207 average time/residue: 0.1800 time to fit residues: 61.8634 Evaluate side-chains 191 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 129 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 21 SER Chi-restraints excluded: chain J residue 50 ILE 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 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 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 960 ASN 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 336 CYS 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 617 CYS 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 1 GLU Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain K residue 68 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 328 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 288 optimal weight: 5.9990 chunk 52 optimal weight: 40.0000 chunk 110 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 225 optimal weight: 1.9990 chunk 259 optimal weight: 0.6980 chunk 242 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 ASN ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN B1005 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN H 6 GLN ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.105757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.067040 restraints weight = 140297.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.065770 restraints weight = 88516.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.066247 restraints weight = 64803.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.066159 restraints weight = 45326.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.066193 restraints weight = 43293.662| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30922 Z= 0.143 Angle : 0.594 12.601 42250 Z= 0.306 Chirality : 0.044 0.224 4948 Planarity : 0.004 0.064 5371 Dihedral : 5.667 57.746 4982 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.86 % Allowed : 16.70 % Favored : 80.43 % 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 aren not related in a simple way. whole: -0.71 (0.13), residues: 3871 helix: 1.57 (0.21), residues: 660 sheet: -0.36 (0.15), residues: 1161 loop : -1.23 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 346 TYR 0.015 0.001 TYR O 49 PHE 0.025 0.001 PHE C 888 TRP 0.026 0.001 TRP M 37 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00323 (30876) covalent geometry : angle 0.58771 (42158) SS BOND : bond 0.00451 ( 46) SS BOND : angle 1.91636 ( 92) hydrogen bonds : bond 0.04098 ( 1136) hydrogen bonds : angle 5.43867 ( 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 221 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 131 time to evaluate : 1.007 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 77 LYS cc_start: 0.5155 (tttm) cc_final: 0.4123 (mttt) REVERT: J 50 ILE cc_start: 0.0673 (OUTLIER) cc_final: -0.0383 (mt) REVERT: M 52 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8549 (mm-30) REVERT: O 4 MET cc_start: 0.6291 (tpp) cc_final: 0.5829 (mtt) REVERT: A 740 MET cc_start: 0.9357 (tpp) cc_final: 0.8674 (tpp) REVERT: A 791 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8748 (t) REVERT: A 979 ASP cc_start: 0.9529 (m-30) cc_final: 0.9142 (p0) REVERT: B 200 TYR cc_start: 0.9258 (m-80) cc_final: 0.8792 (m-80) REVERT: B 773 GLU cc_start: 0.9068 (tp30) cc_final: 0.8545 (tp30) REVERT: C 229 LEU cc_start: 0.9294 (mt) cc_final: 0.8805 (pp) REVERT: C 242 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8727 (mm) REVERT: C 473 TYR cc_start: 0.5830 (t80) cc_final: 0.5486 (t80) REVERT: C 524 VAL cc_start: 0.5640 (OUTLIER) cc_final: 0.5414 (p) REVERT: C 904 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.8012 (m-10) REVERT: C 960 ASN cc_start: 0.9388 (t0) cc_final: 0.8953 (t0) REVERT: C 1002 GLN cc_start: 0.9247 (tp40) cc_final: 0.8983 (tp40) REVERT: C 1138 TYR cc_start: 0.8475 (m-80) cc_final: 0.7914 (m-10) outliers start: 90 outliers final: 62 residues processed: 209 average time/residue: 0.1653 time to fit residues: 57.0124 Evaluate side-chains 192 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 125 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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 21 SER Chi-restraints excluded: chain J residue 50 ILE 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 50 ILE 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 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 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 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 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 886 TRP Chi-restraints excluded: chain B residue 1031 GLU 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 336 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR 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 869 MET 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 42 GLN Chi-restraints excluded: chain H residue 85 VAL 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: 1.9990 chunk 115 optimal weight: 3.9990 chunk 230 optimal weight: 4.9990 chunk 378 optimal weight: 20.0000 chunk 255 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 329 optimal weight: 0.0670 chunk 130 optimal weight: 0.8980 chunk 91 optimal weight: 30.0000 chunk 182 optimal weight: 0.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 755 GLN A 901 GLN B 960 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.105879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.068193 restraints weight = 140202.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.065787 restraints weight = 90299.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.066591 restraints weight = 66840.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.066278 restraints weight = 49918.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.066349 restraints weight = 48835.282| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3469 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= 0.136 Angle : 0.591 12.419 42250 Z= 0.303 Chirality : 0.044 0.279 4948 Planarity : 0.004 0.065 5371 Dihedral : 5.543 56.250 4982 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.35 % Allowed : 17.18 % Favored : 80.46 % 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 aren not related in a simple way. whole: -0.64 (0.13), residues: 3871 helix: 1.60 (0.21), residues: 656 sheet: -0.31 (0.15), residues: 1155 loop : -1.17 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 18 TYR 0.020 0.001 TYR O 49 PHE 0.024 0.001 PHE C 888 TRP 0.028 0.001 TRP M 37 HIS 0.004 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00308 (30876) covalent geometry : angle 0.58509 (42158) SS BOND : bond 0.00414 ( 46) SS BOND : angle 1.85102 ( 92) hydrogen bonds : bond 0.03995 ( 1136) hydrogen bonds : angle 5.35742 ( 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 209 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 135 time to evaluate : 1.183 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: symmetry clash REVERT: I 77 LYS cc_start: 0.5104 (tttm) cc_final: 0.4097 (mttt) REVERT: J 50 ILE cc_start: 0.0407 (OUTLIER) cc_final: -0.0584 (mt) REVERT: L 55 TRP cc_start: 0.8400 (p-90) cc_final: 0.7783 (p90) REVERT: M 52 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8520 (mm-30) REVERT: P 51 MET cc_start: 0.7104 (tpt) cc_final: 0.6697 (tpt) REVERT: A 239 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7378 (tp40) REVERT: A 740 MET cc_start: 0.9343 (tpp) cc_final: 0.8695 (tpp) REVERT: A 791 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8745 (t) REVERT: A 979 ASP cc_start: 0.9541 (m-30) cc_final: 0.9146 (p0) REVERT: B 200 TYR cc_start: 0.9307 (m-80) cc_final: 0.8824 (m-10) REVERT: B 904 TYR cc_start: 0.8291 (OUTLIER) cc_final: 0.7944 (m-10) REVERT: C 229 LEU cc_start: 0.9275 (mt) cc_final: 0.8784 (pp) REVERT: C 242 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8729 (mm) REVERT: C 473 TYR cc_start: 0.5861 (t80) cc_final: 0.5458 (t80) REVERT: C 524 VAL cc_start: 0.5528 (OUTLIER) cc_final: 0.5291 (p) REVERT: C 904 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.8010 (m-10) REVERT: C 960 ASN cc_start: 0.9373 (t0) cc_final: 0.8945 (t0) REVERT: C 1002 GLN cc_start: 0.9237 (tp40) cc_final: 0.8968 (tp40) REVERT: C 1138 TYR cc_start: 0.8476 (m-80) cc_final: 0.7903 (m-10) REVERT: K 51 MET cc_start: 0.4089 (mpp) cc_final: 0.3753 (mpp) outliers start: 74 outliers final: 58 residues processed: 199 average time/residue: 0.1749 time to fit residues: 57.1832 Evaluate side-chains 191 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 126 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 50 ILE 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 50 ILE 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 59 TYR 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 599 THR 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 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 886 TRP Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1031 GLU 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 336 CYS Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR 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 1 GLU Chi-restraints excluded: chain H residue 42 GLN 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: 20.0000 chunk 375 optimal weight: 40.0000 chunk 19 optimal weight: 2.9990 chunk 310 optimal weight: 8.9990 chunk 121 optimal weight: 0.8980 chunk 364 optimal weight: 0.9990 chunk 306 optimal weight: 9.9990 chunk 292 optimal weight: 9.9990 chunk 291 optimal weight: 20.0000 chunk 194 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 914 ASN B 282 ASN B 901 GLN ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS ** C 544 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.102774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.064279 restraints weight = 137633.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.064845 restraints weight = 82463.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.064661 restraints weight = 61060.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.065051 restraints weight = 53725.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.065202 restraints weight = 45234.267| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 30922 Z= 0.295 Angle : 0.722 12.177 42250 Z= 0.368 Chirality : 0.046 0.253 4948 Planarity : 0.005 0.067 5371 Dihedral : 6.092 58.023 4981 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.39 % Allowed : 17.40 % Favored : 80.21 % 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 aren not related in a simple way. whole: -0.98 (0.13), residues: 3871 helix: 1.05 (0.20), residues: 655 sheet: -0.50 (0.15), residues: 1141 loop : -1.30 (0.13), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 237 TYR 0.023 0.002 TYR A1067 PHE 0.027 0.002 PHE A 238 TRP 0.032 0.002 TRP M 37 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00671 (30876) covalent geometry : angle 0.71639 (42158) SS BOND : bond 0.00565 ( 46) SS BOND : angle 2.08307 ( 92) hydrogen bonds : bond 0.04977 ( 1136) hydrogen bonds : angle 5.87150 ( 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 201 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 126 time to evaluate : 1.203 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: symmetry clash REVERT: J 50 ILE cc_start: -0.0397 (OUTLIER) cc_final: -0.1402 (mt) REVERT: L 55 TRP cc_start: 0.8397 (p-90) cc_final: 0.7811 (p90) REVERT: L 73 LYS cc_start: 0.7782 (pptt) cc_final: 0.7270 (tptm) REVERT: M 52 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8496 (mm-30) REVERT: O 4 MET cc_start: 0.7234 (tpp) cc_final: 0.6203 (mtt) REVERT: A 740 MET cc_start: 0.9350 (tpp) cc_final: 0.8776 (tpp) REVERT: A 791 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8891 (t) REVERT: B 200 TYR cc_start: 0.9239 (m-80) cc_final: 0.8743 (m-10) REVERT: B 773 GLU cc_start: 0.8849 (tp30) cc_final: 0.8493 (tp30) REVERT: C 229 LEU cc_start: 0.9266 (mt) cc_final: 0.8809 (pp) REVERT: C 242 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8433 (mm) REVERT: C 524 VAL cc_start: 0.5411 (OUTLIER) cc_final: 0.5172 (p) REVERT: C 904 TYR cc_start: 0.8349 (OUTLIER) cc_final: 0.8006 (m-10) REVERT: C 960 ASN cc_start: 0.9312 (t0) cc_final: 0.8923 (t0) REVERT: C 1138 TYR cc_start: 0.8317 (m-80) cc_final: 0.7832 (m-10) REVERT: K 51 MET cc_start: 0.3622 (mpp) cc_final: 0.3268 (mpp) outliers start: 75 outliers final: 62 residues processed: 190 average time/residue: 0.1739 time to fit residues: 54.8765 Evaluate side-chains 191 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 124 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 50 ILE 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 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 599 THR 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 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 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 886 TRP Chi-restraints excluded: chain B residue 1031 GLU 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 336 CYS Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 590 CYS 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 869 MET 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 42 GLN Chi-restraints excluded: chain H residue 85 VAL 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: 0.0040 chunk 69 optimal weight: 8.9990 chunk 184 optimal weight: 40.0000 chunk 332 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 chunk 257 optimal weight: 0.9990 chunk 363 optimal weight: 7.9990 chunk 242 optimal weight: 3.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN B 282 ASN B 751 ASN B 901 GLN B 960 ASN C 519 HIS ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.104324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.067650 restraints weight = 135560.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.068560 restraints weight = 66170.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.068316 restraints weight = 44976.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.068640 restraints weight = 44577.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.069008 restraints weight = 38411.307| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30922 Z= 0.120 Angle : 0.592 12.219 42250 Z= 0.303 Chirality : 0.044 0.264 4948 Planarity : 0.004 0.064 5371 Dihedral : 5.655 57.508 4981 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.07 % Allowed : 17.59 % Favored : 80.34 % 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 aren not related in a simple way. whole: -0.69 (0.13), residues: 3871 helix: 1.54 (0.21), residues: 656 sheet: -0.32 (0.15), residues: 1148 loop : -1.20 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 346 TYR 0.018 0.001 TYR A 453 PHE 0.026 0.001 PHE B 201 TRP 0.031 0.001 TRP M 37 HIS 0.003 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00266 (30876) covalent geometry : angle 0.58778 (42158) SS BOND : bond 0.00425 ( 46) SS BOND : angle 1.65602 ( 92) hydrogen bonds : bond 0.04046 ( 1136) hydrogen bonds : angle 5.36013 ( 3117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6759.34 seconds wall clock time: 116 minutes 56.87 seconds (7016.87 seconds total)