Starting phenix.real_space_refine on Thu Jun 26 09:28:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvp_34135/06_2025/7yvp_34135.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvp_34135/06_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_34135/06_2025/7yvp_34135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvp_34135/06_2025/7yvp_34135.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvp_34135/06_2025/7yvp_34135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvp_34135/06_2025/7yvp_34135.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 10, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} 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: {'GLN:plan1': 9, 'TYR:plan': 3, 'ASN:plan1': 7, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 7} 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: {'GLN:plan1': 10, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 5} 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: 17.86, per 1000 atoms: 0.59 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: 7.88 Conformation dependent library (CDL) restraints added in 4.1 seconds 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7332 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 63 sheets defined 20.3% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.61 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: 15.13 Time building geometry restraints manager: 9.63 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 1146 or resid 1301 throug \ h 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 1146 or resid 1301 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 1146 or resid 1301 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: 10.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.150 Check model and map are aligned: 0.230 Set scattering table: 0.270 Process input model: 77.290 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.160 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.770 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.058 0.004 TRP H 94 HIS 0.008 0.002 HIS A1048 PHE 0.031 0.003 PHE B 194 TYR 0.031 0.003 TYR A 873 ARG 0.008 0.001 ARG C1000 Details of bonding type rmsd hydrogen bonds : bond 0.21785 ( 1136) hydrogen bonds : angle 8.61520 ( 3117) SS BOND : bond 0.01210 ( 46) SS BOND : angle 3.24066 ( 92) covalent geometry : bond 0.00851 (30876) covalent geometry : angle 1.03165 (42158) *********************** 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 : 3.852 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: 0.6919 time to fit residues: 288.2697 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 : 3.547 ------------------------------------------------------------------------------- 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 325 optimal weight: 2.9990 chunk 292 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 99 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 chunk 156 optimal weight: 0.7980 chunk 302 optimal weight: 30.0000 chunk 117 optimal weight: 0.9990 chunk 183 optimal weight: 7.9990 chunk 225 optimal weight: 5.9990 chunk 350 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 ** B 762 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.108385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.070254 restraints weight = 139988.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.068952 restraints weight = 75896.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.069932 restraints weight = 59894.953| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1642 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 : 0.684 10.621 42250 Z= 0.357 Chirality : 0.047 0.360 4948 Planarity : 0.005 0.106 5371 Dihedral : 7.064 57.021 4997 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.40 % Favored : 94.47 % Rotamer: Outliers : 1.91 % Allowed : 11.04 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.13), residues: 3871 helix: 1.18 (0.21), residues: 652 sheet: -0.86 (0.14), residues: 1130 loop : -1.98 (0.12), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 886 HIS 0.004 0.001 HIS B1088 PHE 0.023 0.001 PHE B 429 TYR 0.036 0.002 TYR P 107 ARG 0.007 0.001 ARG C 765 Details of bonding type rmsd hydrogen bonds : bond 0.05211 ( 1136) hydrogen bonds : angle 6.41458 ( 3117) SS BOND : bond 0.00593 ( 46) SS BOND : angle 1.93790 ( 92) covalent geometry : bond 0.00328 (30876) covalent geometry : angle 0.67922 (42158) *********************** 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 236 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 176 time to evaluate : 3.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 77 LYS cc_start: 0.5442 (tttm) cc_final: 0.4246 (mttt) REVERT: J 49 MET cc_start: -0.3539 (tpp) cc_final: -0.3781 (tmm) REVERT: M 52 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8601 (mm-30) REVERT: P 1 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7436 (pp20) REVERT: P 82 MET cc_start: 0.5662 (mtm) cc_final: 0.5375 (mtm) REVERT: A 902 MET cc_start: 0.9069 (tpp) cc_final: 0.8792 (tpt) REVERT: A 1135 ASN cc_start: 0.8929 (t0) cc_final: 0.8555 (t0) REVERT: B 200 TYR cc_start: 0.9300 (m-80) cc_final: 0.8901 (m-10) REVERT: B 773 GLU cc_start: 0.9021 (tp30) cc_final: 0.8471 (tp30) REVERT: C 229 LEU cc_start: 0.9347 (mt) cc_final: 0.8927 (pp) REVERT: C 365 TYR cc_start: 0.8222 (m-80) cc_final: 0.7809 (m-80) REVERT: C 902 MET cc_start: 0.9361 (tpp) cc_final: 0.8853 (tpt) REVERT: C 960 ASN cc_start: 0.9391 (t0) cc_final: 0.9011 (t0) REVERT: C 1138 TYR cc_start: 0.8244 (m-80) cc_final: 0.7674 (m-10) REVERT: H 36 TYR cc_start: 0.2990 (m-80) cc_final: 0.2668 (m-80) REVERT: H 38 GLN cc_start: 0.4023 (tp-100) cc_final: 0.3723 (mt0) REVERT: K 36 TRP cc_start: 0.4808 (m100) cc_final: 0.4507 (m100) REVERT: K 94 TYR cc_start: 0.6736 (m-80) cc_final: 0.6519 (m-10) REVERT: K 110 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8114 (pm20) outliers start: 60 outliers final: 24 residues processed: 230 average time/residue: 0.4211 time to fit residues: 157.9062 Evaluate side-chains 163 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 3.105 ------------------------------------------------------------------------------- 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 1 GLU Chi-restraints excluded: chain P residue 38 ARG Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain K residue 110 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 369 optimal weight: 1.9990 chunk 300 optimal weight: 5.9990 chunk 324 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 chunk 107 optimal weight: 50.0000 chunk 340 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 348 optimal weight: 1.9990 chunk 333 optimal weight: 0.0870 chunk 144 optimal weight: 2.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- 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 16 GLN M 39 GLN ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 ASN ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 GLN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 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 = 0.4184 r_free = 0.4184 target = 0.107723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.070443 restraints weight = 140424.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.068097 restraints weight = 81923.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.068775 restraints weight = 61794.934| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2125 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= 0.147 Angle : 0.631 12.727 42250 Z= 0.326 Chirality : 0.045 0.374 4948 Planarity : 0.004 0.060 5371 Dihedral : 6.444 55.673 4986 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.30 % Favored : 94.60 % Rotamer: Outliers : 2.45 % Allowed : 12.85 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.13), residues: 3871 helix: 1.46 (0.21), residues: 659 sheet: -0.71 (0.14), residues: 1132 loop : -1.71 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L 109 HIS 0.003 0.001 HIS L 99 PHE 0.019 0.001 PHE B 201 TYR 0.021 0.001 TYR L 96 ARG 0.006 0.000 ARG L 40 Details of bonding type rmsd hydrogen bonds : bond 0.04612 ( 1136) hydrogen bonds : angle 5.95916 ( 3117) SS BOND : bond 0.00697 ( 46) SS BOND : angle 1.92174 ( 92) covalent geometry : bond 0.00330 (30876) covalent geometry : angle 0.62511 (42158) *********************** 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 231 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 154 time to evaluate : 3.282 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: 0.5303 (tttm) cc_final: 0.4262 (mttt) REVERT: M 52 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8675 (mm-30) REVERT: P 66 ARG cc_start: 0.5341 (ptm160) cc_final: 0.5134 (ttp-170) REVERT: P 79 TYR cc_start: 0.8828 (m-80) cc_final: 0.8514 (m-80) REVERT: A 904 TYR cc_start: 0.8454 (OUTLIER) cc_final: 0.8247 (m-80) REVERT: B 191 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8311 (mt-10) REVERT: B 200 TYR cc_start: 0.9255 (m-80) cc_final: 0.8880 (m-10) REVERT: B 437 ASN cc_start: 0.9109 (m110) cc_final: 0.8770 (m-40) REVERT: B 773 GLU cc_start: 0.8881 (tp30) cc_final: 0.8395 (tp30) REVERT: B 902 MET cc_start: 0.9312 (tpp) cc_final: 0.9045 (tpt) REVERT: C 229 LEU cc_start: 0.9348 (mt) cc_final: 0.8923 (pp) REVERT: C 365 TYR cc_start: 0.8206 (m-80) cc_final: 0.7831 (m-80) REVERT: C 904 TYR cc_start: 0.8522 (OUTLIER) cc_final: 0.8243 (m-10) REVERT: C 960 ASN cc_start: 0.9181 (t0) cc_final: 0.8809 (t0) REVERT: C 1138 TYR cc_start: 0.7983 (m-80) cc_final: 0.7475 (m-10) REVERT: H 36 TYR cc_start: 0.3022 (m-80) cc_final: 0.2717 (m-80) REVERT: H 38 GLN cc_start: 0.4064 (tp-100) cc_final: 0.3717 (mt0) REVERT: K 36 TRP cc_start: 0.4680 (m100) cc_final: 0.4391 (m100) REVERT: K 110 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8320 (pm20) outliers start: 77 outliers final: 39 residues processed: 220 average time/residue: 0.4395 time to fit residues: 159.8573 Evaluate side-chains 173 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 131 time to evaluate : 2.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 LEU 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 98 VAL 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 A residue 886 TRP Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain K residue 110 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 276 optimal weight: 8.9990 chunk 252 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 377 optimal weight: 0.8980 chunk 199 optimal weight: 20.0000 chunk 105 optimal weight: 7.9990 chunk 290 optimal weight: 0.4980 chunk 110 optimal weight: 0.0470 chunk 78 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 overall best weight: 1.0680 ------------------------------------------------------------------------------- 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** O 37 GLN ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN H 102 GLN ** 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 = 0.4190 r_free = 0.4190 target = 0.108015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.068912 restraints weight = 140661.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.068158 restraints weight = 77248.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.068514 restraints weight = 56117.217| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30922 Z= 0.121 Angle : 0.604 11.954 42250 Z= 0.312 Chirality : 0.044 0.324 4948 Planarity : 0.004 0.060 5371 Dihedral : 6.015 54.905 4984 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.17 % Favored : 94.78 % Rotamer: Outliers : 2.39 % Allowed : 14.13 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.13), residues: 3871 helix: 1.63 (0.21), residues: 660 sheet: -0.50 (0.15), residues: 1093 loop : -1.52 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP P 36 HIS 0.004 0.001 HIS A 69 PHE 0.024 0.001 PHE B 429 TYR 0.018 0.001 TYR K 79 ARG 0.017 0.000 ARG L 40 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 1136) hydrogen bonds : angle 5.69595 ( 3117) SS BOND : bond 0.00504 ( 46) SS BOND : angle 1.83239 ( 92) covalent geometry : bond 0.00262 (30876) covalent geometry : angle 0.59869 (42158) *********************** 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 224 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 149 time to evaluate : 3.142 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: 0.5269 (tttm) cc_final: 0.4100 (mttt) REVERT: J 49 MET cc_start: -0.2680 (tmm) cc_final: -0.3624 (tmm) REVERT: L 39 ILE cc_start: 0.7552 (mm) cc_final: 0.7106 (mm) REVERT: L 48 GLU cc_start: 0.3800 (mp0) cc_final: 0.3571 (mp0) REVERT: P 51 MET cc_start: 0.6896 (tpp) cc_final: 0.6591 (tpp) REVERT: A 858 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9224 (mt) REVERT: A 900 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8773 (mtm) REVERT: A 1017 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8631 (tp30) REVERT: B 191 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8248 (mt-10) REVERT: B 200 TYR cc_start: 0.9229 (m-80) cc_final: 0.8871 (m-10) REVERT: B 773 GLU cc_start: 0.9045 (tp30) cc_final: 0.8472 (tp30) REVERT: C 229 LEU cc_start: 0.9343 (mt) cc_final: 0.8910 (pp) REVERT: C 242 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8700 (mm) REVERT: C 365 TYR cc_start: 0.8139 (m-80) cc_final: 0.7743 (m-80) REVERT: C 904 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.8160 (m-10) REVERT: C 960 ASN cc_start: 0.9352 (t0) cc_final: 0.8939 (t0) REVERT: C 1138 TYR cc_start: 0.8226 (m-80) cc_final: 0.7664 (m-10) REVERT: H 36 TYR cc_start: 0.2808 (m-80) cc_final: 0.2532 (m-10) REVERT: H 38 GLN cc_start: 0.4037 (tp-100) cc_final: 0.3681 (mt0) outliers start: 75 outliers final: 36 residues processed: 212 average time/residue: 0.4292 time to fit residues: 150.5221 Evaluate side-chains 174 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 3.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 LEU 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 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 858 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 98 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 31 optimal weight: 8.9990 chunk 211 optimal weight: 1.9990 chunk 323 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 342 optimal weight: 3.9990 chunk 331 optimal weight: 4.9990 chunk 47 optimal weight: 0.3980 chunk 38 optimal weight: 40.0000 chunk 330 optimal weight: 1.9990 chunk 203 optimal weight: 20.0000 overall best weight: 2.4788 ------------------------------------------------------------------------------- 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** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 GLN A 239 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1010 GLN B 409 GLN B1134 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C1125 ASN ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.105304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.066993 restraints weight = 135524.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.067913 restraints weight = 68044.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.067769 restraints weight = 41576.137| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 30922 Z= 0.191 Angle : 0.630 12.498 42250 Z= 0.325 Chirality : 0.045 0.295 4948 Planarity : 0.004 0.093 5371 Dihedral : 5.989 58.586 4982 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.48 % Favored : 94.47 % Rotamer: Outliers : 2.90 % Allowed : 14.73 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.13), residues: 3871 helix: 1.57 (0.21), residues: 652 sheet: -0.47 (0.15), residues: 1128 loop : -1.47 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP K 36 HIS 0.004 0.001 HIS C1064 PHE 0.018 0.002 PHE L 24 TYR 0.022 0.002 TYR M 93 ARG 0.004 0.000 ARG O 54 Details of bonding type rmsd hydrogen bonds : bond 0.04464 ( 1136) hydrogen bonds : angle 5.74599 ( 3117) SS BOND : bond 0.00549 ( 46) SS BOND : angle 1.65200 ( 92) covalent geometry : bond 0.00434 (30876) covalent geometry : angle 0.62632 (42158) *********************** 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 230 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 139 time to evaluate : 3.286 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: 0.4785 (tttm) cc_final: 0.3922 (mttt) REVERT: P 51 MET cc_start: 0.6821 (tpp) cc_final: 0.6501 (tpp) REVERT: A 858 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9076 (mt) REVERT: A 900 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8896 (mtm) REVERT: A 979 ASP cc_start: 0.9500 (m-30) cc_final: 0.9130 (p0) REVERT: B 200 TYR cc_start: 0.9162 (m-80) cc_final: 0.8776 (m-10) REVERT: B 437 ASN cc_start: 0.9041 (m110) cc_final: 0.8466 (m-40) REVERT: B 773 GLU cc_start: 0.8993 (tp30) cc_final: 0.8503 (tp30) REVERT: B 904 TYR cc_start: 0.8188 (OUTLIER) cc_final: 0.7793 (m-10) REVERT: C 229 LEU cc_start: 0.9265 (mt) cc_final: 0.8828 (pp) REVERT: C 501 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.8119 (m-10) REVERT: C 904 TYR cc_start: 0.8394 (OUTLIER) cc_final: 0.8071 (m-10) REVERT: C 909 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8921 (tp) REVERT: C 960 ASN cc_start: 0.9335 (t0) cc_final: 0.8929 (t0) REVERT: C 1138 TYR cc_start: 0.8185 (m-80) cc_final: 0.7691 (m-10) outliers start: 91 outliers final: 54 residues processed: 218 average time/residue: 0.3717 time to fit residues: 136.4711 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 : 3.028 ------------------------------------------------------------------------------- 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 51 TYR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain O residue 98 TYR Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 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 761 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 900 MET Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 303 LEU 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 559 PHE Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 1002 GLN 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 445 VAL Chi-restraints excluded: chain C residue 501 TYR 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 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 5 optimal weight: 10.0000 chunk 256 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 330 optimal weight: 0.6980 chunk 195 optimal weight: 6.9990 chunk 220 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 322 optimal weight: 5.9990 chunk 298 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 153 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 GLN A 30 ASN A 239 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN B 239 GLN C 450 ASN C 965 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.105393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.066773 restraints weight = 135971.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.067698 restraints weight = 81670.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.067875 restraints weight = 50724.771| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30922 Z= 0.164 Angle : 0.599 10.579 42250 Z= 0.311 Chirality : 0.044 0.277 4948 Planarity : 0.004 0.064 5371 Dihedral : 5.851 56.668 4982 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.55 % Favored : 94.42 % Rotamer: Outliers : 3.02 % Allowed : 15.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.13), residues: 3871 helix: 1.61 (0.21), residues: 652 sheet: -0.42 (0.15), residues: 1122 loop : -1.40 (0.13), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 36 HIS 0.006 0.001 HIS A 69 PHE 0.031 0.001 PHE B 429 TYR 0.020 0.001 TYR P 107 ARG 0.003 0.000 ARG B 34 Details of bonding type rmsd hydrogen bonds : bond 0.04302 ( 1136) hydrogen bonds : angle 5.62650 ( 3117) SS BOND : bond 0.00569 ( 46) SS BOND : angle 1.60594 ( 92) covalent geometry : bond 0.00372 (30876) covalent geometry : angle 0.59521 (42158) *********************** 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 229 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 134 time to evaluate : 3.334 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: 0.4712 (tttm) cc_final: 0.3892 (mttt) REVERT: L 73 LYS cc_start: 0.7729 (pptt) cc_final: 0.7283 (tmtt) REVERT: A 239 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7810 (tp40) REVERT: A 791 THR cc_start: 0.9075 (OUTLIER) cc_final: 0.8825 (t) REVERT: A 900 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8739 (mtm) REVERT: A 979 ASP cc_start: 0.9503 (m-30) cc_final: 0.9122 (p0) REVERT: B 200 TYR cc_start: 0.9082 (m-80) cc_final: 0.8692 (m-80) REVERT: B 773 GLU cc_start: 0.8845 (tp30) cc_final: 0.8419 (tp30) REVERT: B 904 TYR cc_start: 0.8286 (OUTLIER) cc_final: 0.7916 (m-10) REVERT: C 229 LEU cc_start: 0.9270 (mt) cc_final: 0.8885 (pp) REVERT: C 242 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8573 (mm) REVERT: C 501 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.8084 (m-10) REVERT: C 546 LEU cc_start: 0.8840 (tp) cc_final: 0.8517 (pp) REVERT: C 904 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.7880 (m-10) REVERT: C 909 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8982 (tp) REVERT: C 960 ASN cc_start: 0.9195 (t0) cc_final: 0.8801 (t0) REVERT: C 1002 GLN cc_start: 0.9113 (tp40) cc_final: 0.8904 (tp40) REVERT: C 1138 TYR cc_start: 0.8108 (m-80) cc_final: 0.7645 (m-10) outliers start: 95 outliers final: 60 residues processed: 217 average time/residue: 0.5143 time to fit residues: 185.1220 Evaluate side-chains 198 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 130 time to evaluate : 4.098 ------------------------------------------------------------------------------- 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 51 TYR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain O residue 98 TYR Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 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 781 VAL Chi-restraints excluded: chain A residue 791 THR 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 A residue 1077 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 303 LEU 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 396 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 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 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 121 optimal weight: 0.9990 chunk 274 optimal weight: 30.0000 chunk 331 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 chunk 312 optimal weight: 8.9990 chunk 306 optimal weight: 0.9990 chunk 322 optimal weight: 6.9990 chunk 366 optimal weight: 50.0000 chunk 220 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 382 optimal weight: 20.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 ASN ** P 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 417 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 914 ASN B 960 ASN ** 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 = 0.103950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.065545 restraints weight = 136266.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.066599 restraints weight = 66276.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.066301 restraints weight = 45162.667| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 30922 Z= 0.217 Angle : 0.645 15.239 42250 Z= 0.332 Chirality : 0.045 0.252 4948 Planarity : 0.004 0.064 5371 Dihedral : 5.978 56.915 4982 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.67 % Allowed : 16.13 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.13), residues: 3871 helix: 1.45 (0.21), residues: 657 sheet: -0.46 (0.15), residues: 1146 loop : -1.37 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP M 37 HIS 0.006 0.001 HIS C1048 PHE 0.034 0.002 PHE A 238 TYR 0.019 0.002 TYR A1067 ARG 0.004 0.000 ARG P 66 Details of bonding type rmsd hydrogen bonds : bond 0.04587 ( 1136) hydrogen bonds : angle 5.71723 ( 3117) SS BOND : bond 0.00566 ( 46) SS BOND : angle 1.71667 ( 92) covalent geometry : bond 0.00493 (30876) covalent geometry : angle 0.64113 (42158) *********************** 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 216 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 132 time to evaluate : 3.149 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: 0.4657 (tttm) cc_final: 0.3895 (mttt) REVERT: L 40 ARG cc_start: 0.6247 (tmt-80) cc_final: 0.6027 (tmt-80) REVERT: P 79 TYR cc_start: 0.8706 (m-80) cc_final: 0.8402 (m-80) REVERT: A 791 THR cc_start: 0.9079 (OUTLIER) cc_final: 0.8838 (t) REVERT: A 979 ASP cc_start: 0.9530 (m-30) cc_final: 0.9137 (p0) REVERT: B 200 TYR cc_start: 0.9187 (m-80) cc_final: 0.8756 (m-10) REVERT: B 904 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.8019 (m-10) REVERT: C 229 LEU cc_start: 0.9312 (mt) cc_final: 0.8889 (pp) REVERT: C 501 TYR cc_start: 0.8383 (OUTLIER) cc_final: 0.8061 (m-10) REVERT: C 904 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.7955 (m-10) REVERT: C 909 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.9098 (tp) REVERT: C 960 ASN cc_start: 0.9214 (t0) cc_final: 0.8845 (t0) REVERT: C 1002 GLN cc_start: 0.9133 (tp40) cc_final: 0.8905 (tp40) REVERT: C 1138 TYR cc_start: 0.8134 (m-80) cc_final: 0.7689 (m-10) REVERT: K 36 TRP cc_start: 0.4616 (m100) cc_final: 0.4400 (m100) REVERT: K 51 MET cc_start: 0.3525 (mtm) cc_final: 0.3322 (mpp) outliers start: 84 outliers final: 64 residues processed: 203 average time/residue: 0.4756 time to fit residues: 162.4451 Evaluate side-chains 194 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 125 time to evaluate : 3.102 ------------------------------------------------------------------------------- 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 51 TYR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain O residue 98 TYR Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 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 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 781 VAL Chi-restraints excluded: chain A residue 791 THR 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 303 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1002 GLN 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 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 42 GLN 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 280 optimal weight: 5.9990 chunk 215 optimal weight: 0.6980 chunk 2 optimal weight: 8.9990 chunk 18 optimal weight: 20.0000 chunk 222 optimal weight: 4.9990 chunk 11 optimal weight: 30.0000 chunk 223 optimal weight: 1.9990 chunk 343 optimal weight: 0.7980 chunk 299 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 chunk 186 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN C 901 GLN H 6 GLN ** H 27 GLN ** 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 = 0.4124 r_free = 0.4124 target = 0.105337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.067825 restraints weight = 140775.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.064963 restraints weight = 103010.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.065666 restraints weight = 67953.110| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 30922 Z= 0.162 Angle : 0.605 13.177 42250 Z= 0.311 Chirality : 0.044 0.229 4948 Planarity : 0.004 0.064 5371 Dihedral : 5.843 58.990 4982 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.74 % Allowed : 16.26 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.13), residues: 3871 helix: 1.53 (0.21), residues: 656 sheet: -0.39 (0.15), residues: 1159 loop : -1.31 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP M 37 HIS 0.005 0.001 HIS C1048 PHE 0.013 0.001 PHE C 92 TYR 0.017 0.001 TYR A1067 ARG 0.003 0.000 ARG L 40 Details of bonding type rmsd hydrogen bonds : bond 0.04277 ( 1136) hydrogen bonds : angle 5.52501 ( 3117) SS BOND : bond 0.00493 ( 46) SS BOND : angle 1.60308 ( 92) covalent geometry : bond 0.00367 (30876) covalent geometry : angle 0.60058 (42158) *********************** 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 217 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 131 time to evaluate : 5.364 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: J 50 ILE cc_start: 0.0146 (OUTLIER) cc_final: -0.1006 (mt) REVERT: L 55 TRP cc_start: 0.8364 (p-90) cc_final: 0.7752 (p90) REVERT: P 79 TYR cc_start: 0.8822 (m-80) cc_final: 0.8598 (m-80) REVERT: A 791 THR cc_start: 0.9084 (OUTLIER) cc_final: 0.8806 (t) REVERT: B 200 TYR cc_start: 0.9263 (m-80) cc_final: 0.8792 (m-10) REVERT: B 904 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.7889 (m-10) REVERT: C 229 LEU cc_start: 0.9328 (mt) cc_final: 0.8863 (pp) REVERT: C 242 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8592 (mm) REVERT: C 473 TYR cc_start: 0.6116 (t80) cc_final: 0.5603 (t80) REVERT: C 501 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.8054 (m-10) REVERT: C 904 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.8096 (m-10) REVERT: C 960 ASN cc_start: 0.9332 (t0) cc_final: 0.8939 (t0) REVERT: C 1002 GLN cc_start: 0.9149 (tp40) cc_final: 0.8918 (tp40) REVERT: C 1138 TYR cc_start: 0.8345 (m-80) cc_final: 0.7839 (m-10) REVERT: K 51 MET cc_start: 0.3780 (OUTLIER) cc_final: 0.3562 (mpp) outliers start: 86 outliers final: 59 residues processed: 203 average time/residue: 0.7467 time to fit residues: 258.4642 Evaluate side-chains 193 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 127 time to evaluate : 4.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 L residue 87 MET Chi-restraints excluded: chain M residue 51 TYR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain O residue 98 TYR Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 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 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 791 THR 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 227 VAL Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR 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 98 TYR Chi-restraints excluded: chain K residue 51 MET 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 318 optimal weight: 0.8980 chunk 191 optimal weight: 5.9990 chunk 273 optimal weight: 20.0000 chunk 319 optimal weight: 0.3980 chunk 209 optimal weight: 1.9990 chunk 195 optimal weight: 5.9990 chunk 361 optimal weight: 3.9990 chunk 377 optimal weight: 50.0000 chunk 118 optimal weight: 0.6980 chunk 322 optimal weight: 5.9990 chunk 280 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A 901 GLN A1011 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.105720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.068616 restraints weight = 140151.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.065507 restraints weight = 101773.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.066309 restraints weight = 68183.667| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 0.050 30922 Z= 0.138 Angle : 0.606 12.785 42250 Z= 0.310 Chirality : 0.044 0.266 4948 Planarity : 0.004 0.064 5371 Dihedral : 5.677 58.743 4982 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.42 % Allowed : 16.74 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.13), residues: 3871 helix: 1.63 (0.21), residues: 655 sheet: -0.31 (0.15), residues: 1149 loop : -1.26 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP M 37 HIS 0.004 0.001 HIS C1048 PHE 0.031 0.001 PHE C 888 TYR 0.017 0.001 TYR O 49 ARG 0.008 0.000 ARG P 66 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 1136) hydrogen bonds : angle 5.39408 ( 3117) SS BOND : bond 0.00433 ( 46) SS BOND : angle 1.84935 ( 92) covalent geometry : bond 0.00312 (30876) covalent geometry : angle 0.60040 (42158) *********************** 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 215 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 139 time to evaluate : 3.858 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: 0.0120 (OUTLIER) cc_final: -0.1010 (mt) REVERT: L 55 TRP cc_start: 0.8397 (p-90) cc_final: 0.7792 (p90) REVERT: P 51 MET cc_start: 0.6926 (tpp) cc_final: 0.6641 (tpp) REVERT: P 79 TYR cc_start: 0.8834 (m-80) cc_final: 0.8618 (m-80) REVERT: A 791 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8858 (p) REVERT: A 979 ASP cc_start: 0.9536 (m-30) cc_final: 0.9134 (p0) REVERT: B 200 TYR cc_start: 0.9300 (m-80) cc_final: 0.8829 (m-10) REVERT: B 904 TYR cc_start: 0.8281 (OUTLIER) cc_final: 0.7903 (m-10) REVERT: C 200 TYR cc_start: 0.9372 (m-80) cc_final: 0.9050 (m-10) REVERT: C 229 LEU cc_start: 0.9318 (mt) cc_final: 0.8940 (tp) REVERT: C 242 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8626 (mm) REVERT: C 473 TYR cc_start: 0.6065 (t80) cc_final: 0.5566 (t80) REVERT: C 501 TYR cc_start: 0.8332 (OUTLIER) cc_final: 0.8063 (m-10) REVERT: C 904 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.7955 (m-10) REVERT: C 960 ASN cc_start: 0.9264 (t0) cc_final: 0.8870 (t0) REVERT: C 1002 GLN cc_start: 0.9080 (tp40) cc_final: 0.8847 (tp40) REVERT: C 1138 TYR cc_start: 0.8321 (m-80) cc_final: 0.7777 (m-10) outliers start: 76 outliers final: 58 residues processed: 202 average time/residue: 0.4694 time to fit residues: 158.8172 Evaluate side-chains 192 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 128 time to evaluate : 4.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 49 MET Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain O residue 98 TYR Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 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 859 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 1 GLU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 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 118 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 363 optimal weight: 1.9990 chunk 289 optimal weight: 6.9990 chunk 301 optimal weight: 9.9990 chunk 241 optimal weight: 2.9990 chunk 142 optimal weight: 0.3980 chunk 183 optimal weight: 50.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 93 ASN ** P 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.104966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.067384 restraints weight = 140513.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.064425 restraints weight = 98367.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.065199 restraints weight = 65965.342| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 30922 Z= 0.183 Angle : 0.638 12.594 42250 Z= 0.325 Chirality : 0.044 0.262 4948 Planarity : 0.004 0.065 5371 Dihedral : 5.771 57.108 4981 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.29 % Allowed : 16.86 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.13), residues: 3871 helix: 1.46 (0.21), residues: 655 sheet: -0.33 (0.15), residues: 1159 loop : -1.25 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP M 37 HIS 0.004 0.001 HIS C1064 PHE 0.026 0.001 PHE C 888 TYR 0.019 0.001 TYR O 49 ARG 0.004 0.000 ARG P 66 Details of bonding type rmsd hydrogen bonds : bond 0.04384 ( 1136) hydrogen bonds : angle 5.53476 ( 3117) SS BOND : bond 0.00465 ( 46) SS BOND : angle 1.85270 ( 92) covalent geometry : bond 0.00415 (30876) covalent geometry : angle 0.63305 (42158) ********************** 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 200 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 128 time to evaluate : 3.140 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: -0.0245 (OUTLIER) cc_final: -0.1270 (mt) REVERT: L 55 TRP cc_start: 0.8394 (p-90) cc_final: 0.7788 (p90) REVERT: P 51 MET cc_start: 0.6973 (tpp) cc_final: 0.6735 (tpp) REVERT: P 79 TYR cc_start: 0.8827 (m-80) cc_final: 0.8617 (m-80) REVERT: A 979 ASP cc_start: 0.9548 (m-30) cc_final: 0.9134 (p0) REVERT: B 200 TYR cc_start: 0.9319 (m-80) cc_final: 0.8877 (m-10) REVERT: B 904 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7924 (m-10) REVERT: C 200 TYR cc_start: 0.9409 (m-80) cc_final: 0.9122 (m-10) REVERT: C 229 LEU cc_start: 0.9321 (mt) cc_final: 0.8711 (pp) REVERT: C 242 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8562 (mm) REVERT: C 501 TYR cc_start: 0.8329 (OUTLIER) cc_final: 0.8059 (m-10) REVERT: C 904 TYR cc_start: 0.8517 (OUTLIER) cc_final: 0.7984 (m-10) REVERT: C 960 ASN cc_start: 0.9318 (t0) cc_final: 0.8924 (t0) REVERT: C 1002 GLN cc_start: 0.9171 (tp40) cc_final: 0.8938 (tp40) REVERT: C 1138 TYR cc_start: 0.8398 (m-80) cc_final: 0.7873 (m-10) outliers start: 72 outliers final: 58 residues processed: 190 average time/residue: 0.3886 time to fit residues: 124.8000 Evaluate side-chains 189 residues out of total 3413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 126 time to evaluate : 3.473 ------------------------------------------------------------------------------- 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 49 MET Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain O residue 98 TYR Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 105 THR 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 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 1 GLU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 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 88 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 229 optimal weight: 0.9990 chunk 169 optimal weight: 20.0000 chunk 246 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 329 optimal weight: 0.9990 chunk 172 optimal weight: 20.0000 chunk 121 optimal weight: 0.9980 chunk 274 optimal weight: 20.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 ASN ** P 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN B 751 ASN C 519 HIS ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 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 = 0.4141 r_free = 0.4141 target = 0.105931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.067536 restraints weight = 140873.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.066318 restraints weight = 89237.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.066892 restraints weight = 60330.072| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30922 Z= 0.125 Angle : 0.597 12.499 42250 Z= 0.304 Chirality : 0.044 0.262 4948 Planarity : 0.004 0.063 5371 Dihedral : 5.509 58.161 4980 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.32 % Allowed : 17.02 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.13), residues: 3871 helix: 1.65 (0.21), residues: 656 sheet: -0.21 (0.15), residues: 1147 loop : -1.20 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP M 37 HIS 0.003 0.001 HIS A 69 PHE 0.026 0.001 PHE C 888 TYR 0.015 0.001 TYR O 49 ARG 0.002 0.000 ARG B 34 Details of bonding type rmsd hydrogen bonds : bond 0.04001 ( 1136) hydrogen bonds : angle 5.29929 ( 3117) SS BOND : bond 0.00406 ( 46) SS BOND : angle 1.62837 ( 92) covalent geometry : bond 0.00282 (30876) covalent geometry : angle 0.59327 (42158) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14174.42 seconds wall clock time: 256 minutes 31.11 seconds (15391.11 seconds total)