Starting phenix.real_space_refine on Fri Mar 6 11:18:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvo_34134/03_2026/7yvo_34134.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvo_34134/03_2026/7yvo_34134.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yvo_34134/03_2026/7yvo_34134.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvo_34134/03_2026/7yvo_34134.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yvo_34134/03_2026/7yvo_34134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvo_34134/03_2026/7yvo_34134.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.035 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 19336 2.51 5 N 5010 2.21 5 O 5808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 147 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30285 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 7725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7725 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 10, 'GLN:plan1': 10, 'ASN:plan1': 7, 'GLU:plan': 8, 'PHE:plan': 2, 'ARG:plan': 5, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 174 Chain: "B" Number of atoms: 7413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7413 Classifications: {'peptide': 987} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 54, 'TRANS': 932} Chain breaks: 10 Unresolved non-hydrogen bonds: 316 Unresolved non-hydrogen angles: 388 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 11, 'GLN:plan1': 9, 'ASN:plan1': 7, 'GLU:plan': 10, 'PHE:plan': 2, 'ARG:plan': 7, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 198 Chain: "C" Number of atoms: 7719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7719 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 359 Unresolved non-hydrogen dihedrals: 237 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 10, 'GLN:plan1': 10, 'ASN:plan1': 7, 'GLU:plan': 8, 'PHE:plan': 3, 'ARG:plan': 5, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 180 Chain: "H" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 818 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 865 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: "J" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 818 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 865 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: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "M" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 956 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "N" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "O" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 956 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} 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: 6.34, per 1000 atoms: 0.21 Number of scatterers: 30285 At special positions: 0 Unit cell: (183.68, 151.7, 226.32, 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 5808 8.00 N 5010 7.00 C 19336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.01 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 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=2.04 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=2.06 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.01 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 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=2.05 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=2.01 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=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 97 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 89 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.3 seconds 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7340 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 57 sheets defined 20.3% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.160A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.653A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.510A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.542A 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 816 through 826 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.508A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.594A 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: 3.937A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.973A 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: 3.505A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.053A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.163A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.811A 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 345 removed outlier: 4.653A pdb=" N THR B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' 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 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.609A 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: 3.882A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.874A 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: 3.541A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.882A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' 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: 3.645A 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: 4.082A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.581A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.607A 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 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 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: 3.790A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.822A 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: 3.558A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.889A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.829A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.104A pdb=" N SER H 83 " --> pdb=" O SER H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 75 No H-bonds generated for 'chain 'I' and resid 73 through 75' Processing helix chain 'I' and resid 86 through 90 removed outlier: 4.085A pdb=" N THR I 90 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 4.053A pdb=" N SER J 83 " --> pdb=" O SER J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 75 No H-bonds generated for 'chain 'K' and resid 73 through 75' Processing helix chain 'K' and resid 86 through 90 removed outlier: 3.954A pdb=" N THR K 90 " --> pdb=" O ALA K 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 66 Processing helix chain 'M' and resid 88 through 92 Processing helix chain 'O' and resid 63 through 66 Processing helix chain 'O' and resid 88 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 8.612A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.571A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN C 542 " --> pdb=" O ILE C 326 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.875A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.537A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.004A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.723A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.913A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.345A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.985A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.801A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.801A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.371A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.029A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.537A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 29 through 31 removed outlier: 8.704A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.900A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.879A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.376A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 324 through 328 removed outlier: 5.579A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.661A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.732A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.008A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.783A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.783A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.354A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.470A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 29 through 31 removed outlier: 8.787A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.839A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.785A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.958A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.701A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.986A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.762A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.762A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.409A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.755A pdb=" N GLU H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.545A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'I' and resid 10 through 12 removed outlier: 5.898A pdb=" N GLY I 10 " --> pdb=" O THR I 115 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.684A pdb=" N GLU J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.067A pdb=" N LEU J 11 " --> pdb=" O GLU J 107 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.765A pdb=" N GLY K 10 " --> pdb=" O THR K 115 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.765A pdb=" N GLY K 10 " --> pdb=" O THR K 115 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR K 107 " --> pdb=" O ARG K 97 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AF6, first strand: chain 'L' and resid 46 through 49 removed outlier: 5.263A pdb=" N LEU L 47 " --> pdb=" O HIS L 38 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N HIS L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 3 through 8 Processing sheet with id=AF8, first strand: chain 'M' and resid 59 through 61 removed outlier: 5.185A pdb=" N TRP M 49 " --> pdb=" O ARG M 40 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG M 40 " --> pdb=" O TRP M 49 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA M 51 " --> pdb=" O TRP M 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 18 through 23 Processing sheet with id=AG1, first strand: chain 'N' and resid 46 through 49 removed outlier: 6.751A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 3 through 8 Processing sheet with id=AG3, first strand: chain 'O' and resid 11 through 12 removed outlier: 6.668A pdb=" N VAL O 36 " --> pdb=" O LEU O 52 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU O 52 " --> pdb=" O VAL O 36 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TRP O 38 " --> pdb=" O LEU O 50 " (cutoff:3.500A) 1241 hydrogen bonds defined for protein. 3297 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.91 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 8232 1.33 - 1.46: 9896 1.46 - 1.59: 12699 1.59 - 1.73: 6 1.73 - 1.86: 161 Bond restraints: 30994 Sorted by residual: bond pdb=" C LEU B 223 " pdb=" N GLU B 224 " ideal model delta sigma weight residual 1.331 1.213 0.118 2.07e-02 2.33e+03 3.25e+01 bond pdb=" CB TRP C 886 " pdb=" CG TRP C 886 " ideal model delta sigma weight residual 1.498 1.336 0.162 3.10e-02 1.04e+03 2.74e+01 bond pdb=" CB CYS C 649 " pdb=" SG CYS C 649 " ideal model delta sigma weight residual 1.808 1.648 0.160 3.30e-02 9.18e+02 2.34e+01 bond pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " ideal model delta sigma weight residual 1.808 1.664 0.144 3.30e-02 9.18e+02 1.90e+01 bond pdb=" CA SER B 884 " pdb=" CB SER B 884 " ideal model delta sigma weight residual 1.534 1.468 0.067 1.55e-02 4.16e+03 1.85e+01 ... (remaining 30989 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 40698 3.30 - 6.61: 1436 6.61 - 9.91: 136 9.91 - 13.22: 33 13.22 - 16.52: 9 Bond angle restraints: 42312 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 121.97 134.84 -12.87 1.80e+00 3.09e-01 5.11e+01 angle pdb=" CA CYS B 432 " pdb=" CB CYS B 432 " pdb=" SG CYS B 432 " ideal model delta sigma weight residual 114.40 130.29 -15.89 2.30e+00 1.89e-01 4.77e+01 angle pdb=" C SER J 30 " pdb=" N SER J 31 " pdb=" CA SER J 31 " ideal model delta sigma weight residual 122.14 111.34 10.80 1.67e+00 3.59e-01 4.18e+01 angle pdb=" CA CYS A 538 " pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " ideal model delta sigma weight residual 114.40 128.70 -14.30 2.30e+00 1.89e-01 3.87e+01 angle pdb=" N PHE C 329 " pdb=" CA PHE C 329 " pdb=" C PHE C 329 " ideal model delta sigma weight residual 108.82 119.22 -10.40 1.69e+00 3.50e-01 3.79e+01 ... (remaining 42307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.32: 17615 22.32 - 44.64: 929 44.64 - 66.96: 168 66.96 - 89.28: 34 89.28 - 111.61: 3 Dihedral angle restraints: 18749 sinusoidal: 7321 harmonic: 11428 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 -68.39 -111.61 0 5.00e+00 4.00e-02 4.98e+02 dihedral pdb=" CA PRO J 95 " pdb=" C PRO J 95 " pdb=" N PRO J 96 " pdb=" CA PRO J 96 " ideal model delta harmonic sigma weight residual -180.00 -68.47 -111.53 0 5.00e+00 4.00e-02 4.98e+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 -6.13 -79.87 1 1.00e+01 1.00e-02 7.91e+01 ... (remaining 18746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3632 0.080 - 0.161: 1148 0.161 - 0.241: 135 0.241 - 0.321: 22 0.321 - 0.401: 3 Chirality restraints: 4940 Sorted by residual: chirality pdb=" CA CYS C 649 " pdb=" N CYS C 649 " pdb=" C CYS C 649 " pdb=" CB CYS C 649 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CA ASN A 709 " pdb=" N ASN A 709 " pdb=" C ASN A 709 " pdb=" CB ASN A 709 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA CYS C 617 " pdb=" N CYS C 617 " pdb=" C CYS C 617 " pdb=" CB CYS C 617 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 ... (remaining 4937 not shown) Planarity restraints: 5409 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 94 " 0.036 2.00e-02 2.50e+03 2.48e-02 1.53e+01 pdb=" CG TRP H 94 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP H 94 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP H 94 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 94 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP H 94 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 94 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 94 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP H 94 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 526 " -0.062 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO C 527 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO C 527 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 527 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 380 " -0.035 2.00e-02 2.50e+03 2.51e-02 1.26e+01 pdb=" CG TYR B 380 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 TYR B 380 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 380 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 380 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 380 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 380 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR B 380 " -0.003 2.00e-02 2.50e+03 ... (remaining 5406 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 448 2.56 - 3.15: 27503 3.15 - 3.73: 46195 3.73 - 4.32: 64140 4.32 - 4.90: 106871 Nonbonded interactions: 245157 Sorted by model distance: nonbonded pdb=" O TRP C 353 " pdb=" NH1 ARG C 466 " model vdw 1.977 3.120 nonbonded pdb=" OG1 THR N 5 " pdb=" OG SER N 23 " model vdw 1.993 3.040 nonbonded pdb=" O SER J 28 " pdb=" ND2 ASN J 92 " model vdw 2.057 3.120 nonbonded pdb=" O GLN N 1 " pdb=" ND2 ASN N 28 " model vdw 2.071 3.120 nonbonded pdb=" O VAL I 50 " pdb=" OG1 THR I 57 " model vdw 2.081 3.040 ... (remaining 245152 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 328 or (resid 329 and (name N or name CA or nam \ e C or name O or name CB )) or resid 330 through 368 or (resid 369 and (name N o \ r name CA or name C or name O or name CB )) or resid 370 through 402 or (resid 4 \ 03 and (name N or name CA or name C or name O or name CB )) or resid 404 through \ 405 or (resid 406 and (name N or name CA or name C or name O or name CB )) or r \ esid 407 through 423 or (resid 424 and (name N or name CA or name C or name O or \ name CB )) or resid 425 through 438 or (resid 439 and (name N or name CA or nam \ e C or name O or name CB )) or resid 440 through 441 or (resid 442 and (name N o \ r name CA or name C or name O or name CB )) or resid 443 or resid 451 through 46 \ 4 or (resid 465 and (name N or name CA or name C or name O or name CB )) or resi \ d 491 through 497 or resid 503 through 508 or (resid 509 and (name N or name CA \ or name C or name O or name CB )) or resid 510 through 1312)) selection = (chain 'B' and (resid 27 through 328 or (resid 329 and (name N or name CA or nam \ e C or name O or name CB )) or resid 330 through 1312)) selection = (chain 'C' and (resid 27 through 368 or (resid 369 and (name N or name CA or nam \ e C or name O or name CB )) or resid 370 through 402 or (resid 403 and (name N o \ r name CA or name C or name O or name CB )) or resid 404 through 405 or (resid 4 \ 06 and (name N or name CA or name C or name O or name CB )) or resid 407 through \ 423 or (resid 424 and (name N or name CA or name C or name O or name CB )) or r \ esid 425 through 438 or (resid 439 and (name N or name CA or name C or name O or \ name CB )) or resid 440 through 441 or (resid 442 and (name N or name CA or nam \ e C or name O or name CB )) or resid 443 or resid 451 through 464 or (resid 465 \ and (name N or name CA or name C or name O or name CB )) or resid 491 through 49 \ 7 or resid 503 through 508 or (resid 509 and (name N or name CA or name C or nam \ e O or name CB )) or resid 510 through 1312)) } ncs_group { reference = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'M' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.060 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: 0.030 Extract box with map and model: 0.660 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 28.140 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 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 : 0.020 0.163 31040 Z= 0.860 Angle : 1.447 16.524 42404 Z= 0.786 Chirality : 0.075 0.401 4940 Planarity : 0.007 0.096 5409 Dihedral : 13.558 111.605 11271 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 23.23 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.59 % Favored : 94.03 % Rotamer: Outliers : 1.33 % Allowed : 8.83 % Favored : 89.83 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.12), residues: 3883 helix: -0.09 (0.19), residues: 669 sheet: -1.43 (0.14), residues: 1066 loop : -2.40 (0.12), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.002 ARG O 100 TYR 0.061 0.004 TYR B 380 PHE 0.055 0.005 PHE B 559 TRP 0.066 0.004 TRP H 94 HIS 0.009 0.003 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.01969 (30994) covalent geometry : angle 1.43486 (42312) SS BOND : bond 0.01282 ( 46) SS BOND : angle 4.30554 ( 92) hydrogen bonds : bond 0.14330 ( 1201) hydrogen bonds : angle 7.86322 ( 3297) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 253 time to evaluate : 1.060 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: A 106 PHE cc_start: 0.7461 (m-80) cc_final: 0.7203 (m-80) REVERT: A 238 PHE cc_start: 0.7227 (p90) cc_final: 0.6274 (p90) REVERT: A 776 LYS cc_start: 0.9031 (ttpp) cc_final: 0.8795 (ttpp) REVERT: B 129 LYS cc_start: 0.8142 (mtpt) cc_final: 0.7813 (tttp) REVERT: B 200 TYR cc_start: 0.8834 (m-80) cc_final: 0.8467 (m-80) REVERT: B 231 ILE cc_start: 0.6811 (mm) cc_final: 0.6581 (tt) REVERT: B 338 PHE cc_start: 0.9225 (m-80) cc_final: 0.8910 (m-80) REVERT: B 354 ASN cc_start: 0.7364 (t0) cc_final: 0.6959 (t0) REVERT: B 357 ARG cc_start: 0.7330 (mtt180) cc_final: 0.6495 (mtt180) REVERT: B 436 TRP cc_start: 0.5841 (m-10) cc_final: 0.5345 (m-10) REVERT: C 365 TYR cc_start: 0.8254 (m-80) cc_final: 0.8031 (m-80) REVERT: C 960 ASN cc_start: 0.8695 (t0) cc_final: 0.8273 (t0) REVERT: I 34 MET cc_start: 0.4810 (mmm) cc_final: 0.4119 (tpt) REVERT: J 94 TRP cc_start: 0.6931 (t-100) cc_final: 0.5614 (t-100) REVERT: K 34 MET cc_start: 0.5387 (mmm) cc_final: 0.4771 (mtm) REVERT: O 29 LEU cc_start: 0.6699 (tp) cc_final: 0.5533 (pp) outliers start: 42 outliers final: 16 residues processed: 286 average time/residue: 0.1880 time to fit residues: 87.3595 Evaluate side-chains 160 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain O residue 16 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN A 388 ASN A 450 ASN A 477 ASN A 505 HIS A 657 ASN A 955 ASN A1002 GLN A1134 ASN B 334 ASN B 388 ASN B 437 ASN B 506 GLN B 955 ASN B1002 GLN B1074 ASN C 282 ASN C 448 ASN C 450 ASN ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 657 ASN C 762 GLN C1002 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN I 81 GLN J 79 GLN ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 1 GLN L 6 GLN L 32 ASN L 50 HIS ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 99 HIS N 6 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 50 HIS O 86 ASN ** O 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 105 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.155009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.092891 restraints weight = 77830.817| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 4.47 r_work: 0.3043 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 31040 Z= 0.169 Angle : 0.692 10.632 42404 Z= 0.361 Chirality : 0.047 0.284 4940 Planarity : 0.005 0.108 5409 Dihedral : 7.406 60.610 5016 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.92 % Favored : 94.98 % Rotamer: Outliers : 2.16 % Allowed : 12.20 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 1.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.13), residues: 3883 helix: 1.36 (0.21), residues: 653 sheet: -0.52 (0.15), residues: 1094 loop : -1.95 (0.12), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 55 TYR 0.024 0.002 TYR J 98 PHE 0.026 0.002 PHE H 71 TRP 0.014 0.002 TRP B 353 HIS 0.005 0.001 HIS M 99 Details of bonding type rmsd covalent geometry : bond 0.00387 (30994) covalent geometry : angle 0.68505 (42312) SS BOND : bond 0.00635 ( 46) SS BOND : angle 2.13751 ( 92) hydrogen bonds : bond 0.05501 ( 1201) hydrogen bonds : angle 6.11506 ( 3297) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 190 time to evaluate : 0.949 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: A 238 PHE cc_start: 0.7013 (p90) cc_final: 0.6240 (p90) REVERT: A 298 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8437 (tm-30) REVERT: A 486 VAL cc_start: -0.1878 (OUTLIER) cc_final: -0.2121 (m) REVERT: B 166 CYS cc_start: 0.5675 (OUTLIER) cc_final: 0.5243 (t) REVERT: B 200 TYR cc_start: 0.9000 (m-80) cc_final: 0.8588 (m-80) REVERT: B 224 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7552 (mp0) REVERT: B 231 ILE cc_start: 0.6833 (mm) cc_final: 0.6566 (tt) REVERT: B 354 ASN cc_start: 0.7034 (t0) cc_final: 0.6725 (t0) REVERT: B 402 ILE cc_start: 0.7015 (OUTLIER) cc_final: 0.6661 (tp) REVERT: B 436 TRP cc_start: 0.5632 (m-10) cc_final: 0.5359 (m-10) REVERT: B 577 ARG cc_start: 0.6627 (OUTLIER) cc_final: 0.6125 (ttm110) REVERT: B 712 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8990 (tt) REVERT: B 1138 TYR cc_start: 0.8301 (m-80) cc_final: 0.8027 (t80) REVERT: C 135 PHE cc_start: 0.6450 (t80) cc_final: 0.5997 (t80) REVERT: C 298 GLU cc_start: 0.8508 (tt0) cc_final: 0.8273 (tt0) REVERT: C 365 TYR cc_start: 0.8217 (m-80) cc_final: 0.7820 (m-80) REVERT: C 524 VAL cc_start: 0.8137 (p) cc_final: 0.7571 (p) REVERT: C 960 ASN cc_start: 0.8830 (t0) cc_final: 0.8425 (t0) REVERT: I 34 MET cc_start: 0.5168 (mmm) cc_final: 0.4716 (tpt) REVERT: J 4 MET cc_start: 0.1764 (mmm) cc_final: 0.1381 (mmp) REVERT: J 73 LEU cc_start: 0.2686 (tt) cc_final: 0.2430 (tp) REVERT: K 34 MET cc_start: 0.5954 (mmm) cc_final: 0.5747 (tpp) REVERT: O 29 LEU cc_start: 0.7357 (tp) cc_final: 0.7043 (pp) outliers start: 68 outliers final: 24 residues processed: 245 average time/residue: 0.1800 time to fit residues: 73.2748 Evaluate side-chains 186 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 16 GLN Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 80 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 323 optimal weight: 50.0000 chunk 124 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 154 optimal weight: 8.9990 chunk 265 optimal weight: 2.9990 chunk 309 optimal weight: 40.0000 chunk 72 optimal weight: 0.7980 chunk 255 optimal weight: 4.9990 chunk 271 optimal weight: 0.0000 chunk 213 optimal weight: 5.9990 chunk 307 optimal weight: 40.0000 overall best weight: 2.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 801 ASN B 334 ASN ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1134 ASN C 448 ASN ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** C 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN J 89 GLN ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 104 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.152515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.088694 restraints weight = 76483.781| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 4.17 r_work: 0.2975 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 31040 Z= 0.244 Angle : 0.686 12.775 42404 Z= 0.358 Chirality : 0.047 0.193 4940 Planarity : 0.005 0.068 5409 Dihedral : 6.897 61.680 5002 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.97 % Favored : 94.95 % Rotamer: Outliers : 2.57 % Allowed : 13.50 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.13), residues: 3883 helix: 1.53 (0.21), residues: 661 sheet: -0.49 (0.15), residues: 1092 loop : -1.68 (0.13), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 498 TYR 0.024 0.002 TYR C1067 PHE 0.020 0.002 PHE H 71 TRP 0.011 0.002 TRP C 64 HIS 0.005 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00586 (30994) covalent geometry : angle 0.67863 (42312) SS BOND : bond 0.00671 ( 46) SS BOND : angle 2.22634 ( 92) hydrogen bonds : bond 0.05851 ( 1201) hydrogen bonds : angle 5.87496 ( 3297) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 156 time to evaluate : 0.934 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: A 101 ILE cc_start: 0.9040 (mp) cc_final: 0.8637 (tp) REVERT: A 106 PHE cc_start: 0.6795 (m-80) cc_final: 0.6440 (m-80) REVERT: A 238 PHE cc_start: 0.7316 (p90) cc_final: 0.6303 (p90) REVERT: A 298 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8524 (tm-30) REVERT: A 486 VAL cc_start: -0.1728 (OUTLIER) cc_final: -0.1965 (m) REVERT: B 200 TYR cc_start: 0.9002 (m-80) cc_final: 0.8639 (m-80) REVERT: B 224 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7610 (mp0) REVERT: B 231 ILE cc_start: 0.6998 (mm) cc_final: 0.6681 (tt) REVERT: B 309 GLU cc_start: 0.8505 (mp0) cc_final: 0.8217 (pm20) REVERT: B 354 ASN cc_start: 0.7051 (t0) cc_final: 0.6832 (t0) REVERT: B 436 TRP cc_start: 0.5314 (m-10) cc_final: 0.5032 (m-10) REVERT: B 505 HIS cc_start: 0.8036 (OUTLIER) cc_final: 0.7805 (t-90) REVERT: B 1138 TYR cc_start: 0.8299 (m-80) cc_final: 0.7977 (t80) REVERT: C 135 PHE cc_start: 0.6514 (t80) cc_final: 0.6268 (t80) REVERT: C 369 TYR cc_start: 0.8627 (m-80) cc_final: 0.8268 (m-80) REVERT: C 960 ASN cc_start: 0.8854 (t0) cc_final: 0.8423 (t0) REVERT: H 4 MET cc_start: 0.3639 (mtt) cc_final: 0.2854 (ttt) REVERT: H 71 PHE cc_start: 0.3745 (m-10) cc_final: 0.3271 (m-10) REVERT: I 34 MET cc_start: 0.5290 (mmm) cc_final: 0.3607 (tpp) REVERT: J 4 MET cc_start: 0.2135 (mmm) cc_final: 0.1662 (mmp) REVERT: J 24 ARG cc_start: 0.7937 (ttp-170) cc_final: 0.7696 (ttp80) REVERT: J 73 LEU cc_start: 0.2562 (tt) cc_final: 0.2309 (tp) REVERT: J 94 TRP cc_start: 0.6293 (t-100) cc_final: 0.4659 (t-100) REVERT: K 95 CYS cc_start: 0.7306 (OUTLIER) cc_final: 0.5389 (p) REVERT: O 29 LEU cc_start: 0.7294 (tp) cc_final: 0.6861 (pp) outliers start: 81 outliers final: 39 residues processed: 227 average time/residue: 0.1611 time to fit residues: 62.7433 Evaluate side-chains 173 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 131 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 95 CYS Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain O residue 16 GLN Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 80 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 244 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 chunk 360 optimal weight: 20.0000 chunk 148 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 264 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 183 optimal weight: 0.0020 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1083 HIS C 448 ASN ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 99 HIS ** 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 = 0.4372 r_free = 0.4372 target = 0.154066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.091637 restraints weight = 76220.653| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 4.27 r_work: 0.3009 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 31040 Z= 0.137 Angle : 0.600 11.387 42404 Z= 0.313 Chirality : 0.044 0.215 4940 Planarity : 0.004 0.066 5409 Dihedral : 6.378 62.387 5002 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.64 % Favored : 95.31 % Rotamer: Outliers : 2.22 % Allowed : 14.90 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.13), residues: 3883 helix: 1.68 (0.21), residues: 668 sheet: -0.25 (0.15), residues: 1048 loop : -1.57 (0.13), residues: 2167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 328 TYR 0.021 0.001 TYR A1067 PHE 0.035 0.001 PHE B 342 TRP 0.015 0.001 TRP C 886 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00316 (30994) covalent geometry : angle 0.59125 (42312) SS BOND : bond 0.00562 ( 46) SS BOND : angle 2.26184 ( 92) hydrogen bonds : bond 0.04756 ( 1201) hydrogen bonds : angle 5.48607 ( 3297) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 153 time to evaluate : 1.059 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: A 106 PHE cc_start: 0.6773 (m-80) cc_final: 0.6487 (m-80) REVERT: A 238 PHE cc_start: 0.7229 (p90) cc_final: 0.6602 (p90) REVERT: A 298 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8502 (tm-30) REVERT: A 486 VAL cc_start: -0.1562 (OUTLIER) cc_final: -0.1787 (m) REVERT: B 200 TYR cc_start: 0.9005 (m-80) cc_final: 0.8665 (m-80) REVERT: B 224 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7558 (mp0) REVERT: B 231 ILE cc_start: 0.6932 (mm) cc_final: 0.6582 (tt) REVERT: B 309 GLU cc_start: 0.8515 (mp0) cc_final: 0.8167 (pm20) REVERT: B 342 PHE cc_start: 0.8733 (m-80) cc_final: 0.8111 (m-80) REVERT: B 354 ASN cc_start: 0.6951 (t0) cc_final: 0.6744 (t0) REVERT: B 505 HIS cc_start: 0.7973 (OUTLIER) cc_final: 0.7755 (t-90) REVERT: B 752 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9292 (tt) REVERT: B 1138 TYR cc_start: 0.8349 (m-80) cc_final: 0.8004 (t80) REVERT: C 135 PHE cc_start: 0.6345 (t80) cc_final: 0.6036 (t80) REVERT: C 369 TYR cc_start: 0.8645 (m-80) cc_final: 0.8163 (m-80) REVERT: C 451 TYR cc_start: 0.7696 (m-80) cc_final: 0.7139 (m-80) REVERT: C 960 ASN cc_start: 0.8813 (t0) cc_final: 0.8409 (t0) REVERT: I 34 MET cc_start: 0.5121 (mmm) cc_final: 0.3756 (tpp) REVERT: I 51 MET cc_start: 0.4385 (tmm) cc_final: 0.4166 (tmm) REVERT: I 80 LEU cc_start: 0.1436 (OUTLIER) cc_final: 0.0898 (tp) REVERT: I 82 MET cc_start: -0.0488 (mpp) cc_final: -0.3297 (ttp) REVERT: J 90 GLN cc_start: 0.3874 (pp30) cc_final: 0.3527 (pp30) REVERT: J 94 TRP cc_start: 0.6208 (t-100) cc_final: 0.4654 (t-100) REVERT: M 52 LEU cc_start: -0.4736 (OUTLIER) cc_final: -0.4977 (mt) REVERT: O 29 LEU cc_start: 0.7234 (tp) cc_final: 0.6911 (pp) outliers start: 70 outliers final: 35 residues processed: 213 average time/residue: 0.1754 time to fit residues: 63.3039 Evaluate side-chains 174 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain O residue 16 GLN Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 80 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 171 optimal weight: 2.9990 chunk 37 optimal weight: 30.0000 chunk 104 optimal weight: 0.7980 chunk 177 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 312 optimal weight: 50.0000 chunk 249 optimal weight: 5.9990 chunk 370 optimal weight: 8.9990 chunk 384 optimal weight: 40.0000 chunk 234 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN B 282 ASN ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 ASN ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 110 GLN N 32 ASN O 99 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.151740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.088316 restraints weight = 76255.649| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 4.36 r_work: 0.2947 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 31040 Z= 0.264 Angle : 0.676 10.711 42404 Z= 0.350 Chirality : 0.047 0.249 4940 Planarity : 0.005 0.060 5409 Dihedral : 6.473 62.993 5000 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.28 % Favored : 94.67 % Rotamer: Outliers : 3.11 % Allowed : 15.89 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.13), residues: 3883 helix: 1.38 (0.20), residues: 673 sheet: -0.36 (0.15), residues: 1109 loop : -1.56 (0.13), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 346 TYR 0.024 0.002 TYR C1067 PHE 0.025 0.002 PHE B 342 TRP 0.015 0.001 TRP B 436 HIS 0.005 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00636 (30994) covalent geometry : angle 0.66585 (42312) SS BOND : bond 0.00596 ( 46) SS BOND : angle 2.56088 ( 92) hydrogen bonds : bond 0.05763 ( 1201) hydrogen bonds : angle 5.68331 ( 3297) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 136 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.6796 (m-80) cc_final: 0.6517 (m-80) REVERT: A 238 PHE cc_start: 0.7385 (p90) cc_final: 0.6708 (p90) REVERT: A 298 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8563 (tm-30) REVERT: A 486 VAL cc_start: -0.1894 (OUTLIER) cc_final: -0.2131 (m) REVERT: B 200 TYR cc_start: 0.9007 (m-80) cc_final: 0.8713 (m-80) REVERT: B 224 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7587 (mp0) REVERT: B 231 ILE cc_start: 0.7123 (mm) cc_final: 0.6730 (tt) REVERT: B 309 GLU cc_start: 0.8646 (mp0) cc_final: 0.8321 (pm20) REVERT: B 342 PHE cc_start: 0.8703 (m-80) cc_final: 0.8305 (m-80) REVERT: B 505 HIS cc_start: 0.8021 (OUTLIER) cc_final: 0.7810 (t-90) REVERT: B 752 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9291 (tt) REVERT: B 1138 TYR cc_start: 0.8362 (m-80) cc_final: 0.8029 (t80) REVERT: C 369 TYR cc_start: 0.8810 (m-80) cc_final: 0.8520 (m-80) REVERT: C 451 TYR cc_start: 0.7803 (m-80) cc_final: 0.7394 (m-80) REVERT: C 960 ASN cc_start: 0.8883 (t0) cc_final: 0.8445 (t0) REVERT: I 34 MET cc_start: 0.4884 (mmm) cc_final: 0.3478 (tpp) REVERT: I 51 MET cc_start: 0.4229 (tmm) cc_final: 0.4019 (tmm) REVERT: I 80 LEU cc_start: 0.1607 (OUTLIER) cc_final: 0.1070 (tp) REVERT: I 82 MET cc_start: -0.1044 (mpp) cc_final: -0.3596 (ttp) REVERT: J 94 TRP cc_start: 0.6226 (t-100) cc_final: 0.4847 (t-100) REVERT: K 108 TRP cc_start: 0.3983 (m-90) cc_final: 0.3781 (m-90) REVERT: M 52 LEU cc_start: -0.4905 (OUTLIER) cc_final: -0.5110 (mt) REVERT: O 29 LEU cc_start: 0.7122 (tp) cc_final: 0.6704 (pp) outliers start: 98 outliers final: 66 residues processed: 223 average time/residue: 0.1601 time to fit residues: 61.9685 Evaluate side-chains 195 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 124 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain O residue 16 GLN Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 80 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 99 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 239 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 253 optimal weight: 0.8980 chunk 212 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 28 optimal weight: 30.0000 chunk 291 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 388 ASN ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 110 GLN L 16 GLN ** O 79 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 = 0.4335 r_free = 0.4335 target = 0.151550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.087370 restraints weight = 75772.434| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 4.40 r_work: 0.2934 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31040 Z= 0.188 Angle : 0.617 10.350 42404 Z= 0.320 Chirality : 0.045 0.341 4940 Planarity : 0.004 0.058 5409 Dihedral : 6.229 63.235 4999 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.97 % Favored : 94.98 % Rotamer: Outliers : 3.15 % Allowed : 16.56 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.13), residues: 3883 helix: 1.49 (0.21), residues: 673 sheet: -0.28 (0.15), residues: 1088 loop : -1.46 (0.13), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 346 TYR 0.022 0.001 TYR A1067 PHE 0.026 0.001 PHE B 342 TRP 0.015 0.001 TRP A 436 HIS 0.006 0.001 HIS O 99 Details of bonding type rmsd covalent geometry : bond 0.00449 (30994) covalent geometry : angle 0.60779 (42312) SS BOND : bond 0.00657 ( 46) SS BOND : angle 2.36207 ( 92) hydrogen bonds : bond 0.05145 ( 1201) hydrogen bonds : angle 5.49306 ( 3297) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 132 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.6750 (m-80) cc_final: 0.6521 (m-80) REVERT: A 238 PHE cc_start: 0.7297 (p90) cc_final: 0.6622 (p90) REVERT: A 298 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8530 (tm-30) REVERT: A 486 VAL cc_start: -0.1749 (OUTLIER) cc_final: -0.1974 (m) REVERT: A 720 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.9009 (mp) REVERT: B 200 TYR cc_start: 0.8991 (m-80) cc_final: 0.8706 (m-80) REVERT: B 224 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7544 (mp0) REVERT: B 231 ILE cc_start: 0.7070 (mm) cc_final: 0.6689 (tt) REVERT: B 309 GLU cc_start: 0.8659 (mp0) cc_final: 0.8286 (pm20) REVERT: B 342 PHE cc_start: 0.8757 (m-80) cc_final: 0.8387 (m-80) REVERT: B 752 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9290 (tt) REVERT: B 981 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8914 (pp) REVERT: B 1138 TYR cc_start: 0.8384 (m-80) cc_final: 0.7989 (t80) REVERT: C 369 TYR cc_start: 0.8846 (m-80) cc_final: 0.8424 (m-80) REVERT: C 960 ASN cc_start: 0.8849 (t0) cc_final: 0.8409 (t0) REVERT: I 34 MET cc_start: 0.4951 (mmm) cc_final: 0.3652 (tpp) REVERT: J 94 TRP cc_start: 0.6222 (t-100) cc_final: 0.4792 (t-100) REVERT: K 34 MET cc_start: 0.5900 (tpp) cc_final: 0.5400 (mmt) REVERT: M 52 LEU cc_start: -0.4870 (OUTLIER) cc_final: -0.5088 (mt) REVERT: O 29 LEU cc_start: 0.7084 (tp) cc_final: 0.6768 (pp) REVERT: O 87 MET cc_start: -0.0999 (tpp) cc_final: -0.1300 (tpt) outliers start: 99 outliers final: 65 residues processed: 223 average time/residue: 0.1572 time to fit residues: 61.3429 Evaluate side-chains 195 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 125 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 345 THR 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 720 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain K residue 110 GLN Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain O residue 16 GLN Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 80 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 351 optimal weight: 50.0000 chunk 129 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 368 optimal weight: 0.3980 chunk 133 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 346 optimal weight: 50.0000 chunk 91 optimal weight: 0.9990 chunk 384 optimal weight: 30.0000 chunk 304 optimal weight: 30.0000 chunk 186 optimal weight: 0.8980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 ASN C 448 ASN ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.153096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.089006 restraints weight = 76145.566| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.95 r_work: 0.2980 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 31040 Z= 0.196 Angle : 0.619 11.524 42404 Z= 0.319 Chirality : 0.045 0.284 4940 Planarity : 0.004 0.054 5409 Dihedral : 6.151 62.884 4999 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.51 % Favored : 94.46 % Rotamer: Outliers : 3.15 % Allowed : 16.84 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.13), residues: 3883 helix: 1.47 (0.20), residues: 678 sheet: -0.29 (0.16), residues: 1035 loop : -1.41 (0.13), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 346 TYR 0.022 0.001 TYR A1067 PHE 0.029 0.001 PHE C 497 TRP 0.023 0.001 TRP O 38 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00470 (30994) covalent geometry : angle 0.61202 (42312) SS BOND : bond 0.00527 ( 46) SS BOND : angle 2.04847 ( 92) hydrogen bonds : bond 0.05156 ( 1201) hydrogen bonds : angle 5.44085 ( 3297) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 137 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.6745 (m-80) cc_final: 0.6537 (m-80) REVERT: A 238 PHE cc_start: 0.7339 (p90) cc_final: 0.6704 (p90) REVERT: A 298 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8548 (tm-30) REVERT: B 200 TYR cc_start: 0.8969 (m-80) cc_final: 0.8687 (m-80) REVERT: B 224 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7563 (mp0) REVERT: B 231 ILE cc_start: 0.7079 (mm) cc_final: 0.6694 (tt) REVERT: B 309 GLU cc_start: 0.8636 (mp0) cc_final: 0.8262 (pm20) REVERT: B 342 PHE cc_start: 0.8863 (m-80) cc_final: 0.8567 (m-80) REVERT: B 752 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9284 (tt) REVERT: B 981 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8923 (pp) REVERT: C 140 PHE cc_start: 0.7593 (p90) cc_final: 0.7154 (p90) REVERT: C 369 TYR cc_start: 0.8932 (m-80) cc_final: 0.8723 (m-80) REVERT: C 960 ASN cc_start: 0.8859 (t0) cc_final: 0.8417 (t0) REVERT: I 82 MET cc_start: -0.1041 (mpp) cc_final: -0.3229 (ttp) REVERT: K 108 TRP cc_start: 0.4350 (m-90) cc_final: 0.3916 (m-90) REVERT: M 52 LEU cc_start: -0.4881 (OUTLIER) cc_final: -0.5106 (mt) REVERT: O 29 LEU cc_start: 0.6966 (tp) cc_final: 0.6505 (pp) outliers start: 99 outliers final: 74 residues processed: 227 average time/residue: 0.1651 time to fit residues: 64.0873 Evaluate side-chains 206 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 129 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain O residue 16 GLN Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 80 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 227 optimal weight: 0.8980 chunk 300 optimal weight: 1.9990 chunk 374 optimal weight: 40.0000 chunk 355 optimal weight: 40.0000 chunk 133 optimal weight: 5.9990 chunk 253 optimal weight: 0.8980 chunk 312 optimal weight: 40.0000 chunk 204 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 159 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 ASN ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 13 GLN ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 GLN ** 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 = 0.4371 r_free = 0.4371 target = 0.155077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.092120 restraints weight = 75556.428| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 4.14 r_work: 0.3018 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 31040 Z= 0.129 Angle : 0.586 12.917 42404 Z= 0.303 Chirality : 0.044 0.264 4940 Planarity : 0.004 0.054 5409 Dihedral : 5.826 61.805 4999 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.84 % Favored : 95.13 % Rotamer: Outliers : 2.41 % Allowed : 17.67 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.13), residues: 3883 helix: 1.65 (0.21), residues: 675 sheet: -0.14 (0.16), residues: 1032 loop : -1.31 (0.13), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 346 TYR 0.034 0.001 TYR C 449 PHE 0.016 0.001 PHE B 342 TRP 0.017 0.001 TRP O 38 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00298 (30994) covalent geometry : angle 0.57929 (42312) SS BOND : bond 0.00495 ( 46) SS BOND : angle 2.03402 ( 92) hydrogen bonds : bond 0.04465 ( 1201) hydrogen bonds : angle 5.21842 ( 3297) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 142 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7252 (p90) cc_final: 0.6671 (p90) REVERT: A 298 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8518 (tm-30) REVERT: B 200 TYR cc_start: 0.8942 (m-80) cc_final: 0.8661 (m-80) REVERT: B 231 ILE cc_start: 0.7134 (mm) cc_final: 0.6744 (tt) REVERT: B 309 GLU cc_start: 0.8636 (mp0) cc_final: 0.8244 (pm20) REVERT: B 342 PHE cc_start: 0.8862 (m-80) cc_final: 0.8247 (m-80) REVERT: B 752 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9275 (tt) REVERT: B 791 THR cc_start: 0.8443 (OUTLIER) cc_final: 0.8222 (p) REVERT: B 981 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8833 (pp) REVERT: C 140 PHE cc_start: 0.7490 (p90) cc_final: 0.7099 (p90) REVERT: C 346 ARG cc_start: 0.7571 (tmt170) cc_final: 0.6678 (tpt90) REVERT: C 369 TYR cc_start: 0.8886 (m-80) cc_final: 0.8449 (m-80) REVERT: C 960 ASN cc_start: 0.8818 (t0) cc_final: 0.8400 (t0) REVERT: I 34 MET cc_start: 0.4466 (mmm) cc_final: 0.2280 (tpp) REVERT: I 82 MET cc_start: -0.0832 (mpp) cc_final: -0.3034 (ttp) REVERT: J 94 TRP cc_start: 0.6164 (t-100) cc_final: 0.4825 (t-100) REVERT: K 108 TRP cc_start: 0.4197 (m-90) cc_final: 0.3851 (m-90) REVERT: M 52 LEU cc_start: -0.4841 (OUTLIER) cc_final: -0.5089 (mt) REVERT: O 29 LEU cc_start: 0.7009 (tp) cc_final: 0.6640 (pp) REVERT: O 87 MET cc_start: -0.0737 (tpp) cc_final: -0.1023 (tpt) outliers start: 76 outliers final: 55 residues processed: 214 average time/residue: 0.1630 time to fit residues: 59.3112 Evaluate side-chains 189 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 130 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain O residue 16 GLN Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 80 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 184 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 282 optimal weight: 2.9990 chunk 231 optimal weight: 7.9990 chunk 383 optimal weight: 20.0000 chunk 215 optimal weight: 0.0070 chunk 372 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 272 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 448 ASN ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.153276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.089951 restraints weight = 75853.599| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 4.12 r_work: 0.2996 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 31040 Z= 0.193 Angle : 0.629 13.464 42404 Z= 0.324 Chirality : 0.045 0.268 4940 Planarity : 0.004 0.051 5409 Dihedral : 5.887 62.074 4995 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.35 % Allowed : 18.02 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.13), residues: 3883 helix: 1.59 (0.21), residues: 668 sheet: -0.10 (0.16), residues: 1038 loop : -1.33 (0.13), residues: 2177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 983 TYR 0.023 0.001 TYR A 170 PHE 0.018 0.001 PHE B 342 TRP 0.013 0.001 TRP A 436 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00462 (30994) covalent geometry : angle 0.62142 (42312) SS BOND : bond 0.00493 ( 46) SS BOND : angle 2.21990 ( 92) hydrogen bonds : bond 0.05020 ( 1201) hydrogen bonds : angle 5.37249 ( 3297) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 137 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7347 (p90) cc_final: 0.6774 (p90) REVERT: A 298 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8564 (tm-30) REVERT: B 200 TYR cc_start: 0.8945 (m-80) cc_final: 0.8667 (m-80) REVERT: B 231 ILE cc_start: 0.7204 (mm) cc_final: 0.6800 (tt) REVERT: B 309 GLU cc_start: 0.8697 (mp0) cc_final: 0.8319 (pm20) REVERT: B 752 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9291 (tt) REVERT: B 981 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8816 (pp) REVERT: C 140 PHE cc_start: 0.7530 (p90) cc_final: 0.7168 (p90) REVERT: C 369 TYR cc_start: 0.8961 (m-80) cc_final: 0.8512 (m-80) REVERT: C 960 ASN cc_start: 0.8847 (t0) cc_final: 0.8412 (t0) REVERT: H 4 MET cc_start: 0.3685 (ttt) cc_final: 0.3456 (ttt) REVERT: I 34 MET cc_start: 0.4568 (mmm) cc_final: 0.2667 (tpt) REVERT: I 82 MET cc_start: -0.1511 (mpp) cc_final: -0.3561 (ttp) REVERT: K 108 TRP cc_start: 0.4245 (m-90) cc_final: 0.3870 (m-90) REVERT: O 29 LEU cc_start: 0.6801 (tp) cc_final: 0.6297 (pp) outliers start: 74 outliers final: 65 residues processed: 206 average time/residue: 0.1570 time to fit residues: 55.9843 Evaluate side-chains 196 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 129 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain O residue 16 GLN Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 80 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 344 optimal weight: 4.9990 chunk 223 optimal weight: 0.5980 chunk 113 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 294 optimal weight: 1.9990 chunk 313 optimal weight: 8.9990 chunk 214 optimal weight: 7.9990 chunk 243 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1011 GLN ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.151798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.088629 restraints weight = 75447.743| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 4.28 r_work: 0.2956 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 31040 Z= 0.244 Angle : 0.658 12.204 42404 Z= 0.340 Chirality : 0.046 0.259 4940 Planarity : 0.004 0.053 5409 Dihedral : 6.093 62.330 4995 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.45 % Allowed : 17.89 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.13), residues: 3883 helix: 1.39 (0.20), residues: 675 sheet: -0.14 (0.16), residues: 1026 loop : -1.38 (0.13), residues: 2182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 983 TYR 0.034 0.002 TYR C 449 PHE 0.024 0.002 PHE B 342 TRP 0.022 0.001 TRP A 436 HIS 0.004 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00588 (30994) covalent geometry : angle 0.65129 (42312) SS BOND : bond 0.00578 ( 46) SS BOND : angle 2.17595 ( 92) hydrogen bonds : bond 0.05501 ( 1201) hydrogen bonds : angle 5.46122 ( 3297) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 135 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7462 (p90) cc_final: 0.6878 (p90) REVERT: A 298 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8587 (tm-30) REVERT: B 129 LYS cc_start: 0.7224 (pptt) cc_final: 0.7015 (pptt) REVERT: B 200 TYR cc_start: 0.8933 (m-80) cc_final: 0.8655 (m-80) REVERT: B 231 ILE cc_start: 0.7253 (mm) cc_final: 0.6870 (tt) REVERT: B 309 GLU cc_start: 0.8721 (mp0) cc_final: 0.8371 (pm20) REVERT: B 338 PHE cc_start: 0.9142 (t80) cc_final: 0.8841 (t80) REVERT: B 752 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9287 (tt) REVERT: B 981 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8851 (pp) REVERT: C 140 PHE cc_start: 0.7674 (p90) cc_final: 0.7293 (p90) REVERT: C 346 ARG cc_start: 0.7674 (tmt170) cc_final: 0.6804 (tpt90) REVERT: C 369 TYR cc_start: 0.8980 (m-80) cc_final: 0.8572 (m-80) REVERT: C 497 PHE cc_start: 0.6603 (m-80) cc_final: 0.6386 (m-80) REVERT: C 960 ASN cc_start: 0.8888 (t0) cc_final: 0.8452 (t0) REVERT: K 108 TRP cc_start: 0.4183 (m-90) cc_final: 0.3813 (m-90) REVERT: O 29 LEU cc_start: 0.6857 (tp) cc_final: 0.6358 (pp) outliers start: 77 outliers final: 71 residues processed: 202 average time/residue: 0.1629 time to fit residues: 56.3167 Evaluate side-chains 207 residues out of total 3417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 134 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain O residue 16 GLN Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 80 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 270 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 326 optimal weight: 50.0000 chunk 18 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 chunk 209 optimal weight: 5.9990 chunk 174 optimal weight: 0.0980 chunk 57 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 213 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 218 GLN C 448 ASN ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.154449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.091854 restraints weight = 77255.498| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 4.29 r_work: 0.3018 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31040 Z= 0.127 Angle : 0.589 11.058 42404 Z= 0.303 Chirality : 0.044 0.244 4940 Planarity : 0.004 0.052 5409 Dihedral : 5.689 61.660 4995 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.26 % Allowed : 18.27 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.13), residues: 3883 helix: 1.69 (0.21), residues: 672 sheet: -0.03 (0.16), residues: 1021 loop : -1.30 (0.13), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 983 TYR 0.022 0.001 TYR A 170 PHE 0.028 0.001 PHE B 342 TRP 0.019 0.001 TRP A 436 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00292 (30994) covalent geometry : angle 0.58256 (42312) SS BOND : bond 0.00518 ( 46) SS BOND : angle 1.95949 ( 92) hydrogen bonds : bond 0.04510 ( 1201) hydrogen bonds : angle 5.17049 ( 3297) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11474.28 seconds wall clock time: 195 minutes 42.85 seconds (11742.85 seconds total)