Starting phenix.real_space_refine on Mon Aug 25 14:15:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvn_34133/08_2025/7yvn_34133.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvn_34133/08_2025/7yvn_34133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yvn_34133/08_2025/7yvn_34133.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvn_34133/08_2025/7yvn_34133.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yvn_34133/08_2025/7yvn_34133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvn_34133/08_2025/7yvn_34133.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 18210 2.51 5 N 4695 2.21 5 O 5469 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 177 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28503 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 7649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7649 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 364 Unresolved non-hydrogen angles: 450 Unresolved non-hydrogen dihedrals: 296 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASP:plan': 13, 'GLN:plan1': 9, 'ASN:plan1': 9, 'GLU:plan': 11, 'PHE:plan': 3, 'ARG:plan': 9, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 237 Chain: "B" Number of atoms: 7643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7643 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASP:plan': 13, 'GLN:plan1': 9, 'ASN:plan1': 9, 'GLU:plan': 11, 'PHE:plan': 3, 'ARG:plan': 10, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 242 Chain: "A" Number of atoms: 7634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7634 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 470 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 13, 'GLN:plan1': 9, 'ASN:plan1': 9, 'GLU:plan': 11, 'PHE:plan': 4, 'ARG:plan': 10, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 248 Chain: "H" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 821 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 870 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "K" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 821 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 870 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "N" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 821 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "O" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 870 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 4.93, per 1000 atoms: 0.17 Number of scatterers: 28503 At special positions: 0 Unit cell: (145.14, 149.24, 225.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 5469 8.00 N 4695 7.00 C 18210 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.05 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.01 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 95 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 95 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 928.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6972 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 52 sheets defined 21.3% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 344 Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.876A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.686A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.532A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.634A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.682A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.967A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.097A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.934A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 403 through 410 removed outlier: 4.852A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.585A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.626A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.867A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.956A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.078A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.845A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 344 Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.888A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.650A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.647A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.782A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.015A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.139A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.791A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.134A pdb=" N SER H 83 " --> pdb=" O SER H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 75 Processing helix chain 'I' and resid 86 through 90 removed outlier: 4.050A pdb=" N THR I 90 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 4.060A pdb=" N SER K 83 " --> pdb=" O SER K 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 75 Processing helix chain 'L' and resid 86 through 90 removed outlier: 3.982A pdb=" N THR L 90 " --> pdb=" O ALA L 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.026A pdb=" N SER N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 72 through 75 Processing helix chain 'O' and resid 86 through 90 removed outlier: 3.952A pdb=" N THR O 90 " --> pdb=" O ALA O 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.814A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 3.611A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.471A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.169A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.320A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.933A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.949A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.125A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 702 through 703 Processing sheet with id=AB2, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.100A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C1052 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.100A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.465A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 788 through 789 removed outlier: 6.150A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.455A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.568A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.210A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.550A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.877A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.144A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.646A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 3.852A pdb=" N CYS B 525 " --> pdb=" O CYS B 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.940A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.133A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.133A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.441A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 788 through 789 removed outlier: 6.221A pdb=" N ILE B 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.440A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.527A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.609A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.830A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.157A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.854A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AD9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.988A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.091A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.091A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.565A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.505A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.815A pdb=" N GLU H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.772A pdb=" N LEU H 11 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL H 85 " --> pdb=" O GLN H 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 3 through 7 removed outlier: 4.075A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL I 5 " --> pdb=" O ALA I 23 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 10 through 12 removed outlier: 5.808A pdb=" N GLY I 10 " --> pdb=" O THR I 115 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR I 112 " --> pdb=" O TYR I 93 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 5 through 7 removed outlier: 3.782A pdb=" N GLU K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.408A pdb=" N LEU K 11 " --> pdb=" O GLU K 107 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 3 through 7 removed outlier: 4.029A pdb=" N GLN L 3 " --> pdb=" O SER L 25 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER L 25 " --> pdb=" O GLN L 3 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 11 through 12 removed outlier: 3.593A pdb=" N VAL L 12 " --> pdb=" O THR L 115 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N MET L 34 " --> pdb=" O VAL L 50 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL L 50 " --> pdb=" O MET L 34 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.587A pdb=" N PHE N 71 " --> pdb=" O CYS N 23 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.334A pdb=" N LEU N 11 " --> pdb=" O GLU N 107 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AF7, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.450A pdb=" N GLY O 10 " --> pdb=" O THR O 115 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) 1145 hydrogen bonds defined for protein. 3075 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.44 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9150 1.35 - 1.49: 8156 1.49 - 1.62: 11688 1.62 - 1.76: 14 1.76 - 1.90: 151 Bond restraints: 29159 Sorted by residual: bond pdb=" C PHE B 329 " pdb=" N PRO B 330 " ideal model delta sigma weight residual 1.334 1.416 -0.082 2.34e-02 1.83e+03 1.22e+01 bond pdb=" CB CYS B 749 " pdb=" SG CYS B 749 " ideal model delta sigma weight residual 1.808 1.711 0.097 3.30e-02 9.18e+02 8.64e+00 bond pdb=" C PHE A 329 " pdb=" N PRO A 330 " ideal model delta sigma weight residual 1.334 1.401 -0.067 2.34e-02 1.83e+03 8.15e+00 bond pdb=" CB CYS B 743 " pdb=" SG CYS B 743 " ideal model delta sigma weight residual 1.808 1.716 0.092 3.30e-02 9.18e+02 7.79e+00 bond pdb=" CB CYS B 649 " pdb=" SG CYS B 649 " ideal model delta sigma weight residual 1.808 1.718 0.090 3.30e-02 9.18e+02 7.50e+00 ... (remaining 29154 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 39239 3.19 - 6.38: 507 6.38 - 9.57: 56 9.57 - 12.76: 18 12.76 - 15.95: 8 Bond angle restraints: 39828 Sorted by residual: angle pdb=" CA CYS A 432 " pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 114.40 130.35 -15.95 2.30e+00 1.89e-01 4.81e+01 angle pdb=" CA CYS C 432 " pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 114.40 130.27 -15.87 2.30e+00 1.89e-01 4.76e+01 angle pdb=" N GLY C 526 " pdb=" CA GLY C 526 " pdb=" C GLY C 526 " ideal model delta sigma weight residual 112.34 125.56 -13.22 2.04e+00 2.40e-01 4.20e+01 angle pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " ideal model delta sigma weight residual 114.40 128.20 -13.80 2.30e+00 1.89e-01 3.60e+01 angle pdb=" CA TYR H 49 " pdb=" CB TYR H 49 " pdb=" CG TYR H 49 " ideal model delta sigma weight residual 113.90 124.41 -10.51 1.80e+00 3.09e-01 3.41e+01 ... (remaining 39823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 16121 17.53 - 35.06: 1219 35.06 - 52.59: 219 52.59 - 70.12: 73 70.12 - 87.65: 27 Dihedral angle restraints: 17659 sinusoidal: 6799 harmonic: 10860 Sorted by residual: dihedral pdb=" CA PRO N 95 " pdb=" C PRO N 95 " pdb=" N PRO N 96 " pdb=" CA PRO N 96 " ideal model delta harmonic sigma weight residual -180.00 -126.72 -53.28 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA PRO H 95 " pdb=" C PRO H 95 " pdb=" N PRO H 96 " pdb=" CA PRO H 96 " ideal model delta harmonic sigma weight residual -180.00 -130.73 -49.27 0 5.00e+00 4.00e-02 9.71e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 5.62 87.38 1 1.00e+01 1.00e-02 9.16e+01 ... (remaining 17656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3904 0.077 - 0.154: 713 0.154 - 0.231: 46 0.231 - 0.308: 7 0.308 - 0.385: 6 Chirality restraints: 4676 Sorted by residual: chirality pdb=" CA CYS A 432 " pdb=" N CYS A 432 " pdb=" C CYS A 432 " pdb=" CB CYS A 432 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CA PRO A 330 " pdb=" N PRO A 330 " pdb=" C PRO A 330 " pdb=" CB PRO A 330 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA CYS B 432 " pdb=" N CYS B 432 " pdb=" C CYS B 432 " pdb=" CB CYS B 432 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.35e+00 ... (remaining 4673 not shown) Planarity restraints: 5100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP H 94 " -0.062 5.00e-02 4.00e+02 9.38e-02 1.41e+01 pdb=" N PRO H 95 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO H 95 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO H 95 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP K 94 " 0.062 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO K 95 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO K 95 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO K 95 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO K 95 " 0.051 5.00e-02 4.00e+02 7.86e-02 9.88e+00 pdb=" N PRO K 96 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO K 96 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO K 96 " 0.043 5.00e-02 4.00e+02 ... (remaining 5097 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 2080 2.72 - 3.27: 28529 3.27 - 3.81: 43994 3.81 - 4.36: 51979 4.36 - 4.90: 91411 Nonbonded interactions: 217993 Sorted by model distance: nonbonded pdb=" O LEU B 455 " pdb=" OH TYR I 107 " model vdw 2.179 3.040 nonbonded pdb=" NH2 ARG C 454 " pdb=" O ASP C 467 " model vdw 2.192 3.120 nonbonded pdb=" OH TYR H 49 " pdb=" O VAL I 5 " model vdw 2.203 3.040 nonbonded pdb=" OG SER H 83 " pdb=" OE1 GLU H 107 " model vdw 2.205 3.040 nonbonded pdb=" NH1 ARG C 34 " pdb=" O GLY C 219 " model vdw 2.211 3.120 ... (remaining 217988 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 27 through 328 or (resid 329 and (name N or name CA or nam \ e C or name O or name CB )) or resid 330 through 532 or (resid 533 and (name N o \ r name CA or name C or name O or name CB )) or resid 534 through 1311)) selection = (chain 'C' and (resid 27 through 327 or (resid 328 through 329 and (name N or na \ me CA or name C or name O or name CB )) or resid 330 through 532 or (resid 533 a \ nd (name N or name CA or name C or name O or name CB )) or resid 534 through 131 \ 1)) } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.260 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 29204 Z= 0.297 Angle : 1.006 15.951 39918 Z= 0.542 Chirality : 0.058 0.385 4676 Planarity : 0.005 0.094 5100 Dihedral : 13.109 87.648 10552 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.62 % Allowed : 5.28 % Favored : 94.10 % Rotamer: Outliers : 1.06 % Allowed : 7.27 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.39 (0.12), residues: 3693 helix: 0.20 (0.20), residues: 649 sheet: -1.20 (0.14), residues: 997 loop : -2.48 (0.12), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 61 TYR 0.051 0.002 TYR H 49 PHE 0.029 0.003 PHE B 456 TRP 0.036 0.003 TRP N 94 HIS 0.011 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00705 (29159) covalent geometry : angle 0.98566 (39828) SS BOND : bond 0.00881 ( 45) SS BOND : angle 4.38168 ( 90) hydrogen bonds : bond 0.21089 ( 1130) hydrogen bonds : angle 7.96083 ( 3075) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 306 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 200 TYR cc_start: 0.8625 (m-80) cc_final: 0.8375 (m-80) REVERT: C 241 LEU cc_start: 0.7744 (pp) cc_final: 0.6926 (mp) REVERT: C 776 LYS cc_start: 0.8763 (ttpp) cc_final: 0.8434 (ttpp) REVERT: C 950 ASP cc_start: 0.7986 (m-30) cc_final: 0.7784 (m-30) REVERT: B 258 TRP cc_start: 0.5537 (t-100) cc_final: 0.4423 (m-90) REVERT: B 497 PHE cc_start: 0.4025 (m-80) cc_final: 0.3478 (m-80) REVERT: I 78 LEU cc_start: 0.4378 (mm) cc_final: 0.3953 (mt) REVERT: K 32 ASP cc_start: 0.7633 (m-30) cc_final: 0.7194 (p0) REVERT: K 38 GLN cc_start: 0.6756 (tt0) cc_final: 0.6454 (tt0) REVERT: K 92 ASN cc_start: 0.5695 (p0) cc_final: 0.5441 (t0) REVERT: L 85 LEU cc_start: 0.2907 (OUTLIER) cc_final: 0.1988 (tp) REVERT: N 37 GLN cc_start: 0.8258 (tt0) cc_final: 0.7988 (tm-30) REVERT: N 99 THR cc_start: 0.7704 (m) cc_final: 0.7487 (m) REVERT: O 3 GLN cc_start: 0.7408 (tp-100) cc_final: 0.7126 (pp30) REVERT: O 36 TRP cc_start: 0.4306 (m100) cc_final: 0.3656 (m100) REVERT: O 45 LEU cc_start: 0.7651 (tp) cc_final: 0.7424 (tp) REVERT: O 108 TRP cc_start: 0.6578 (m100) cc_final: 0.5882 (m100) outliers start: 31 outliers final: 6 residues processed: 333 average time/residue: 0.1764 time to fit residues: 90.8671 Evaluate side-chains 193 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 186 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 85 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 50.0000 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 GLN C 417 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN C 540 ASN C 657 ASN C 762 GLN C1074 ASN C1134 ASN B 360 ASN B 493 GLN B 505 HIS B 506 GLN B 657 ASN B 762 GLN A 354 ASN A 417 ASN A 493 GLN A 506 GLN A 657 ASN A 762 GLN A 953 ASN A 955 ASN A1005 GLN A1074 ASN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN N 92 ASN N 102 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.147631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.091330 restraints weight = 67496.149| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 4.97 r_work: 0.3093 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 29204 Z= 0.179 Angle : 0.692 10.460 39918 Z= 0.360 Chirality : 0.047 0.241 4676 Planarity : 0.005 0.077 5100 Dihedral : 6.493 57.972 4758 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.33 % Favored : 95.56 % Rotamer: Outliers : 2.30 % Allowed : 11.01 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.13), residues: 3693 helix: 1.52 (0.21), residues: 660 sheet: -0.70 (0.15), residues: 953 loop : -1.84 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 61 TYR 0.018 0.002 TYR C 449 PHE 0.025 0.002 PHE A 970 TRP 0.021 0.002 TRP K 94 HIS 0.005 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00422 (29159) covalent geometry : angle 0.68361 (39828) SS BOND : bond 0.00568 ( 45) SS BOND : angle 2.41335 ( 90) hydrogen bonds : bond 0.05466 ( 1130) hydrogen bonds : angle 6.03539 ( 3075) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 206 time to evaluate : 0.928 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: C 200 TYR cc_start: 0.8923 (m-80) cc_final: 0.8612 (m-80) REVERT: C 241 LEU cc_start: 0.8310 (pp) cc_final: 0.7639 (mp) REVERT: C 712 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8859 (tt) REVERT: C 755 GLN cc_start: 0.8605 (mp10) cc_final: 0.8282 (pm20) REVERT: B 237 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.6659 (ptm-80) REVERT: B 497 PHE cc_start: 0.4538 (m-80) cc_final: 0.4001 (m-80) REVERT: B 740 MET cc_start: 0.8221 (tpp) cc_final: 0.7985 (tpp) REVERT: A 135 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7126 (m-80) REVERT: A 578 ASP cc_start: 0.4689 (m-30) cc_final: 0.3949 (t0) REVERT: A 856 ASN cc_start: 0.8847 (m-40) cc_final: 0.8114 (t0) REVERT: A 868 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8216 (tp30) REVERT: K 92 ASN cc_start: 0.6934 (p0) cc_final: 0.6631 (t0) REVERT: L 82 MET cc_start: 0.5833 (mtm) cc_final: 0.5552 (ptm) REVERT: L 85 LEU cc_start: 0.4105 (OUTLIER) cc_final: 0.2947 (tp) REVERT: N 37 GLN cc_start: 0.8221 (tt0) cc_final: 0.8007 (tm-30) REVERT: O 51 MET cc_start: 0.5857 (ppp) cc_final: 0.5541 (ptm) outliers start: 67 outliers final: 33 residues processed: 258 average time/residue: 0.1607 time to fit residues: 68.3992 Evaluate side-chains 217 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain K residue 71 PHE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain O residue 4 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 47 optimal weight: 2.9990 chunk 265 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 351 optimal weight: 20.0000 chunk 331 optimal weight: 10.0000 chunk 19 optimal weight: 0.0970 chunk 94 optimal weight: 0.3980 chunk 37 optimal weight: 9.9990 chunk 339 optimal weight: 8.9990 chunk 330 optimal weight: 6.9990 chunk 229 optimal weight: 5.9990 overall best weight: 2.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 801 ASN B 334 ASN A 125 ASN A 417 ASN A 762 GLN A 801 ASN A1134 ASN N 92 ASN O 81 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.144722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.087970 restraints weight = 67798.479| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 4.94 r_work: 0.3060 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 29204 Z= 0.207 Angle : 0.675 15.060 39918 Z= 0.349 Chirality : 0.047 0.233 4676 Planarity : 0.005 0.054 5100 Dihedral : 5.945 56.100 4750 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.12 % Favored : 94.86 % Rotamer: Outliers : 3.12 % Allowed : 12.73 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.13), residues: 3693 helix: 1.76 (0.20), residues: 666 sheet: -0.50 (0.15), residues: 966 loop : -1.57 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 346 TYR 0.023 0.002 TYR I 79 PHE 0.028 0.002 PHE B 392 TRP 0.020 0.002 TRP H 94 HIS 0.005 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00496 (29159) covalent geometry : angle 0.66504 (39828) SS BOND : bond 0.00521 ( 45) SS BOND : angle 2.49693 ( 90) hydrogen bonds : bond 0.05353 ( 1130) hydrogen bonds : angle 5.78622 ( 3075) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 190 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 200 TYR cc_start: 0.8882 (m-80) cc_final: 0.8623 (m-80) REVERT: C 756 TYR cc_start: 0.8427 (m-10) cc_final: 0.8111 (m-80) REVERT: B 237 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.6649 (ptm-80) REVERT: B 365 TYR cc_start: 0.7931 (m-80) cc_final: 0.6803 (t80) REVERT: B 432 CYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7320 (p) REVERT: B 497 PHE cc_start: 0.4789 (m-80) cc_final: 0.4206 (m-80) REVERT: B 534 VAL cc_start: 0.8409 (t) cc_final: 0.8184 (p) REVERT: B 902 MET cc_start: 0.9194 (tpt) cc_final: 0.8819 (tpt) REVERT: A 118 LEU cc_start: 0.7222 (mp) cc_final: 0.7012 (tp) REVERT: A 135 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.6813 (m-80) REVERT: A 377 PHE cc_start: 0.7611 (t80) cc_final: 0.7350 (t80) REVERT: A 525 CYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6941 (m) REVERT: A 762 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8341 (mp10) REVERT: A 856 ASN cc_start: 0.8868 (m-40) cc_final: 0.8210 (t0) REVERT: A 950 ASP cc_start: 0.8752 (m-30) cc_final: 0.8507 (m-30) REVERT: A 1096 VAL cc_start: 0.9315 (OUTLIER) cc_final: 0.9080 (p) REVERT: K 47 LEU cc_start: 0.5335 (OUTLIER) cc_final: 0.4998 (pp) REVERT: K 86 TYR cc_start: 0.6242 (m-80) cc_final: 0.5833 (m-10) REVERT: K 92 ASN cc_start: 0.7461 (p0) cc_final: 0.6890 (t0) REVERT: L 85 LEU cc_start: 0.4181 (OUTLIER) cc_final: 0.3210 (tp) REVERT: O 38 ARG cc_start: 0.4830 (ptt180) cc_final: 0.4591 (ptm-80) REVERT: O 45 LEU cc_start: 0.7747 (tp) cc_final: 0.7367 (mt) REVERT: O 107 TYR cc_start: 0.7447 (m-80) cc_final: 0.7176 (m-80) outliers start: 91 outliers final: 47 residues processed: 267 average time/residue: 0.1433 time to fit residues: 63.3913 Evaluate side-chains 224 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 169 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 417 ASN Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 236 optimal weight: 9.9990 chunk 90 optimal weight: 0.6980 chunk 58 optimal weight: 0.4980 chunk 87 optimal weight: 0.7980 chunk 322 optimal weight: 40.0000 chunk 194 optimal weight: 0.9990 chunk 148 optimal weight: 10.0000 chunk 309 optimal weight: 50.0000 chunk 262 optimal weight: 0.9990 chunk 36 optimal weight: 50.0000 chunk 132 optimal weight: 20.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 953 ASN N 92 ASN O 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.143497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.084592 restraints weight = 69566.763| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.43 r_work: 0.3142 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 29204 Z= 0.124 Angle : 0.603 11.617 39918 Z= 0.311 Chirality : 0.044 0.203 4676 Planarity : 0.004 0.074 5100 Dihedral : 5.434 55.215 4750 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.41 % Favored : 95.56 % Rotamer: Outliers : 2.57 % Allowed : 14.44 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.14), residues: 3693 helix: 2.07 (0.21), residues: 664 sheet: -0.24 (0.16), residues: 971 loop : -1.41 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 983 TYR 0.027 0.001 TYR I 79 PHE 0.027 0.001 PHE B 392 TRP 0.021 0.001 TRP A 104 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00281 (29159) covalent geometry : angle 0.59550 (39828) SS BOND : bond 0.00443 ( 45) SS BOND : angle 2.08877 ( 90) hydrogen bonds : bond 0.04452 ( 1130) hydrogen bonds : angle 5.43681 ( 3075) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 188 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 200 TYR cc_start: 0.8911 (m-80) cc_final: 0.8596 (m-80) REVERT: B 237 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.6676 (ptm-80) REVERT: B 365 TYR cc_start: 0.7786 (m-80) cc_final: 0.6977 (t80) REVERT: B 497 PHE cc_start: 0.5112 (m-80) cc_final: 0.4454 (m-80) REVERT: B 534 VAL cc_start: 0.8409 (t) cc_final: 0.8157 (p) REVERT: B 902 MET cc_start: 0.9068 (tpt) cc_final: 0.8759 (tpt) REVERT: B 983 ARG cc_start: 0.8703 (ttp80) cc_final: 0.8390 (tmm160) REVERT: A 856 ASN cc_start: 0.8824 (m-40) cc_final: 0.8181 (t0) REVERT: A 868 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8316 (mp0) REVERT: A 950 ASP cc_start: 0.8706 (m-30) cc_final: 0.8444 (m-30) REVERT: A 1096 VAL cc_start: 0.9227 (OUTLIER) cc_final: 0.9001 (p) REVERT: I 82 MET cc_start: -0.1438 (ptp) cc_final: -0.1732 (ppp) REVERT: K 86 TYR cc_start: 0.6243 (m-80) cc_final: 0.5880 (m-10) REVERT: K 92 ASN cc_start: 0.7474 (p0) cc_final: 0.7098 (t0) REVERT: O 45 LEU cc_start: 0.7636 (tp) cc_final: 0.7270 (mt) outliers start: 75 outliers final: 43 residues processed: 249 average time/residue: 0.1554 time to fit residues: 64.4425 Evaluate side-chains 213 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 319 optimal weight: 10.0000 chunk 167 optimal weight: 0.4980 chunk 15 optimal weight: 10.0000 chunk 293 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 345 optimal weight: 30.0000 chunk 174 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 244 optimal weight: 0.1980 chunk 67 optimal weight: 0.6980 chunk 332 optimal weight: 0.1980 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 519 HIS A 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.157041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.100326 restraints weight = 69229.827| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 4.67 r_work: 0.3112 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29204 Z= 0.108 Angle : 0.585 14.352 39918 Z= 0.300 Chirality : 0.044 0.219 4676 Planarity : 0.004 0.047 5100 Dihedral : 5.038 54.353 4747 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.44 % Favored : 95.53 % Rotamer: Outliers : 2.98 % Allowed : 14.96 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.14), residues: 3693 helix: 2.24 (0.21), residues: 660 sheet: -0.05 (0.16), residues: 960 loop : -1.29 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 102 TYR 0.022 0.001 TYR I 79 PHE 0.025 0.001 PHE K 71 TRP 0.021 0.001 TRP A 104 HIS 0.004 0.000 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00236 (29159) covalent geometry : angle 0.57805 (39828) SS BOND : bond 0.00557 ( 45) SS BOND : angle 2.03947 ( 90) hydrogen bonds : bond 0.04073 ( 1130) hydrogen bonds : angle 5.19797 ( 3075) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 187 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 200 TYR cc_start: 0.8874 (m-80) cc_final: 0.8657 (m-80) REVERT: C 759 PHE cc_start: 0.8062 (m-80) cc_final: 0.7861 (m-80) REVERT: C 780 GLU cc_start: 0.9112 (tt0) cc_final: 0.8878 (tt0) REVERT: C 1019 ARG cc_start: 0.8610 (tpt170) cc_final: 0.8392 (tpt170) REVERT: B 237 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.6705 (ptm-80) REVERT: B 365 TYR cc_start: 0.7785 (m-80) cc_final: 0.6957 (t80) REVERT: B 497 PHE cc_start: 0.5178 (m-80) cc_final: 0.4468 (m-80) REVERT: B 534 VAL cc_start: 0.8369 (t) cc_final: 0.8080 (p) REVERT: B 773 GLU cc_start: 0.8410 (tt0) cc_final: 0.8040 (tt0) REVERT: B 918 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8267 (mp0) REVERT: B 983 ARG cc_start: 0.8694 (ttp80) cc_final: 0.8428 (tmm160) REVERT: A 242 LEU cc_start: 0.8105 (mt) cc_final: 0.7833 (mt) REVERT: A 317 ASN cc_start: 0.8656 (p0) cc_final: 0.8154 (t0) REVERT: A 856 ASN cc_start: 0.8892 (m-40) cc_final: 0.8178 (t0) REVERT: A 950 ASP cc_start: 0.8761 (m-30) cc_final: 0.8520 (m-30) REVERT: A 1096 VAL cc_start: 0.9222 (OUTLIER) cc_final: 0.8978 (p) REVERT: K 86 TYR cc_start: 0.6253 (m-80) cc_final: 0.6049 (m-10) REVERT: K 100 PHE cc_start: 0.5638 (m-80) cc_final: 0.5403 (t80) REVERT: L 85 LEU cc_start: 0.3118 (OUTLIER) cc_final: 0.1931 (tp) REVERT: O 45 LEU cc_start: 0.7629 (tp) cc_final: 0.7277 (mt) outliers start: 87 outliers final: 52 residues processed: 256 average time/residue: 0.1540 time to fit residues: 65.6133 Evaluate side-chains 227 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 171 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 51 MET Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 277 optimal weight: 20.0000 chunk 317 optimal weight: 20.0000 chunk 116 optimal weight: 6.9990 chunk 53 optimal weight: 0.4980 chunk 134 optimal weight: 5.9990 chunk 344 optimal weight: 0.9990 chunk 64 optimal weight: 0.0670 chunk 261 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 313 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 overall best weight: 1.1124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1005 GLN A 953 ASN K 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.149592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.091888 restraints weight = 65082.505| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 4.91 r_work: 0.3083 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29204 Z= 0.133 Angle : 0.610 18.666 39918 Z= 0.313 Chirality : 0.045 0.288 4676 Planarity : 0.004 0.047 5100 Dihedral : 4.969 53.731 4747 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.52 % Favored : 95.45 % Rotamer: Outliers : 2.81 % Allowed : 15.71 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.14), residues: 3693 helix: 2.25 (0.21), residues: 661 sheet: -0.02 (0.16), residues: 963 loop : -1.26 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 346 TYR 0.024 0.001 TYR I 79 PHE 0.018 0.001 PHE C 238 TRP 0.019 0.001 TRP A 104 HIS 0.003 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00310 (29159) covalent geometry : angle 0.59647 (39828) SS BOND : bond 0.00460 ( 45) SS BOND : angle 2.71391 ( 90) hydrogen bonds : bond 0.04259 ( 1130) hydrogen bonds : angle 5.14833 ( 3075) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 179 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 258 TRP cc_start: 0.3438 (OUTLIER) cc_final: 0.2887 (m100) REVERT: C 351 TYR cc_start: 0.8139 (t80) cc_final: 0.7838 (t80) REVERT: C 983 ARG cc_start: 0.8702 (ttp80) cc_final: 0.8232 (ttp80) REVERT: B 237 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.6757 (ptm-80) REVERT: B 365 TYR cc_start: 0.7881 (m-80) cc_final: 0.7085 (t80) REVERT: B 455 LEU cc_start: 0.6255 (OUTLIER) cc_final: 0.5975 (tt) REVERT: B 497 PHE cc_start: 0.5215 (m-80) cc_final: 0.4515 (m-80) REVERT: B 534 VAL cc_start: 0.8442 (t) cc_final: 0.8176 (p) REVERT: B 773 GLU cc_start: 0.8515 (tt0) cc_final: 0.8134 (tt0) REVERT: B 918 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8335 (mp0) REVERT: A 317 ASN cc_start: 0.8613 (p0) cc_final: 0.8151 (t0) REVERT: A 762 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8488 (mp10) REVERT: A 856 ASN cc_start: 0.8923 (m-40) cc_final: 0.8180 (t0) REVERT: A 868 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8365 (mp0) REVERT: A 950 ASP cc_start: 0.8761 (m-30) cc_final: 0.8505 (m-30) REVERT: A 1096 VAL cc_start: 0.9244 (OUTLIER) cc_final: 0.9000 (p) REVERT: K 92 ASN cc_start: 0.7757 (p0) cc_final: 0.7534 (m-40) REVERT: L 85 LEU cc_start: 0.3594 (OUTLIER) cc_final: 0.2395 (tp) REVERT: O 45 LEU cc_start: 0.7583 (tp) cc_final: 0.7257 (mt) outliers start: 82 outliers final: 52 residues processed: 245 average time/residue: 0.1545 time to fit residues: 62.6852 Evaluate side-chains 225 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 166 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain O residue 68 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 69 optimal weight: 0.8980 chunk 268 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 357 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 337 optimal weight: 20.0000 chunk 207 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 334 ASN B1005 GLN A 751 ASN A 762 GLN A 953 ASN K 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.155430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.095926 restraints weight = 68805.443| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 3.56 r_work: 0.3108 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29204 Z= 0.161 Angle : 0.615 12.348 39918 Z= 0.316 Chirality : 0.045 0.241 4676 Planarity : 0.004 0.054 5100 Dihedral : 5.016 53.914 4747 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.79 % Favored : 95.18 % Rotamer: Outliers : 2.88 % Allowed : 15.85 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.14), residues: 3693 helix: 2.15 (0.21), residues: 668 sheet: 0.02 (0.16), residues: 964 loop : -1.24 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 346 TYR 0.034 0.001 TYR I 79 PHE 0.025 0.001 PHE C 238 TRP 0.020 0.001 TRP A 104 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00382 (29159) covalent geometry : angle 0.60309 (39828) SS BOND : bond 0.00440 ( 45) SS BOND : angle 2.57246 ( 90) hydrogen bonds : bond 0.04552 ( 1130) hydrogen bonds : angle 5.18696 ( 3075) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 171 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 200 TYR cc_start: 0.8732 (m-80) cc_final: 0.8402 (m-80) REVERT: C 258 TRP cc_start: 0.3393 (OUTLIER) cc_final: 0.2750 (m100) REVERT: C 351 TYR cc_start: 0.8157 (t80) cc_final: 0.7899 (t80) REVERT: C 791 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8651 (p) REVERT: C 983 ARG cc_start: 0.8738 (ttp80) cc_final: 0.8271 (ttp80) REVERT: B 237 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.6839 (ptm-80) REVERT: B 365 TYR cc_start: 0.7894 (m-80) cc_final: 0.7118 (t80) REVERT: B 455 LEU cc_start: 0.6434 (OUTLIER) cc_final: 0.6177 (tt) REVERT: B 497 PHE cc_start: 0.5283 (m-80) cc_final: 0.4657 (m-80) REVERT: B 534 VAL cc_start: 0.8579 (t) cc_final: 0.8360 (p) REVERT: B 902 MET cc_start: 0.9139 (tpt) cc_final: 0.8777 (tpt) REVERT: B 918 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8328 (mp0) REVERT: A 101 ILE cc_start: 0.6885 (OUTLIER) cc_final: 0.6385 (tp) REVERT: A 317 ASN cc_start: 0.8573 (p0) cc_final: 0.8189 (t0) REVERT: A 856 ASN cc_start: 0.8906 (m-40) cc_final: 0.8255 (t0) REVERT: A 950 ASP cc_start: 0.8738 (m-30) cc_final: 0.8463 (m-30) REVERT: A 1096 VAL cc_start: 0.9235 (OUTLIER) cc_final: 0.8993 (p) REVERT: L 85 LEU cc_start: 0.3813 (OUTLIER) cc_final: 0.2595 (tp) REVERT: O 38 ARG cc_start: 0.3907 (ptm-80) cc_final: 0.3613 (ptm160) REVERT: O 45 LEU cc_start: 0.7626 (tp) cc_final: 0.7330 (mt) outliers start: 84 outliers final: 57 residues processed: 240 average time/residue: 0.1552 time to fit residues: 61.7945 Evaluate side-chains 228 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 163 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 51 MET Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 148 optimal weight: 0.9980 chunk 238 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 265 optimal weight: 0.9980 chunk 262 optimal weight: 0.9980 chunk 198 optimal weight: 0.9990 chunk 171 optimal weight: 0.8980 chunk 293 optimal weight: 0.9980 chunk 233 optimal weight: 40.0000 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 751 ASN B1005 GLN A 953 ASN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.142850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.084824 restraints weight = 69755.657| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.90 r_work: 0.3106 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29204 Z= 0.125 Angle : 0.594 10.580 39918 Z= 0.306 Chirality : 0.044 0.233 4676 Planarity : 0.004 0.046 5100 Dihedral : 4.886 54.550 4747 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.58 % Favored : 95.40 % Rotamer: Outliers : 2.40 % Allowed : 16.74 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.14), residues: 3693 helix: 2.30 (0.21), residues: 662 sheet: 0.04 (0.16), residues: 995 loop : -1.21 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 45 TYR 0.028 0.001 TYR I 79 PHE 0.029 0.001 PHE C 238 TRP 0.029 0.001 TRP L 36 HIS 0.004 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00291 (29159) covalent geometry : angle 0.58393 (39828) SS BOND : bond 0.00415 ( 45) SS BOND : angle 2.36060 ( 90) hydrogen bonds : bond 0.04229 ( 1130) hydrogen bonds : angle 5.06580 ( 3075) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 173 time to evaluate : 1.073 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: C 88 ASP cc_start: 0.8390 (m-30) cc_final: 0.8014 (p0) REVERT: C 200 TYR cc_start: 0.8721 (m-80) cc_final: 0.8365 (m-80) REVERT: C 258 TRP cc_start: 0.3383 (OUTLIER) cc_final: 0.2754 (m100) REVERT: C 351 TYR cc_start: 0.8180 (t80) cc_final: 0.7900 (t80) REVERT: C 791 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8640 (p) REVERT: C 983 ARG cc_start: 0.8704 (ttp80) cc_final: 0.8245 (ttp80) REVERT: B 237 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.6840 (ptm-80) REVERT: B 365 TYR cc_start: 0.7887 (m-80) cc_final: 0.7075 (t80) REVERT: B 455 LEU cc_start: 0.6398 (OUTLIER) cc_final: 0.6137 (tt) REVERT: B 497 PHE cc_start: 0.5289 (m-80) cc_final: 0.4671 (m-80) REVERT: B 534 VAL cc_start: 0.8601 (t) cc_final: 0.8391 (p) REVERT: B 773 GLU cc_start: 0.8486 (tt0) cc_final: 0.8107 (tt0) REVERT: B 902 MET cc_start: 0.9100 (tpt) cc_final: 0.8722 (tpt) REVERT: B 918 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8352 (mp0) REVERT: A 101 ILE cc_start: 0.6892 (OUTLIER) cc_final: 0.6421 (tp) REVERT: A 317 ASN cc_start: 0.8571 (p0) cc_final: 0.8179 (t0) REVERT: A 368 LEU cc_start: 0.8840 (mm) cc_final: 0.8470 (tp) REVERT: A 950 ASP cc_start: 0.8760 (m-30) cc_final: 0.8482 (m-30) REVERT: A 1096 VAL cc_start: 0.9242 (OUTLIER) cc_final: 0.8994 (p) REVERT: I 82 MET cc_start: 0.0377 (ppp) cc_final: 0.0147 (ppp) REVERT: K 100 PHE cc_start: 0.5962 (m-80) cc_final: 0.5713 (t80) REVERT: L 85 LEU cc_start: 0.4226 (OUTLIER) cc_final: 0.3004 (tp) REVERT: O 45 LEU cc_start: 0.7635 (tp) cc_final: 0.7344 (mt) outliers start: 70 outliers final: 57 residues processed: 234 average time/residue: 0.1542 time to fit residues: 59.6799 Evaluate side-chains 230 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 165 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 51 MET Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 261 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 309 optimal weight: 20.0000 chunk 125 optimal weight: 0.1980 chunk 50 optimal weight: 0.5980 chunk 138 optimal weight: 30.0000 chunk 24 optimal weight: 3.9990 chunk 266 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 281 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 505 HIS B1005 GLN A 953 ASN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.145764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.088359 restraints weight = 68406.364| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 4.47 r_work: 0.3095 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29204 Z= 0.112 Angle : 0.586 9.901 39918 Z= 0.301 Chirality : 0.044 0.223 4676 Planarity : 0.004 0.039 5100 Dihedral : 4.728 54.302 4747 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.44 % Favored : 95.53 % Rotamer: Outliers : 2.57 % Allowed : 16.67 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.14), residues: 3693 helix: 2.32 (0.21), residues: 661 sheet: 0.19 (0.16), residues: 973 loop : -1.19 (0.13), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 346 TYR 0.027 0.001 TYR I 79 PHE 0.026 0.001 PHE C 238 TRP 0.046 0.001 TRP L 36 HIS 0.006 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00254 (29159) covalent geometry : angle 0.57679 (39828) SS BOND : bond 0.00451 ( 45) SS BOND : angle 2.27981 ( 90) hydrogen bonds : bond 0.03977 ( 1130) hydrogen bonds : angle 4.95160 ( 3075) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 169 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ASP cc_start: 0.8442 (m-30) cc_final: 0.8024 (p0) REVERT: C 200 TYR cc_start: 0.8736 (m-80) cc_final: 0.8379 (m-80) REVERT: C 258 TRP cc_start: 0.3201 (OUTLIER) cc_final: 0.2614 (m100) REVERT: C 351 TYR cc_start: 0.8222 (t80) cc_final: 0.7929 (t80) REVERT: C 643 PHE cc_start: 0.7600 (t80) cc_final: 0.6912 (t80) REVERT: C 791 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8628 (p) REVERT: C 983 ARG cc_start: 0.8705 (ttp80) cc_final: 0.8230 (ttp80) REVERT: B 237 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.6823 (ptm-80) REVERT: B 365 TYR cc_start: 0.7849 (m-80) cc_final: 0.7060 (t80) REVERT: B 455 LEU cc_start: 0.6406 (OUTLIER) cc_final: 0.6149 (tt) REVERT: B 497 PHE cc_start: 0.5245 (m-80) cc_final: 0.4612 (m-80) REVERT: B 534 VAL cc_start: 0.8606 (t) cc_final: 0.8387 (p) REVERT: B 773 GLU cc_start: 0.8451 (tt0) cc_final: 0.8087 (tt0) REVERT: B 918 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8365 (mp0) REVERT: A 317 ASN cc_start: 0.8628 (p0) cc_final: 0.8231 (t0) REVERT: A 368 LEU cc_start: 0.8853 (mm) cc_final: 0.8493 (tp) REVERT: A 856 ASN cc_start: 0.8873 (m-40) cc_final: 0.8141 (t0) REVERT: A 950 ASP cc_start: 0.8780 (m-30) cc_final: 0.8551 (m-30) REVERT: K 45 ARG cc_start: 0.8395 (mmm160) cc_final: 0.7960 (tmt170) REVERT: K 94 TRP cc_start: 0.6727 (t60) cc_final: 0.5982 (t-100) REVERT: K 100 PHE cc_start: 0.6057 (m-80) cc_final: 0.5795 (t80) REVERT: L 82 MET cc_start: 0.5985 (mtm) cc_final: 0.5561 (mtt) REVERT: L 85 LEU cc_start: 0.4529 (OUTLIER) cc_final: 0.3019 (tp) REVERT: L 93 TYR cc_start: 0.3733 (m-80) cc_final: 0.3015 (m-80) REVERT: O 45 LEU cc_start: 0.7650 (tp) cc_final: 0.7395 (mp) outliers start: 75 outliers final: 59 residues processed: 235 average time/residue: 0.1497 time to fit residues: 58.8377 Evaluate side-chains 228 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 163 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain O residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 294 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 280 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 205 optimal weight: 0.7980 chunk 214 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 213 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 269 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1005 GLN A 953 ASN ** K 38 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 = 0.4280 r_free = 0.4280 target = 0.142137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.082510 restraints weight = 68271.117| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 3.50 r_work: 0.3112 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29204 Z= 0.145 Angle : 0.602 11.307 39918 Z= 0.310 Chirality : 0.044 0.222 4676 Planarity : 0.004 0.046 5100 Dihedral : 4.774 53.977 4747 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.71 % Favored : 95.26 % Rotamer: Outliers : 2.33 % Allowed : 17.08 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.14), residues: 3693 helix: 2.35 (0.21), residues: 662 sheet: 0.11 (0.16), residues: 994 loop : -1.16 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG N 24 TYR 0.033 0.001 TYR I 79 PHE 0.027 0.001 PHE C 238 TRP 0.060 0.002 TRP L 36 HIS 0.003 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00343 (29159) covalent geometry : angle 0.59257 (39828) SS BOND : bond 0.00466 ( 45) SS BOND : angle 2.31367 ( 90) hydrogen bonds : bond 0.04318 ( 1130) hydrogen bonds : angle 5.00856 ( 3075) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 169 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ASP cc_start: 0.8366 (m-30) cc_final: 0.8039 (p0) REVERT: C 200 TYR cc_start: 0.8730 (m-80) cc_final: 0.8347 (m-80) REVERT: C 258 TRP cc_start: 0.3086 (OUTLIER) cc_final: 0.2539 (m100) REVERT: C 351 TYR cc_start: 0.8247 (t80) cc_final: 0.7958 (t80) REVERT: C 791 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8664 (p) REVERT: C 983 ARG cc_start: 0.8745 (ttp80) cc_final: 0.8285 (ttp80) REVERT: B 237 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.6831 (ptm-80) REVERT: B 365 TYR cc_start: 0.7884 (m-80) cc_final: 0.7036 (t80) REVERT: B 497 PHE cc_start: 0.5292 (m-80) cc_final: 0.4665 (m-80) REVERT: B 534 VAL cc_start: 0.8675 (t) cc_final: 0.8468 (p) REVERT: B 773 GLU cc_start: 0.8504 (tt0) cc_final: 0.8125 (tt0) REVERT: B 918 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8362 (mp0) REVERT: A 317 ASN cc_start: 0.8530 (p0) cc_final: 0.8187 (t0) REVERT: A 368 LEU cc_start: 0.8867 (mm) cc_final: 0.8523 (tp) REVERT: A 856 ASN cc_start: 0.8840 (m-40) cc_final: 0.8172 (t0) REVERT: A 950 ASP cc_start: 0.8738 (m-30) cc_final: 0.8463 (m-30) REVERT: K 45 ARG cc_start: 0.8463 (mmm160) cc_final: 0.8013 (tmt170) REVERT: K 94 TRP cc_start: 0.6695 (t60) cc_final: 0.6007 (t-100) REVERT: K 100 PHE cc_start: 0.6105 (m-80) cc_final: 0.5885 (t80) REVERT: L 82 MET cc_start: 0.5964 (mtm) cc_final: 0.5525 (mtt) REVERT: L 85 LEU cc_start: 0.4112 (OUTLIER) cc_final: 0.2583 (tp) REVERT: L 93 TYR cc_start: 0.3251 (m-80) cc_final: 0.2939 (m-80) REVERT: O 45 LEU cc_start: 0.7652 (tp) cc_final: 0.7344 (mp) outliers start: 68 outliers final: 58 residues processed: 230 average time/residue: 0.1536 time to fit residues: 58.9128 Evaluate side-chains 227 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 164 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain O residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 115 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 137 optimal weight: 0.0970 chunk 2 optimal weight: 1.9990 chunk 278 optimal weight: 0.6980 chunk 292 optimal weight: 2.9990 chunk 214 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 184 optimal weight: 0.8980 chunk 215 optimal weight: 9.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 ASN B1005 GLN A 953 ASN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.142928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.083494 restraints weight = 68552.951| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.57 r_work: 0.3134 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29204 Z= 0.117 Angle : 0.590 9.467 39918 Z= 0.302 Chirality : 0.044 0.242 4676 Planarity : 0.004 0.085 5100 Dihedral : 4.679 54.451 4747 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.58 % Favored : 95.40 % Rotamer: Outliers : 2.30 % Allowed : 17.22 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.14), residues: 3693 helix: 2.33 (0.21), residues: 671 sheet: 0.22 (0.16), residues: 1006 loop : -1.12 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 97 TYR 0.031 0.001 TYR I 79 PHE 0.026 0.001 PHE C 329 TRP 0.047 0.001 TRP L 36 HIS 0.003 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00269 (29159) covalent geometry : angle 0.58129 (39828) SS BOND : bond 0.00509 ( 45) SS BOND : angle 2.16955 ( 90) hydrogen bonds : bond 0.04006 ( 1130) hydrogen bonds : angle 4.91396 ( 3075) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8443.86 seconds wall clock time: 144 minutes 26.93 seconds (8666.93 seconds total)