Starting phenix.real_space_refine on Tue Jun 24 15:54:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvn_34133/06_2025/7yvn_34133.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvn_34133/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yvn_34133/06_2025/7yvn_34133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvn_34133/06_2025/7yvn_34133.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvn_34133/06_2025/7yvn_34133.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvn_34133/06_2025/7yvn_34133.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.033 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): 2.40s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 9, 'TYR:plan': 4, 'ASN:plan1': 9, 'ASP:plan': 13, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 9} 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: {'GLN:plan1': 9, 'TYR:plan': 4, 'ASN:plan1': 9, 'ASP:plan': 13, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 10} 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: {'GLN:plan1': 9, 'TYR:plan': 4, 'ASN:plan1': 9, 'ASP:plan': 13, 'PHE:plan': 4, 'GLU:plan': 11, 'ARG:plan': 10} 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: 19.32, per 1000 atoms: 0.68 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: 7.60 Conformation dependent library (CDL) restraints added in 3.9 seconds 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: 4.42 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: 15.61 Time building geometry restraints manager: 9.03 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 1146 or resid 1 \ 301 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 114 \ 6 or resid 1301 through 1311)) } 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: 9.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.210 Check model and map are aligned: 0.240 Set scattering table: 0.310 Process input model: 72.790 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.480 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (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 TRP 0.036 0.003 TRP N 94 HIS 0.011 0.001 HIS B 505 PHE 0.029 0.003 PHE B 456 TYR 0.051 0.002 TYR H 49 ARG 0.012 0.001 ARG H 61 Details of bonding type rmsd hydrogen bonds : bond 0.21089 ( 1130) hydrogen bonds : angle 7.96083 ( 3075) SS BOND : bond 0.00881 ( 45) SS BOND : angle 4.38168 ( 90) covalent geometry : bond 0.00705 (29159) covalent geometry : angle 0.98566 (39828) *********************** 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 : 4.169 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: 0.8376 (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: 0.3477 (m-80) REVERT: I 78 LEU cc_start: 0.4378 (mm) cc_final: 0.3953 (mt) REVERT: K 38 GLN cc_start: 0.6756 (tt0) cc_final: 0.6454 (tt0) 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: 0.4517 time to fit residues: 234.0321 Evaluate side-chains 192 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 185 time to evaluate : 2.879 ------------------------------------------------------------------------------- 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 311 optimal weight: 9.9990 chunk 279 optimal weight: 0.6980 chunk 155 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 188 optimal weight: 0.4980 chunk 149 optimal weight: 0.6980 chunk 289 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 335 optimal weight: 50.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 ** 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** K 90 GLN N 92 ASN N 102 GLN ** O 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.148024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.088789 restraints weight = 67809.928| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.60 r_work: 0.3175 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 29204 Z= 0.148 Angle : 0.674 10.277 39918 Z= 0.350 Chirality : 0.047 0.247 4676 Planarity : 0.005 0.066 5100 Dihedral : 6.368 58.642 4758 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.36 % Favored : 95.53 % Rotamer: Outliers : 2.09 % Allowed : 11.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.13), residues: 3693 helix: 1.56 (0.21), residues: 660 sheet: -0.62 (0.15), residues: 949 loop : -1.82 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 94 HIS 0.005 0.001 HIS B 505 PHE 0.026 0.002 PHE A 970 TYR 0.017 0.001 TYR C 449 ARG 0.007 0.001 ARG H 61 Details of bonding type rmsd hydrogen bonds : bond 0.05202 ( 1130) hydrogen bonds : angle 5.95755 ( 3075) SS BOND : bond 0.00539 ( 45) SS BOND : angle 2.38642 ( 90) covalent geometry : bond 0.00338 (29159) covalent geometry : angle 0.66528 (39828) *********************** 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 276 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 215 time to evaluate : 3.708 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: 0.8921 (m-80) cc_final: 0.8601 (m-80) REVERT: C 241 LEU cc_start: 0.8300 (pp) cc_final: 0.7654 (mp) REVERT: C 749 CYS cc_start: 0.7242 (OUTLIER) cc_final: 0.6973 (t) REVERT: C 755 GLN cc_start: 0.8574 (mp10) cc_final: 0.8257 (pm20) REVERT: B 237 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.6659 (ptm-80) REVERT: B 258 TRP cc_start: 0.5956 (t-100) cc_final: 0.4649 (m-90) REVERT: B 497 PHE cc_start: 0.4593 (m-80) cc_final: 0.4058 (m-80) REVERT: B 740 MET cc_start: 0.8155 (tpp) cc_final: 0.7910 (tpp) REVERT: A 135 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.6984 (m-80) REVERT: A 578 ASP cc_start: 0.4280 (m-30) cc_final: 0.3505 (t0) REVERT: A 582 LEU cc_start: 0.7812 (mm) cc_final: 0.7475 (pp) REVERT: A 856 ASN cc_start: 0.8790 (m-40) cc_final: 0.8127 (t0) REVERT: A 868 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8344 (mp0) REVERT: A 950 ASP cc_start: 0.8757 (m-30) cc_final: 0.8465 (m-30) REVERT: K 90 GLN cc_start: 0.6727 (OUTLIER) cc_final: 0.6285 (pp30) REVERT: L 85 LEU cc_start: 0.4687 (OUTLIER) cc_final: 0.3977 (tp) REVERT: N 4 MET cc_start: 0.3898 (mtp) cc_final: 0.3674 (mtp) REVERT: O 51 MET cc_start: 0.5682 (ppp) cc_final: 0.5405 (ptm) outliers start: 61 outliers final: 28 residues processed: 262 average time/residue: 0.4198 time to fit residues: 182.1867 Evaluate side-chains 211 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 3.363 ------------------------------------------------------------------------------- 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 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 749 CYS Chi-restraints excluded: chain C residue 762 GLN 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 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 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 K residue 71 PHE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 90 GLN 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 13 optimal weight: 10.0000 chunk 349 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 366 optimal weight: 30.0000 chunk 10 optimal weight: 2.9990 chunk 291 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 330 optimal weight: 40.0000 chunk 334 optimal weight: 7.9990 chunk 219 optimal weight: 0.7980 chunk 259 optimal weight: 0.8980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 417 ASN C 801 ASN B 334 ASN A 417 ASN A 762 GLN A 801 ASN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.146262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.089430 restraints weight = 67644.108| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 5.06 r_work: 0.3058 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 29204 Z= 0.193 Angle : 0.668 15.322 39918 Z= 0.344 Chirality : 0.047 0.288 4676 Planarity : 0.005 0.054 5100 Dihedral : 5.900 54.335 4750 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.87 % Favored : 95.10 % Rotamer: Outliers : 2.92 % Allowed : 12.49 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.13), residues: 3693 helix: 1.89 (0.21), residues: 660 sheet: -0.47 (0.15), residues: 961 loop : -1.58 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 94 HIS 0.005 0.001 HIS A1088 PHE 0.027 0.002 PHE B 392 TYR 0.022 0.002 TYR I 79 ARG 0.006 0.001 ARG C 346 Details of bonding type rmsd hydrogen bonds : bond 0.05191 ( 1130) hydrogen bonds : angle 5.72431 ( 3075) SS BOND : bond 0.00528 ( 45) SS BOND : angle 2.40378 ( 90) covalent geometry : bond 0.00460 (29159) covalent geometry : angle 0.65867 (39828) *********************** 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 272 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 187 time to evaluate : 3.064 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: 0.8903 (m-80) cc_final: 0.8632 (m-80) REVERT: C 755 GLN cc_start: 0.8634 (mp10) cc_final: 0.8360 (mp10) REVERT: B 237 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.6581 (ptm-80) REVERT: B 365 TYR cc_start: 0.7784 (m-80) cc_final: 0.6734 (t80) REVERT: B 497 PHE cc_start: 0.4798 (m-80) cc_final: 0.4143 (m-80) REVERT: B 515 PHE cc_start: 0.7044 (OUTLIER) cc_final: 0.6687 (m-10) REVERT: B 534 VAL cc_start: 0.8413 (t) cc_final: 0.8161 (p) REVERT: A 135 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.6968 (m-80) REVERT: A 525 CYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6972 (m) REVERT: A 582 LEU cc_start: 0.7923 (mm) cc_final: 0.7688 (pp) REVERT: A 950 ASP cc_start: 0.8799 (m-30) cc_final: 0.8538 (m-30) REVERT: A 1096 VAL cc_start: 0.9252 (OUTLIER) cc_final: 0.9013 (p) REVERT: K 45 ARG cc_start: 0.8467 (mmm160) cc_final: 0.8201 (mmm160) REVERT: K 47 LEU cc_start: 0.5185 (OUTLIER) cc_final: 0.4914 (pp) REVERT: K 86 TYR cc_start: 0.6092 (m-80) cc_final: 0.5683 (m-10) REVERT: L 20 LEU cc_start: 0.2472 (OUTLIER) cc_final: 0.2141 (tt) REVERT: L 82 MET cc_start: 0.6070 (ptm) cc_final: 0.5828 (mpp) REVERT: L 85 LEU cc_start: 0.3384 (OUTLIER) cc_final: 0.1861 (tp) REVERT: O 45 LEU cc_start: 0.7718 (tp) cc_final: 0.7325 (mt) REVERT: O 51 MET cc_start: 0.5684 (ppp) cc_final: 0.5387 (ptm) REVERT: O 107 TYR cc_start: 0.7405 (m-80) cc_final: 0.7168 (m-80) outliers start: 85 outliers final: 43 residues processed: 259 average time/residue: 0.3819 time to fit residues: 164.4581 Evaluate side-chains 216 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 165 time to evaluate : 3.243 ------------------------------------------------------------------------------- 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 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 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 515 PHE 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 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 650 LEU 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 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 20 LEU 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 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 327 optimal weight: 6.9990 chunk 263 optimal weight: 5.9990 chunk 299 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 198 optimal weight: 0.6980 chunk 174 optimal weight: 0.8980 chunk 165 optimal weight: 0.9980 chunk 324 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 762 GLN A 762 GLN A 953 ASN K 38 GLN K 89 GLN N 92 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.157182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.098115 restraints weight = 69777.522| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.55 r_work: 0.3151 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29204 Z= 0.124 Angle : 0.600 11.816 39918 Z= 0.309 Chirality : 0.044 0.205 4676 Planarity : 0.004 0.049 5100 Dihedral : 5.317 55.178 4749 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.66 % Favored : 95.32 % Rotamer: Outliers : 2.71 % Allowed : 14.58 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.14), residues: 3693 helix: 2.18 (0.21), residues: 656 sheet: -0.22 (0.16), residues: 971 loop : -1.41 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 104 HIS 0.004 0.001 HIS A1088 PHE 0.022 0.001 PHE B 392 TYR 0.030 0.001 TYR L 79 ARG 0.008 0.000 ARG C 346 Details of bonding type rmsd hydrogen bonds : bond 0.04367 ( 1130) hydrogen bonds : angle 5.37077 ( 3075) SS BOND : bond 0.00603 ( 45) SS BOND : angle 2.11072 ( 90) covalent geometry : bond 0.00283 (29159) covalent geometry : angle 0.59271 (39828) *********************** 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 267 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 188 time to evaluate : 3.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 200 TYR cc_start: 0.8875 (m-80) cc_final: 0.8590 (m-80) REVERT: B 237 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.6656 (ptm-80) REVERT: B 365 TYR cc_start: 0.7850 (m-80) cc_final: 0.6984 (t80) REVERT: B 497 PHE cc_start: 0.4952 (m-80) cc_final: 0.4396 (m-80) REVERT: B 534 VAL cc_start: 0.8396 (t) cc_final: 0.8117 (p) REVERT: A 762 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8421 (mp10) REVERT: A 856 ASN cc_start: 0.8847 (m-40) cc_final: 0.8186 (t0) REVERT: A 868 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8296 (mp0) REVERT: A 950 ASP cc_start: 0.8733 (m-30) cc_final: 0.8455 (m-30) REVERT: A 1096 VAL cc_start: 0.9196 (OUTLIER) cc_final: 0.8962 (p) REVERT: I 82 MET cc_start: -0.1470 (ptp) cc_final: -0.1766 (ppp) REVERT: K 86 TYR cc_start: 0.6207 (m-80) cc_final: 0.5877 (m-10) REVERT: K 100 PHE cc_start: 0.6101 (m-80) cc_final: 0.5709 (t80) REVERT: L 85 LEU cc_start: 0.4271 (OUTLIER) cc_final: 0.3639 (mm) REVERT: N 27 GLN cc_start: 0.6746 (mp10) cc_final: 0.6472 (mp10) REVERT: O 45 LEU cc_start: 0.7624 (tp) cc_final: 0.7299 (mt) REVERT: O 67 PHE cc_start: 0.2773 (m-80) cc_final: 0.2541 (m-10) outliers start: 79 outliers final: 40 residues processed: 249 average time/residue: 0.3767 time to fit residues: 157.0555 Evaluate side-chains 212 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 3.045 ------------------------------------------------------------------------------- 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 775 ASP Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 887 THR 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 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 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 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 756 TYR 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 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 I residue 51 MET 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 85 LEU Chi-restraints excluded: chain L residue 102 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 65 optimal weight: 0.9990 chunk 188 optimal weight: 0.8980 chunk 236 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 274 optimal weight: 2.9990 chunk 363 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 294 optimal weight: 2.9990 chunk 319 optimal weight: 9.9990 chunk 252 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.4328 r_free = 0.4328 target = 0.156913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.100847 restraints weight = 69221.668| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 4.83 r_work: 0.3092 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29204 Z= 0.124 Angle : 0.620 20.806 39918 Z= 0.316 Chirality : 0.045 0.301 4676 Planarity : 0.004 0.069 5100 Dihedral : 5.069 53.970 4749 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.47 % Favored : 95.51 % Rotamer: Outliers : 2.71 % Allowed : 15.09 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 3693 helix: 2.25 (0.21), residues: 658 sheet: -0.06 (0.16), residues: 954 loop : -1.31 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 104 HIS 0.004 0.001 HIS C 69 PHE 0.018 0.001 PHE C 238 TYR 0.026 0.001 TYR I 79 ARG 0.011 0.000 ARG C 983 Details of bonding type rmsd hydrogen bonds : bond 0.04268 ( 1130) hydrogen bonds : angle 5.25091 ( 3075) SS BOND : bond 0.00456 ( 45) SS BOND : angle 2.77348 ( 90) covalent geometry : bond 0.00286 (29159) covalent geometry : angle 0.60615 (39828) *********************** 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 259 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 180 time to evaluate : 2.836 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: 0.8852 (m-80) cc_final: 0.8629 (m-80) REVERT: C 759 PHE cc_start: 0.7993 (m-80) cc_final: 0.7791 (m-80) REVERT: B 237 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.6741 (ptm-80) REVERT: B 365 TYR cc_start: 0.7819 (m-80) cc_final: 0.7010 (t80) REVERT: B 497 PHE cc_start: 0.5184 (m-80) cc_final: 0.4484 (m-80) REVERT: B 534 VAL cc_start: 0.8388 (t) cc_final: 0.8097 (p) REVERT: B 918 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8292 (mp0) REVERT: B 983 ARG cc_start: 0.8644 (ttp80) cc_final: 0.8342 (tmm160) REVERT: A 242 LEU cc_start: 0.8120 (mt) cc_final: 0.7850 (mt) REVERT: A 317 ASN cc_start: 0.8622 (p0) cc_final: 0.8149 (t0) REVERT: A 856 ASN cc_start: 0.8892 (m-40) cc_final: 0.8178 (t0) REVERT: A 950 ASP cc_start: 0.8784 (m-30) cc_final: 0.8530 (m-30) REVERT: A 1096 VAL cc_start: 0.9249 (OUTLIER) cc_final: 0.9014 (p) REVERT: K 45 ARG cc_start: 0.8488 (mmm160) cc_final: 0.8239 (ptm160) REVERT: K 86 TYR cc_start: 0.6093 (m-80) cc_final: 0.5880 (m-10) REVERT: L 82 MET cc_start: 0.4386 (ptp) cc_final: 0.4144 (pmm) REVERT: O 6 GLU cc_start: 0.6180 (OUTLIER) cc_final: 0.5468 (tm-30) REVERT: O 45 LEU cc_start: 0.7652 (tp) cc_final: 0.7302 (mt) REVERT: O 51 MET cc_start: 0.5814 (ppp) cc_final: 0.5466 (ppp) outliers start: 79 outliers final: 49 residues processed: 243 average time/residue: 0.3644 time to fit residues: 147.2889 Evaluate side-chains 222 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 169 time to evaluate : 2.782 ------------------------------------------------------------------------------- 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 775 ASP Chi-restraints excluded: chain C residue 860 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 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 950 ASP 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 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 615 VAL 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 886 TRP Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain I residue 51 MET 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 102 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain O residue 6 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 59 optimal weight: 3.9990 chunk 282 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 198 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 217 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 204 optimal weight: 10.0000 chunk 301 optimal weight: 1.9990 chunk 347 optimal weight: 50.0000 chunk 63 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1005 GLN A 125 ASN A 762 GLN A 953 ASN A1134 ASN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.149131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.088953 restraints weight = 65196.871| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 4.39 r_work: 0.3085 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29204 Z= 0.151 Angle : 0.609 13.740 39918 Z= 0.313 Chirality : 0.045 0.274 4676 Planarity : 0.004 0.054 5100 Dihedral : 5.041 53.796 4747 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.74 % Favored : 95.23 % Rotamer: Outliers : 2.78 % Allowed : 15.64 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.14), residues: 3693 helix: 2.17 (0.21), residues: 665 sheet: -0.03 (0.16), residues: 971 loop : -1.25 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 104 HIS 0.004 0.001 HIS A1088 PHE 0.020 0.001 PHE C 329 TYR 0.025 0.001 TYR I 79 ARG 0.010 0.000 ARG C 346 Details of bonding type rmsd hydrogen bonds : bond 0.04456 ( 1130) hydrogen bonds : angle 5.24073 ( 3075) SS BOND : bond 0.00491 ( 45) SS BOND : angle 2.65622 ( 90) covalent geometry : bond 0.00355 (29159) covalent geometry : angle 0.59606 (39828) *********************** 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 255 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 174 time to evaluate : 3.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 200 TYR cc_start: 0.8819 (m-80) cc_final: 0.8615 (m-80) REVERT: C 258 TRP cc_start: 0.3434 (OUTLIER) cc_final: 0.2892 (m100) REVERT: C 351 TYR cc_start: 0.8166 (t80) cc_final: 0.7860 (t80) REVERT: B 237 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.6780 (ptm-80) REVERT: B 365 TYR cc_start: 0.8024 (m-80) cc_final: 0.7181 (t80) REVERT: B 455 LEU cc_start: 0.6392 (OUTLIER) cc_final: 0.6142 (tt) REVERT: B 497 PHE cc_start: 0.5180 (m-80) cc_final: 0.4554 (m-80) REVERT: B 534 VAL cc_start: 0.8451 (t) cc_final: 0.8181 (p) REVERT: B 918 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8292 (mp0) REVERT: A 317 ASN cc_start: 0.8583 (p0) cc_final: 0.8093 (t0) REVERT: A 368 LEU cc_start: 0.8816 (mm) cc_final: 0.8455 (tp) REVERT: A 856 ASN cc_start: 0.8868 (m-40) cc_final: 0.8129 (t0) REVERT: A 950 ASP cc_start: 0.8776 (m-30) cc_final: 0.8492 (m-30) REVERT: A 1096 VAL cc_start: 0.9234 (OUTLIER) cc_final: 0.8988 (p) REVERT: K 45 ARG cc_start: 0.8568 (mmm160) cc_final: 0.8319 (ptm160) REVERT: K 100 PHE cc_start: 0.6143 (t80) cc_final: 0.5575 (t80) REVERT: L 82 MET cc_start: 0.4666 (ptp) cc_final: 0.4429 (pmm) REVERT: O 67 PHE cc_start: 0.2859 (m-10) cc_final: 0.2533 (m-80) outliers start: 81 outliers final: 56 residues processed: 241 average time/residue: 0.3586 time to fit residues: 147.4189 Evaluate side-chains 226 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 165 time to evaluate : 3.153 ------------------------------------------------------------------------------- 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 327 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 887 THR 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 950 ASP 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 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 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 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 1072 GLU 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 102 VAL Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 48 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 184 optimal weight: 3.9990 chunk 367 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 chunk 314 optimal weight: 40.0000 chunk 21 optimal weight: 5.9990 chunk 235 optimal weight: 9.9990 chunk 231 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 ASN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN B 422 ASN ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1134 ASN A 30 ASN A 751 ASN A 762 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN O 81 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.139895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.081186 restraints weight = 68164.344| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 4.42 r_work: 0.2951 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.119 29204 Z= 0.450 Angle : 0.831 12.047 39918 Z= 0.434 Chirality : 0.053 0.267 4676 Planarity : 0.005 0.053 5100 Dihedral : 6.141 54.517 4747 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.01 % Favored : 93.96 % Rotamer: Outliers : 3.46 % Allowed : 15.92 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.13), residues: 3693 helix: 1.47 (0.20), residues: 671 sheet: -0.37 (0.16), residues: 958 loop : -1.54 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 886 HIS 0.007 0.001 HIS A1088 PHE 0.038 0.003 PHE C 92 TYR 0.029 0.003 TYR A 170 ARG 0.012 0.001 ARG C 346 Details of bonding type rmsd hydrogen bonds : bond 0.06605 ( 1130) hydrogen bonds : angle 5.93634 ( 3075) SS BOND : bond 0.00630 ( 45) SS BOND : angle 3.25796 ( 90) covalent geometry : bond 0.01088 (29159) covalent geometry : angle 0.81759 (39828) *********************** 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 259 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 158 time to evaluate : 3.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ASP cc_start: 0.8455 (m-30) cc_final: 0.8239 (p0) REVERT: C 200 TYR cc_start: 0.8948 (m-80) cc_final: 0.8600 (m-80) REVERT: C 238 PHE cc_start: 0.6826 (OUTLIER) cc_final: 0.6073 (p90) REVERT: C 258 TRP cc_start: 0.3407 (OUTLIER) cc_final: 0.2682 (t60) REVERT: C 791 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.8757 (p) REVERT: C 856 ASN cc_start: 0.9171 (OUTLIER) cc_final: 0.8051 (t0) REVERT: B 237 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.6849 (ptm-80) REVERT: B 318 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.7917 (p90) REVERT: B 497 PHE cc_start: 0.5389 (m-80) cc_final: 0.4879 (m-80) REVERT: B 534 VAL cc_start: 0.8797 (t) cc_final: 0.8565 (p) REVERT: B 902 MET cc_start: 0.9263 (tpt) cc_final: 0.8990 (tpt) REVERT: B 918 GLU cc_start: 0.9214 (OUTLIER) cc_final: 0.8442 (mp0) REVERT: B 950 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8602 (t0) REVERT: A 318 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.8866 (p90) REVERT: A 368 LEU cc_start: 0.8859 (mm) cc_final: 0.8509 (tp) REVERT: A 756 TYR cc_start: 0.9229 (OUTLIER) cc_final: 0.8867 (t80) REVERT: A 762 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8305 (mp10) REVERT: K 90 GLN cc_start: 0.6764 (OUTLIER) cc_final: 0.6379 (pp30) REVERT: K 100 PHE cc_start: 0.6639 (t80) cc_final: 0.6187 (t80) REVERT: L 85 LEU cc_start: 0.4430 (OUTLIER) cc_final: 0.4111 (mm) REVERT: O 45 LEU cc_start: 0.7704 (tp) cc_final: 0.7348 (mp) outliers start: 101 outliers final: 63 residues processed: 243 average time/residue: 0.3564 time to fit residues: 149.8785 Evaluate side-chains 221 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 145 time to evaluate : 2.990 ------------------------------------------------------------------------------- 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 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 327 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR 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 318 PHE 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 599 THR Chi-restraints excluded: chain B residue 608 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 950 ASP 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 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 318 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 503 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR 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 826 VAL 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 69 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 68 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 322 optimal weight: 40.0000 chunk 70 optimal weight: 0.9980 chunk 231 optimal weight: 7.9990 chunk 310 optimal weight: 30.0000 chunk 179 optimal weight: 2.9990 chunk 315 optimal weight: 20.0000 chunk 161 optimal weight: 0.9990 chunk 129 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 chunk 249 optimal weight: 0.0770 chunk 195 optimal weight: 0.8980 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 505 HIS C 544 ASN B 422 ASN A 762 GLN A 953 ASN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.144408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.086561 restraints weight = 67465.914| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 4.54 r_work: 0.3040 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 29204 Z= 0.145 Angle : 0.628 10.952 39918 Z= 0.325 Chirality : 0.045 0.230 4676 Planarity : 0.004 0.058 5100 Dihedral : 5.504 56.690 4747 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.66 % Favored : 95.32 % Rotamer: Outliers : 2.33 % Allowed : 17.74 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3693 helix: 2.05 (0.21), residues: 663 sheet: -0.14 (0.16), residues: 987 loop : -1.40 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 104 HIS 0.004 0.001 HIS A1088 PHE 0.028 0.001 PHE C 329 TYR 0.024 0.001 TYR I 79 ARG 0.014 0.000 ARG C 346 Details of bonding type rmsd hydrogen bonds : bond 0.04837 ( 1130) hydrogen bonds : angle 5.39638 ( 3075) SS BOND : bond 0.00522 ( 45) SS BOND : angle 2.43039 ( 90) covalent geometry : bond 0.00339 (29159) covalent geometry : angle 0.61845 (39828) *********************** 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 232 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 164 time to evaluate : 3.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ASP cc_start: 0.8472 (m-30) cc_final: 0.8092 (p0) REVERT: C 200 TYR cc_start: 0.8988 (m-80) cc_final: 0.8703 (m-80) REVERT: C 238 PHE cc_start: 0.6787 (OUTLIER) cc_final: 0.6225 (p90) REVERT: C 258 TRP cc_start: 0.3214 (OUTLIER) cc_final: 0.2624 (m100) REVERT: C 351 TYR cc_start: 0.8180 (t80) cc_final: 0.7860 (t80) REVERT: C 791 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8678 (p) REVERT: B 237 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.6874 (ptm-80) REVERT: B 497 PHE cc_start: 0.5156 (m-80) cc_final: 0.4646 (m-80) REVERT: B 534 VAL cc_start: 0.8780 (t) cc_final: 0.8535 (p) REVERT: B 740 MET cc_start: 0.8480 (tpp) cc_final: 0.8215 (tpp) REVERT: B 918 GLU cc_start: 0.9146 (OUTLIER) cc_final: 0.8381 (mp0) REVERT: A 368 LEU cc_start: 0.8876 (mm) cc_final: 0.8525 (tp) REVERT: A 762 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8314 (mp10) REVERT: A 950 ASP cc_start: 0.8823 (m-30) cc_final: 0.8564 (m-30) REVERT: A 1096 VAL cc_start: 0.9251 (OUTLIER) cc_final: 0.9019 (p) REVERT: I 82 MET cc_start: 0.0389 (ppp) cc_final: 0.0147 (ppp) REVERT: K 100 PHE cc_start: 0.6318 (OUTLIER) cc_final: 0.5688 (t80) REVERT: O 45 LEU cc_start: 0.7645 (tp) cc_final: 0.7310 (mt) outliers start: 68 outliers final: 52 residues processed: 223 average time/residue: 0.3397 time to fit residues: 131.3204 Evaluate side-chains 215 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 155 time to evaluate : 3.038 ------------------------------------------------------------------------------- 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 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 327 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 887 THR 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 549 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 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 950 ASP 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 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 425 LEU Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 565 PHE 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 749 CYS Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL 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 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 100 PHE Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 48 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 168 optimal weight: 0.4980 chunk 305 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 254 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 225 optimal weight: 4.9990 chunk 211 optimal weight: 5.9990 chunk 280 optimal weight: 3.9990 chunk 138 optimal weight: 0.0060 chunk 228 optimal weight: 2.9990 overall best weight: 2.1002 ------------------------------------------------------------------------------- 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 ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.139768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.079583 restraints weight = 69168.204| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 3.49 r_work: 0.3058 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 29204 Z= 0.204 Angle : 0.643 11.848 39918 Z= 0.333 Chirality : 0.046 0.227 4676 Planarity : 0.004 0.066 5100 Dihedral : 5.436 54.390 4747 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.47 % Favored : 94.50 % Rotamer: Outliers : 2.68 % Allowed : 17.60 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.14), residues: 3693 helix: 2.03 (0.21), residues: 664 sheet: -0.12 (0.16), residues: 1007 loop : -1.38 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 36 HIS 0.004 0.001 HIS A 954 PHE 0.027 0.002 PHE C 238 TYR 0.029 0.002 TYR I 79 ARG 0.015 0.001 ARG C 346 Details of bonding type rmsd hydrogen bonds : bond 0.05094 ( 1130) hydrogen bonds : angle 5.40551 ( 3075) SS BOND : bond 0.00484 ( 45) SS BOND : angle 2.09365 ( 90) covalent geometry : bond 0.00488 (29159) covalent geometry : angle 0.63561 (39828) *********************** 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 232 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 154 time to evaluate : 4.026 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: 0.8374 (m-30) cc_final: 0.8123 (p0) REVERT: C 200 TYR cc_start: 0.8993 (m-80) cc_final: 0.8718 (m-80) REVERT: C 238 PHE cc_start: 0.6980 (OUTLIER) cc_final: 0.6407 (p90) REVERT: C 258 TRP cc_start: 0.3280 (OUTLIER) cc_final: 0.2654 (m100) REVERT: C 351 TYR cc_start: 0.8289 (t80) cc_final: 0.7997 (t80) REVERT: C 791 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8699 (p) REVERT: B 237 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.6854 (ptm-80) REVERT: B 497 PHE cc_start: 0.5263 (m-80) cc_final: 0.4756 (m-80) REVERT: B 534 VAL cc_start: 0.8832 (t) cc_final: 0.8592 (p) REVERT: B 740 MET cc_start: 0.8493 (tpp) cc_final: 0.8246 (tpp) REVERT: B 902 MET cc_start: 0.9182 (tpt) cc_final: 0.8779 (tpt) REVERT: B 918 GLU cc_start: 0.9128 (OUTLIER) cc_final: 0.8339 (mp0) REVERT: A 175 PHE cc_start: 0.7646 (m-80) cc_final: 0.7131 (p90) REVERT: A 368 LEU cc_start: 0.8902 (mm) cc_final: 0.8575 (tp) REVERT: A 950 ASP cc_start: 0.8769 (m-30) cc_final: 0.8507 (m-30) REVERT: A 1096 VAL cc_start: 0.9233 (OUTLIER) cc_final: 0.8999 (p) REVERT: K 90 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.6740 (pp30) REVERT: K 100 PHE cc_start: 0.6411 (OUTLIER) cc_final: 0.5915 (t80) REVERT: L 85 LEU cc_start: 0.3916 (OUTLIER) cc_final: 0.3542 (mm) REVERT: O 45 LEU cc_start: 0.7588 (tp) cc_final: 0.7259 (mt) outliers start: 78 outliers final: 58 residues processed: 222 average time/residue: 0.3520 time to fit residues: 135.0090 Evaluate side-chains 220 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 153 time to evaluate : 3.072 ------------------------------------------------------------------------------- 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 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 378 LYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 565 PHE 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 887 THR 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 391 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 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 950 ASP 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 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 503 VAL Chi-restraints excluded: chain A residue 565 PHE 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 749 CYS Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL 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 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 K residue 90 GLN Chi-restraints excluded: chain K residue 100 PHE 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 4 MET Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 53 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 210 optimal weight: 7.9990 chunk 342 optimal weight: 20.0000 chunk 177 optimal weight: 0.7980 chunk 19 optimal weight: 40.0000 chunk 242 optimal weight: 30.0000 chunk 191 optimal weight: 0.9990 chunk 24 optimal weight: 0.0970 chunk 38 optimal weight: 3.9990 chunk 327 optimal weight: 0.9980 chunk 132 optimal weight: 20.0000 chunk 323 optimal weight: 5.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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 I 81 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.140682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.081475 restraints weight = 69491.951| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.43 r_work: 0.3080 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29204 Z= 0.152 Angle : 0.613 12.104 39918 Z= 0.316 Chirality : 0.045 0.221 4676 Planarity : 0.004 0.065 5100 Dihedral : 5.244 55.632 4747 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.01 % Favored : 94.96 % Rotamer: Outliers : 2.47 % Allowed : 18.08 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.14), residues: 3693 helix: 2.15 (0.21), residues: 664 sheet: -0.03 (0.16), residues: 1017 loop : -1.31 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP L 36 HIS 0.004 0.001 HIS A1088 PHE 0.027 0.001 PHE C 238 TYR 0.028 0.001 TYR I 79 ARG 0.014 0.000 ARG C 346 Details of bonding type rmsd hydrogen bonds : bond 0.04656 ( 1130) hydrogen bonds : angle 5.26973 ( 3075) SS BOND : bond 0.00440 ( 45) SS BOND : angle 1.99115 ( 90) covalent geometry : bond 0.00358 (29159) covalent geometry : angle 0.60646 (39828) ********************** 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: 72 poor density : 165 time to evaluate : 3.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ASP cc_start: 0.8421 (m-30) cc_final: 0.8084 (p0) REVERT: C 200 TYR cc_start: 0.8991 (m-80) cc_final: 0.8734 (m-80) REVERT: C 238 PHE cc_start: 0.7002 (OUTLIER) cc_final: 0.6471 (p90) REVERT: C 258 TRP cc_start: 0.3008 (OUTLIER) cc_final: 0.2525 (m100) REVERT: C 318 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8547 (p90) REVERT: C 351 TYR cc_start: 0.8286 (t80) cc_final: 0.8006 (t80) REVERT: B 237 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.6849 (ptm-80) REVERT: B 497 PHE cc_start: 0.5257 (m-80) cc_final: 0.4705 (m-80) REVERT: B 534 VAL cc_start: 0.8881 (t) cc_final: 0.8647 (p) REVERT: B 740 MET cc_start: 0.8460 (tpp) cc_final: 0.8220 (tpp) REVERT: B 918 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8352 (mp0) REVERT: A 175 PHE cc_start: 0.7768 (m-80) cc_final: 0.7174 (p90) REVERT: A 368 LEU cc_start: 0.8925 (mm) cc_final: 0.8583 (tp) REVERT: A 950 ASP cc_start: 0.8776 (m-30) cc_final: 0.8513 (m-30) REVERT: A 1096 VAL cc_start: 0.9226 (OUTLIER) cc_final: 0.8994 (p) REVERT: K 100 PHE cc_start: 0.6361 (OUTLIER) cc_final: 0.5837 (t80) REVERT: L 85 LEU cc_start: 0.3910 (OUTLIER) cc_final: 0.3527 (mm) REVERT: O 45 LEU cc_start: 0.7565 (tp) cc_final: 0.7132 (mt) outliers start: 72 outliers final: 57 residues processed: 224 average time/residue: 0.3532 time to fit residues: 135.5285 Evaluate side-chains 224 residues out of total 3237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 159 time to evaluate : 2.870 ------------------------------------------------------------------------------- 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 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 318 PHE 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 565 PHE 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 887 THR 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 549 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 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 950 ASP 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 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 503 VAL Chi-restraints excluded: chain A residue 565 PHE 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 749 CYS Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL 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 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 K residue 100 PHE Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 53 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 29 optimal weight: 0.7980 chunk 188 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 339 optimal weight: 30.0000 chunk 345 optimal weight: 20.0000 chunk 276 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 69 optimal weight: 0.2980 chunk 52 optimal weight: 0.0270 chunk 278 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 334 ASN A 801 ASN A 953 ASN ** K 89 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 = 0.4295 r_free = 0.4295 target = 0.142259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.087366 restraints weight = 69476.397| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 5.13 r_work: 0.3076 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 29204 Z= 0.106 Angle : 0.581 10.891 39918 Z= 0.299 Chirality : 0.044 0.211 4676 Planarity : 0.004 0.057 5100 Dihedral : 4.875 55.598 4747 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.79 % Favored : 95.18 % Rotamer: Outliers : 2.02 % Allowed : 18.42 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.14), residues: 3693 helix: 2.29 (0.21), residues: 666 sheet: 0.06 (0.16), residues: 1025 loop : -1.20 (0.14), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP L 36 HIS 0.004 0.001 HIS C 69 PHE 0.025 0.001 PHE C 238 TYR 0.027 0.001 TYR I 79 ARG 0.012 0.000 ARG C 346 Details of bonding type rmsd hydrogen bonds : bond 0.04020 ( 1130) hydrogen bonds : angle 5.05439 ( 3075) SS BOND : bond 0.00390 ( 45) SS BOND : angle 1.74064 ( 90) covalent geometry : bond 0.00234 (29159) covalent geometry : angle 0.57611 (39828) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19375.56 seconds wall clock time: 334 minutes 4.21 seconds (20044.21 seconds total)