Starting phenix.real_space_refine on Wed Jun 25 04:49:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvi_34128/06_2025/7yvi_34128.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvi_34128/06_2025/7yvi_34128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yvi_34128/06_2025/7yvi_34128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvi_34128/06_2025/7yvi_34128.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvi_34128/06_2025/7yvi_34128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvi_34128/06_2025/7yvi_34128.cif" } resolution = 3.7 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= 0.041 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 18479 2.51 5 N 4774 2.21 5 O 5579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 131 residue(s): 2.30s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28961 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 7705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7705 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 3, 'ASN:plan1': 7, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 187 Chain: "B" Number of atoms: 7705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7705 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 3, 'ASN:plan1': 7, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 187 Chain: "A" Number of atoms: 7705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7705 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 3, 'ASN:plan1': 7, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 187 Chain: "H" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "J" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "O" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "I" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 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: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 17.70, per 1000 atoms: 0.61 Number of scatterers: 28961 At special positions: 0 Unit cell: (171.38, 147.6, 201.72, 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 5579 8.00 N 4774 7.00 C 18479 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=2.06 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.05 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.01 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.05 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 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=2.02 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=2.06 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=2.04 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=2.06 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.06 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.06 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 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=2.06 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 90 " distance=2.02 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.02 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: 6.44 Conformation dependent library (CDL) restraints added in 3.4 seconds 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6996 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 57 sheets defined 20.5% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.10 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.503A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.432A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.592A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.702A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.833A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.876A 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 removed outlier: 3.690A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.348A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.996A 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 349 through 353 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 410 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 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.540A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.902A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 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: 3.802A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.884A 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: 4.146A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.831A 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 349 through 353 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.515A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.639A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.780A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.972A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.048A 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 removed outlier: 3.600A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.188A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.988A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.978A pdb=" N ASP J 31 " --> pdb=" O MET J 28 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER J 32 " --> pdb=" O ILE J 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 28 through 32' Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.729A pdb=" N THR J 91 " --> pdb=" O VAL J 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.623A pdb=" N ASP O 31 " --> pdb=" O MET O 28 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER O 32 " --> pdb=" O ILE O 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 28 through 32' Processing helix chain 'O' and resid 87 through 91 removed outlier: 3.754A pdb=" N THR O 91 " --> pdb=" O VAL O 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 4.057A pdb=" N ASP K 31 " --> pdb=" O MET K 28 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER K 32 " --> pdb=" O ILE K 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 28 through 32' Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.543A pdb=" N ASP K 90 " --> pdb=" O ARG K 87 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR K 91 " --> pdb=" O VAL K 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'C' and resid 30 through 31 removed outlier: 3.535A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.169A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 removed outlier: 3.556A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.517A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.755A 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: 7.267A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.570A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 6.225A 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 Processing sheet with id=AA8, first strand: chain 'C' and resid 423 through 424 removed outlier: 4.514A pdb=" N LYS C 424 " --> pdb=" O GLU C 465 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU C 465 " --> pdb=" O LYS C 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.011A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 702 through 703 Processing sheet with id=AB3, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.109A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE C1052 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.109A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'C' and resid 788 through 789 removed outlier: 5.990A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.566A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 8.445A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 201 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.030A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.281A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.075A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.339A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.452A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.584A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 3.892A pdb=" N CYS B 525 " --> pdb=" O CYS B 361 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.566A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.950A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.170A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B1052 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.170A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 788 through 789 removed outlier: 6.144A pdb=" N ILE B 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.794A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 29 through 31 removed outlier: 8.789A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.662A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.873A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.195A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.258A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.981A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.286A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A1052 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.286A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 735 through 736 removed outlier: 3.815A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.640A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.571A pdb=" N VAL H 108 " --> pdb=" O ALA H 86 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA H 86 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLN H 39 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU H 48 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.571A pdb=" N VAL H 108 " --> pdb=" O ALA H 86 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA H 86 " --> pdb=" O VAL H 108 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 18 through 22 Processing sheet with id=AF1, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.694A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER J 25 " --> pdb=" O GLN J 3 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR J 80 " --> pdb=" O SER J 71 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER J 71 " --> pdb=" O TYR J 80 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.480A pdb=" N MET J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR J 59 " --> pdb=" O TYR J 50 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 9 through 12 removed outlier: 3.510A pdb=" N THR N 109 " --> pdb=" O VAL N 10 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY N 12 " --> pdb=" O THR N 109 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA N 86 " --> pdb=" O VAL N 108 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP N 37 " --> pdb=" O MET N 49 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 9 through 12 removed outlier: 3.510A pdb=" N THR N 109 " --> pdb=" O VAL N 10 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY N 12 " --> pdb=" O THR N 109 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA N 86 " --> pdb=" O VAL N 108 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER N 92 " --> pdb=" O VAL N 101 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 18 through 22 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 11 through 12 removed outlier: 4.061A pdb=" N SER O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.863A pdb=" N VAL I 108 " --> pdb=" O ALA I 86 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA I 86 " --> pdb=" O VAL I 108 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N GLN I 39 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LEU I 48 " --> pdb=" O GLN I 39 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.863A pdb=" N VAL I 108 " --> pdb=" O ALA I 86 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA I 86 " --> pdb=" O VAL I 108 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 18 through 22 Processing sheet with id=AG2, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AG3, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.904A pdb=" N MET K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N TYR K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) 1139 hydrogen bonds defined for protein. 3009 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: 13.29 Time building geometry restraints manager: 7.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 7874 1.33 - 1.47: 10469 1.47 - 1.60: 11131 1.60 - 1.74: 34 1.74 - 1.88: 131 Bond restraints: 29639 Sorted by residual: bond pdb=" CA THR C1066 " pdb=" CB THR C1066 " ideal model delta sigma weight residual 1.534 1.404 0.130 2.33e-02 1.84e+03 3.11e+01 bond pdb=" CB ASN B 907 " pdb=" CG ASN B 907 " ideal model delta sigma weight residual 1.516 1.380 0.136 2.50e-02 1.60e+03 2.97e+01 bond pdb=" CA THR B1066 " pdb=" CB THR B1066 " ideal model delta sigma weight residual 1.534 1.415 0.120 2.33e-02 1.84e+03 2.65e+01 bond pdb=" CB ILE C 714 " pdb=" CG2 ILE C 714 " ideal model delta sigma weight residual 1.521 1.357 0.164 3.30e-02 9.18e+02 2.48e+01 bond pdb=" CB THR A1077 " pdb=" CG2 THR A1077 " ideal model delta sigma weight residual 1.521 1.358 0.163 3.30e-02 9.18e+02 2.43e+01 ... (remaining 29634 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 38822 3.79 - 7.58: 1443 7.58 - 11.37: 141 11.37 - 15.17: 33 15.17 - 18.96: 8 Bond angle restraints: 40447 Sorted by residual: angle pdb=" N GLY A 416 " pdb=" CA GLY A 416 " pdb=" C GLY A 416 " ideal model delta sigma weight residual 113.18 96.12 17.06 2.37e+00 1.78e-01 5.18e+01 angle pdb=" CA CYS A 649 " pdb=" CB CYS A 649 " pdb=" SG CYS A 649 " ideal model delta sigma weight residual 114.40 129.17 -14.77 2.30e+00 1.89e-01 4.12e+01 angle pdb=" CB LEU B 878 " pdb=" CG LEU B 878 " pdb=" CD2 LEU B 878 " ideal model delta sigma weight residual 110.70 91.74 18.96 3.00e+00 1.11e-01 3.99e+01 angle pdb=" C PHE C 565 " pdb=" CA PHE C 565 " pdb=" CB PHE C 565 " ideal model delta sigma weight residual 109.79 97.14 12.65 2.05e+00 2.38e-01 3.81e+01 angle pdb=" CA CYS C 538 " pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " ideal model delta sigma weight residual 114.40 128.43 -14.03 2.30e+00 1.89e-01 3.72e+01 ... (remaining 40442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 16323 17.69 - 35.38: 1288 35.38 - 53.07: 262 53.07 - 70.76: 63 70.76 - 88.44: 22 Dihedral angle restraints: 17958 sinusoidal: 7026 harmonic: 10932 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -8.84 -77.16 1 1.00e+01 1.00e-02 7.47e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -9.04 -76.96 1 1.00e+01 1.00e-02 7.43e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -11.98 -74.02 1 1.00e+01 1.00e-02 6.96e+01 ... (remaining 17955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 3526 0.103 - 0.206: 988 0.206 - 0.309: 147 0.309 - 0.412: 21 0.412 - 0.515: 5 Chirality restraints: 4687 Sorted by residual: chirality pdb=" CA CYS A 649 " pdb=" N CYS A 649 " pdb=" C CYS A 649 " pdb=" CB CYS A 649 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.52 2.00e-01 2.50e+01 6.63e+00 chirality pdb=" CB VAL C1094 " pdb=" CA VAL C1094 " pdb=" CG1 VAL C1094 " pdb=" CG2 VAL C1094 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.13e+00 chirality pdb=" CB VAL B1094 " pdb=" CA VAL B1094 " pdb=" CG1 VAL B1094 " pdb=" CG2 VAL B1094 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 4.99e+00 ... (remaining 4684 not shown) Planarity restraints: 5188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 67 " -0.074 9.50e-02 1.11e+02 5.93e-02 3.09e+01 pdb=" NE ARG J 67 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG J 67 " -0.094 2.00e-02 2.50e+03 pdb=" NH1 ARG J 67 " 0.032 2.00e-02 2.50e+03 pdb=" NH2 ARG J 67 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP O 115 " -0.021 2.00e-02 2.50e+03 3.08e-02 2.37e+01 pdb=" CG TRP O 115 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 TRP O 115 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP O 115 " -0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP O 115 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP O 115 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP O 115 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP O 115 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP O 115 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP O 115 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 374 " 0.049 2.00e-02 2.50e+03 3.68e-02 2.36e+01 pdb=" CG PHE B 374 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE B 374 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 374 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE B 374 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE B 374 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 374 " 0.017 2.00e-02 2.50e+03 ... (remaining 5185 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 716 2.60 - 3.18: 26798 3.18 - 3.75: 41826 3.75 - 4.33: 55046 4.33 - 4.90: 94985 Nonbonded interactions: 219371 Sorted by model distance: nonbonded pdb=" OG SER O 7 " pdb=" OG SER O 21 " model vdw 2.028 3.040 nonbonded pdb=" O LYS C 440 " pdb=" OH TYR I 32 " model vdw 2.032 3.040 nonbonded pdb=" OD2 ASP B 737 " pdb=" ND2 ASN A 317 " model vdw 2.036 3.120 nonbonded pdb=" NH1 ARG N 63 " pdb=" O GLY N 79 " model vdw 2.051 3.120 nonbonded pdb=" ND2 ASN A1134 " pdb=" O7 NAG A1308 " model vdw 2.053 3.120 ... (remaining 219366 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 1146 or resid 1301 through 1312)) selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'J' selection = chain 'K' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.090 Check model and map are aligned: 0.200 Set scattering table: 0.230 Process input model: 65.620 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.026 0.195 29684 Z= 1.064 Angle : 1.697 18.957 40537 Z= 0.928 Chirality : 0.095 0.515 4687 Planarity : 0.009 0.114 5188 Dihedral : 13.427 88.444 10827 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.62 % Allowed : 5.33 % Favored : 94.05 % Rotamer: Outliers : 1.33 % Allowed : 9.18 % Favored : 89.49 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % 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: -2.56 (0.12), residues: 3717 helix: 0.08 (0.20), residues: 634 sheet: -1.46 (0.14), residues: 987 loop : -2.47 (0.11), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.007 TRP O 115 HIS 0.025 0.005 HIS C1048 PHE 0.080 0.008 PHE B 374 TYR 0.059 0.005 TYR B 674 ARG 0.095 0.003 ARG J 67 Details of bonding type rmsd hydrogen bonds : bond 0.24464 ( 1110) hydrogen bonds : angle 8.83384 ( 3009) SS BOND : bond 0.01308 ( 45) SS BOND : angle 4.56673 ( 90) covalent geometry : bond 0.02581 (29639) covalent geometry : angle 1.68472 (40447) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 257 time to evaluate : 3.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 TRP cc_start: 0.7039 (m-90) cc_final: 0.6770 (m-90) REVERT: C 191 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8135 (mt-10) REVERT: C 202 LYS cc_start: 0.7904 (mmmt) cc_final: 0.7447 (mmtp) REVERT: C 357 ARG cc_start: 0.8598 (ttt-90) cc_final: 0.8354 (tpt-90) REVERT: B 129 LYS cc_start: 0.8534 (mmtt) cc_final: 0.7965 (pttp) REVERT: B 170 TYR cc_start: 0.8236 (t80) cc_final: 0.7851 (t80) REVERT: B 190 ARG cc_start: 0.7728 (mtt-85) cc_final: 0.7101 (mtt90) REVERT: B 202 LYS cc_start: 0.7885 (mttp) cc_final: 0.7327 (mppt) REVERT: B 265 TYR cc_start: 0.6795 (p90) cc_final: 0.6338 (p90) REVERT: B 347 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: B 440 LYS cc_start: 0.7241 (ttpp) cc_final: 0.6836 (tmtt) REVERT: B 1138 TYR cc_start: 0.7574 (m-80) cc_final: 0.7260 (m-80) REVERT: A 105 ILE cc_start: 0.7534 (pt) cc_final: 0.6705 (pt) REVERT: A 239 GLN cc_start: 0.7349 (mp10) cc_final: 0.6352 (mp10) REVERT: A 532 ASN cc_start: 0.9112 (t0) cc_final: 0.8782 (t0) REVERT: A 725 GLU cc_start: 0.7935 (tt0) cc_final: 0.7701 (tt0) REVERT: A 1005 GLN cc_start: 0.8823 (tp-100) cc_final: 0.8292 (tp40) REVERT: H 98 THR cc_start: 0.5261 (m) cc_final: 0.4958 (p) REVERT: J 83 MET cc_start: -0.4471 (mmt) cc_final: -0.4674 (mmm) REVERT: N 108 VAL cc_start: 0.8133 (t) cc_final: 0.7362 (t) REVERT: O 22 CYS cc_start: 0.5603 (t) cc_final: 0.4640 (t) REVERT: O 38 ARG cc_start: 0.4172 (ptt180) cc_final: 0.3747 (ttm170) REVERT: O 67 ARG cc_start: 0.6837 (mtm180) cc_final: 0.6348 (mtm-85) REVERT: K 45 LEU cc_start: 0.4778 (OUTLIER) cc_final: 0.4461 (mm) outliers start: 40 outliers final: 13 residues processed: 292 average time/residue: 0.4781 time to fit residues: 225.3781 Evaluate side-chains 204 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 189 time to evaluate : 3.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain O residue 104 TYR Chi-restraints excluded: chain K residue 45 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 20.0000 chunk 284 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 191 optimal weight: 0.6980 chunk 151 optimal weight: 0.9980 chunk 293 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 178 optimal weight: 0.6980 chunk 218 optimal weight: 0.7980 chunk 340 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 657 ASN C 755 GLN B 188 ASN B 657 ASN B 755 GLN B 762 GLN B1134 ASN A 165 ASN A 234 ASN A 437 ASN A 505 HIS A 540 ASN A 657 ASN A 801 ASN A 965 GLN H 33 ASN H 39 GLN N 39 GLN O 74 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.173852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.104298 restraints weight = 48733.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.104346 restraints weight = 26876.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.103427 restraints weight = 20425.117| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 29684 Z= 0.162 Angle : 0.686 11.299 40537 Z= 0.361 Chirality : 0.047 0.237 4687 Planarity : 0.005 0.058 5188 Dihedral : 6.571 59.118 4849 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.14 % Favored : 94.73 % Rotamer: Outliers : 2.20 % Allowed : 11.88 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.13), residues: 3717 helix: 1.28 (0.21), residues: 635 sheet: -0.86 (0.14), residues: 1059 loop : -2.04 (0.12), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 353 HIS 0.006 0.001 HIS A1064 PHE 0.020 0.002 PHE C 400 TYR 0.023 0.002 TYR B 200 ARG 0.005 0.001 ARG K 72 Details of bonding type rmsd hydrogen bonds : bond 0.06410 ( 1110) hydrogen bonds : angle 6.29909 ( 3009) SS BOND : bond 0.01421 ( 45) SS BOND : angle 2.16171 ( 90) covalent geometry : bond 0.00353 (29639) covalent geometry : angle 0.67881 (40447) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 265 time to evaluate : 2.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ASP cc_start: 0.9040 (t0) cc_final: 0.8674 (t70) REVERT: C 202 LYS cc_start: 0.7656 (mmmt) cc_final: 0.7146 (mmtp) REVERT: C 617 CYS cc_start: 0.6640 (OUTLIER) cc_final: 0.6241 (m) REVERT: C 957 GLN cc_start: 0.7939 (tm-30) cc_final: 0.7738 (tm-30) REVERT: C 960 ASN cc_start: 0.8589 (t0) cc_final: 0.8244 (t0) REVERT: C 1005 GLN cc_start: 0.8948 (tp-100) cc_final: 0.8715 (tp40) REVERT: B 129 LYS cc_start: 0.8473 (mmtt) cc_final: 0.7997 (pttp) REVERT: B 170 TYR cc_start: 0.8113 (t80) cc_final: 0.7886 (t80) REVERT: B 190 ARG cc_start: 0.7925 (mtt-85) cc_final: 0.7339 (mtt90) REVERT: B 202 LYS cc_start: 0.8021 (mttp) cc_final: 0.7786 (mttp) REVERT: B 226 LEU cc_start: 0.7680 (tp) cc_final: 0.7460 (tt) REVERT: B 378 LYS cc_start: 0.7939 (ptpp) cc_final: 0.7704 (ptmt) REVERT: B 440 LYS cc_start: 0.7246 (ttpp) cc_final: 0.6787 (tmtt) REVERT: B 460 ASN cc_start: 0.7453 (m-40) cc_final: 0.7052 (m-40) REVERT: B 987 PRO cc_start: 0.7908 (Cg_exo) cc_final: 0.7701 (Cg_endo) REVERT: B 1005 GLN cc_start: 0.8607 (tp-100) cc_final: 0.8370 (tp40) REVERT: B 1017 GLU cc_start: 0.8464 (tp30) cc_final: 0.8132 (tm-30) REVERT: B 1094 VAL cc_start: 0.9042 (OUTLIER) cc_final: 0.8710 (m) REVERT: B 1135 ASN cc_start: 0.8679 (t0) cc_final: 0.8251 (t0) REVERT: A 88 ASP cc_start: 0.8540 (t0) cc_final: 0.8149 (m-30) REVERT: A 105 ILE cc_start: 0.7403 (pt) cc_final: 0.7172 (pt) REVERT: A 239 GLN cc_start: 0.6983 (mp10) cc_final: 0.6689 (mp10) REVERT: A 1005 GLN cc_start: 0.8464 (tp-100) cc_final: 0.8217 (tp40) REVERT: N 56 ARG cc_start: 0.8480 (ptp90) cc_final: 0.8258 (ptp90) REVERT: N 71 ASN cc_start: 0.7559 (m-40) cc_final: 0.7335 (m-40) REVERT: O 22 CYS cc_start: 0.5037 (t) cc_final: 0.4337 (t) REVERT: O 67 ARG cc_start: 0.7135 (mtm180) cc_final: 0.6405 (mtm-85) REVERT: O 78 PHE cc_start: 0.7504 (m-10) cc_final: 0.7268 (m-10) REVERT: O 87 ARG cc_start: 0.8113 (mmt90) cc_final: 0.7681 (mpt90) REVERT: O 98 ARG cc_start: 0.7097 (tmm160) cc_final: 0.6687 (tmt170) REVERT: K 34 MET cc_start: 0.6658 (pmm) cc_final: 0.6148 (pmm) outliers start: 66 outliers final: 28 residues processed: 316 average time/residue: 0.3760 time to fit residues: 197.9038 Evaluate side-chains 249 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 219 time to evaluate : 3.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain O residue 104 TYR Chi-restraints excluded: chain I residue 99 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 271 optimal weight: 1.9990 chunk 370 optimal weight: 20.0000 chunk 248 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 chunk 325 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 260 optimal weight: 0.8980 chunk 162 optimal weight: 5.9990 chunk 280 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 253 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 234 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS C1134 ASN B 370 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN B 762 GLN ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1074 ASN A 437 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.170184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.097129 restraints weight = 48840.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.100058 restraints weight = 30451.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.100670 restraints weight = 18858.433| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 29684 Z= 0.225 Angle : 0.691 15.150 40537 Z= 0.361 Chirality : 0.047 0.277 4687 Planarity : 0.004 0.049 5188 Dihedral : 6.218 57.384 4844 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.25 % Favored : 94.59 % Rotamer: Outliers : 3.29 % Allowed : 13.74 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.13), residues: 3717 helix: 1.53 (0.21), residues: 642 sheet: -0.52 (0.15), residues: 1059 loop : -1.85 (0.12), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 64 HIS 0.007 0.001 HIS A1064 PHE 0.022 0.002 PHE C 92 TYR 0.025 0.002 TYR B1067 ARG 0.004 0.001 ARG B 34 Details of bonding type rmsd hydrogen bonds : bond 0.06407 ( 1110) hydrogen bonds : angle 5.99764 ( 3009) SS BOND : bond 0.00578 ( 45) SS BOND : angle 2.67225 ( 90) covalent geometry : bond 0.00543 (29639) covalent geometry : angle 0.68062 (40447) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 224 time to evaluate : 4.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ASP cc_start: 0.9043 (t0) cc_final: 0.8732 (t70) REVERT: C 168 PHE cc_start: 0.7519 (t80) cc_final: 0.7257 (t80) REVERT: C 202 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7480 (mmtp) REVERT: C 271 GLN cc_start: 0.8037 (mt0) cc_final: 0.7730 (mt0) REVERT: C 405 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.7956 (p0) REVERT: C 617 CYS cc_start: 0.6647 (OUTLIER) cc_final: 0.6298 (m) REVERT: C 960 ASN cc_start: 0.8651 (t0) cc_final: 0.8266 (t0) REVERT: C 1029 MET cc_start: 0.9157 (tpp) cc_final: 0.8664 (ttm) REVERT: C 1084 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8110 (t70) REVERT: B 170 TYR cc_start: 0.8319 (t80) cc_final: 0.8084 (t80) REVERT: B 190 ARG cc_start: 0.8109 (mtt-85) cc_final: 0.7446 (mtt90) REVERT: B 202 LYS cc_start: 0.8382 (mttp) cc_final: 0.8168 (mttp) REVERT: B 226 LEU cc_start: 0.7958 (tp) cc_final: 0.7699 (tt) REVERT: B 378 LYS cc_start: 0.8239 (ptpp) cc_final: 0.7996 (ptmt) REVERT: B 399 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.8289 (t) REVERT: B 440 LYS cc_start: 0.7151 (ttpp) cc_final: 0.6852 (tttm) REVERT: B 460 ASN cc_start: 0.7507 (m-40) cc_final: 0.7156 (m-40) REVERT: B 493 GLN cc_start: 0.7904 (pt0) cc_final: 0.7573 (pt0) REVERT: B 498 ARG cc_start: 0.8759 (ttm170) cc_final: 0.8537 (tpp80) REVERT: B 1005 GLN cc_start: 0.8725 (tp-100) cc_final: 0.8498 (tp-100) REVERT: B 1017 GLU cc_start: 0.8275 (tp30) cc_final: 0.7934 (tm-30) REVERT: B 1096 VAL cc_start: 0.9433 (OUTLIER) cc_final: 0.9211 (p) REVERT: A 239 GLN cc_start: 0.7676 (mp10) cc_final: 0.7371 (mp10) REVERT: A 957 GLN cc_start: 0.8502 (tm-30) cc_final: 0.8227 (tm-30) REVERT: A 1005 GLN cc_start: 0.8624 (tp-100) cc_final: 0.8343 (tp40) REVERT: A 1096 VAL cc_start: 0.9406 (OUTLIER) cc_final: 0.9146 (p) REVERT: O 22 CYS cc_start: 0.5132 (t) cc_final: 0.4504 (t) REVERT: O 67 ARG cc_start: 0.7449 (mtm180) cc_final: 0.6994 (mtm-85) REVERT: O 78 PHE cc_start: 0.7513 (m-10) cc_final: 0.7201 (m-10) REVERT: K 34 MET cc_start: 0.6924 (pmm) cc_final: 0.6680 (pmm) outliers start: 99 outliers final: 59 residues processed: 308 average time/residue: 0.5345 time to fit residues: 277.1718 Evaluate side-chains 266 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 200 time to evaluate : 2.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain K residue 56 TYR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 341 optimal weight: 10.0000 chunk 218 optimal weight: 3.9990 chunk 360 optimal weight: 7.9990 chunk 204 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 346 optimal weight: 2.9990 chunk 321 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 chunk 92 optimal weight: 0.8980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN A 913 GLN J 82 GLN N 41 HIS ** O 74 ASN ** 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 = 0.173246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.101258 restraints weight = 49565.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.101712 restraints weight = 30640.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.101832 restraints weight = 20478.918| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 29684 Z= 0.188 Angle : 0.644 16.536 40537 Z= 0.336 Chirality : 0.046 0.343 4687 Planarity : 0.004 0.051 5188 Dihedral : 5.861 55.823 4839 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.27 % Favored : 94.62 % Rotamer: Outliers : 3.63 % Allowed : 15.20 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.13), residues: 3717 helix: 1.78 (0.21), residues: 635 sheet: -0.47 (0.15), residues: 1002 loop : -1.71 (0.12), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 436 HIS 0.005 0.001 HIS B1088 PHE 0.019 0.002 PHE C 201 TYR 0.022 0.001 TYR B1067 ARG 0.006 0.000 ARG K 111 Details of bonding type rmsd hydrogen bonds : bond 0.05840 ( 1110) hydrogen bonds : angle 5.74969 ( 3009) SS BOND : bond 0.00565 ( 45) SS BOND : angle 2.72041 ( 90) covalent geometry : bond 0.00450 (29639) covalent geometry : angle 0.63200 (40447) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 220 time to evaluate : 3.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 202 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7317 (mttp) REVERT: C 238 PHE cc_start: 0.6802 (OUTLIER) cc_final: 0.6541 (p90) REVERT: C 405 ASN cc_start: 0.8588 (OUTLIER) cc_final: 0.7997 (p0) REVERT: C 617 CYS cc_start: 0.6628 (OUTLIER) cc_final: 0.6315 (m) REVERT: C 960 ASN cc_start: 0.8552 (t0) cc_final: 0.8124 (t0) REVERT: C 1005 GLN cc_start: 0.8933 (tp40) cc_final: 0.8672 (tp40) REVERT: C 1029 MET cc_start: 0.9061 (tpp) cc_final: 0.8581 (ttm) REVERT: C 1084 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8323 (t70) REVERT: B 190 ARG cc_start: 0.8000 (mtt-85) cc_final: 0.7314 (mtt90) REVERT: B 202 LYS cc_start: 0.8269 (mttp) cc_final: 0.7539 (mppt) REVERT: B 226 LEU cc_start: 0.7749 (tp) cc_final: 0.7501 (tt) REVERT: B 298 GLU cc_start: 0.8572 (tt0) cc_final: 0.8253 (tp30) REVERT: B 378 LYS cc_start: 0.8117 (ptpp) cc_final: 0.7886 (ptmt) REVERT: B 399 SER cc_start: 0.8673 (OUTLIER) cc_final: 0.8221 (t) REVERT: B 440 LYS cc_start: 0.7215 (ttpp) cc_final: 0.6811 (tttm) REVERT: B 460 ASN cc_start: 0.7527 (m-40) cc_final: 0.7140 (m-40) REVERT: B 493 GLN cc_start: 0.7973 (pt0) cc_final: 0.7651 (pt0) REVERT: B 498 ARG cc_start: 0.8735 (ttm170) cc_final: 0.8513 (tpp80) REVERT: B 902 MET cc_start: 0.9159 (tpt) cc_final: 0.8747 (tpt) REVERT: B 957 GLN cc_start: 0.8089 (tm-30) cc_final: 0.7798 (tm-30) REVERT: B 1017 GLU cc_start: 0.8312 (tp30) cc_final: 0.7972 (tm-30) REVERT: B 1094 VAL cc_start: 0.9146 (OUTLIER) cc_final: 0.8807 (m) REVERT: B 1096 VAL cc_start: 0.9342 (OUTLIER) cc_final: 0.9139 (p) REVERT: A 88 ASP cc_start: 0.8421 (t0) cc_final: 0.8040 (m-30) REVERT: A 239 GLN cc_start: 0.7423 (mp10) cc_final: 0.7177 (mp10) REVERT: A 957 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8279 (tm-30) REVERT: A 1005 GLN cc_start: 0.8539 (tp-100) cc_final: 0.8249 (tp40) REVERT: A 1096 VAL cc_start: 0.9365 (OUTLIER) cc_final: 0.9129 (p) REVERT: O 22 CYS cc_start: 0.5329 (t) cc_final: 0.4677 (t) REVERT: O 54 ASN cc_start: 0.8852 (m-40) cc_final: 0.8641 (m110) REVERT: O 67 ARG cc_start: 0.7402 (mtm180) cc_final: 0.6964 (mtm-85) REVERT: O 78 PHE cc_start: 0.7582 (m-10) cc_final: 0.7282 (m-10) REVERT: K 34 MET cc_start: 0.6707 (pmm) cc_final: 0.6475 (pmm) outliers start: 109 outliers final: 68 residues processed: 311 average time/residue: 0.3705 time to fit residues: 192.7098 Evaluate side-chains 281 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 204 time to evaluate : 3.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain K residue 56 TYR Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 123 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 116 optimal weight: 10.0000 chunk 340 optimal weight: 20.0000 chunk 368 optimal weight: 6.9990 chunk 326 optimal weight: 40.0000 chunk 193 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 352 optimal weight: 0.9980 chunk 285 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 1 optimal weight: 0.0050 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN A 913 GLN N 41 HIS ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.182399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.108326 restraints weight = 48353.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.111783 restraints weight = 26838.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.112854 restraints weight = 15698.635| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29684 Z= 0.122 Angle : 0.595 16.956 40537 Z= 0.309 Chirality : 0.045 0.396 4687 Planarity : 0.004 0.050 5188 Dihedral : 5.241 55.320 4837 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.79 % Favored : 95.10 % Rotamer: Outliers : 3.09 % Allowed : 16.20 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.75 (0.13), residues: 3717 helix: 2.05 (0.21), residues: 641 sheet: -0.22 (0.16), residues: 977 loop : -1.52 (0.12), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 64 HIS 0.005 0.001 HIS C 69 PHE 0.018 0.001 PHE A 592 TYR 0.022 0.001 TYR B 170 ARG 0.008 0.000 ARG K 111 Details of bonding type rmsd hydrogen bonds : bond 0.04880 ( 1110) hydrogen bonds : angle 5.37738 ( 3009) SS BOND : bond 0.00431 ( 45) SS BOND : angle 2.55042 ( 90) covalent geometry : bond 0.00271 (29639) covalent geometry : angle 0.58309 (40447) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 233 time to evaluate : 2.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 202 LYS cc_start: 0.7906 (mmmt) cc_final: 0.7294 (mttp) REVERT: C 238 PHE cc_start: 0.6762 (OUTLIER) cc_final: 0.6543 (p90) REVERT: C 740 MET cc_start: 0.8668 (tpp) cc_final: 0.8456 (tpp) REVERT: C 960 ASN cc_start: 0.8517 (t0) cc_final: 0.7889 (t0) REVERT: C 1029 MET cc_start: 0.9121 (tpp) cc_final: 0.8673 (ttm) REVERT: C 1094 VAL cc_start: 0.8766 (OUTLIER) cc_final: 0.8341 (m) REVERT: B 190 ARG cc_start: 0.7987 (mtt-85) cc_final: 0.7356 (mtt90) REVERT: B 202 LYS cc_start: 0.8183 (mttp) cc_final: 0.7452 (mppt) REVERT: B 226 LEU cc_start: 0.7740 (tp) cc_final: 0.7500 (tt) REVERT: B 298 GLU cc_start: 0.8563 (tt0) cc_final: 0.8276 (tp30) REVERT: B 378 LYS cc_start: 0.8147 (ptpp) cc_final: 0.7871 (ptmt) REVERT: B 383 SER cc_start: 0.8406 (m) cc_final: 0.8038 (p) REVERT: B 399 SER cc_start: 0.8630 (OUTLIER) cc_final: 0.8166 (t) REVERT: B 440 LYS cc_start: 0.7059 (ttpp) cc_final: 0.6780 (tttm) REVERT: B 460 ASN cc_start: 0.7604 (m-40) cc_final: 0.6936 (m-40) REVERT: B 493 GLN cc_start: 0.8034 (pt0) cc_final: 0.7741 (pt0) REVERT: B 902 MET cc_start: 0.9173 (tpt) cc_final: 0.8915 (tpt) REVERT: B 964 LYS cc_start: 0.9092 (tptt) cc_final: 0.8865 (tptt) REVERT: B 1017 GLU cc_start: 0.8277 (tp30) cc_final: 0.7933 (tm-30) REVERT: B 1094 VAL cc_start: 0.9178 (OUTLIER) cc_final: 0.8846 (m) REVERT: B 1096 VAL cc_start: 0.9323 (OUTLIER) cc_final: 0.9121 (p) REVERT: A 88 ASP cc_start: 0.8198 (t0) cc_final: 0.7916 (m-30) REVERT: A 239 GLN cc_start: 0.7315 (mp10) cc_final: 0.6654 (mp10) REVERT: A 957 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8214 (tm-30) REVERT: A 1096 VAL cc_start: 0.9270 (OUTLIER) cc_final: 0.9035 (m) REVERT: N 56 ARG cc_start: 0.8080 (ptp90) cc_final: 0.7858 (ptp90) REVERT: O 22 CYS cc_start: 0.5158 (t) cc_final: 0.4496 (t) REVERT: O 67 ARG cc_start: 0.7323 (mtm180) cc_final: 0.6898 (mtm-85) REVERT: O 78 PHE cc_start: 0.7641 (m-10) cc_final: 0.7317 (m-10) REVERT: K 34 MET cc_start: 0.6769 (pmm) cc_final: 0.6494 (pmm) outliers start: 93 outliers final: 58 residues processed: 312 average time/residue: 0.3687 time to fit residues: 192.5177 Evaluate side-chains 272 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 208 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain K residue 56 TYR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 123 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 238 optimal weight: 6.9990 chunk 216 optimal weight: 0.9980 chunk 362 optimal weight: 30.0000 chunk 70 optimal weight: 1.9990 chunk 307 optimal weight: 40.0000 chunk 141 optimal weight: 0.4980 chunk 89 optimal weight: 0.9980 chunk 273 optimal weight: 2.9990 chunk 265 optimal weight: 2.9990 chunk 277 optimal weight: 0.0770 chunk 232 optimal weight: 9.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN N 41 HIS ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 55 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.181660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.107464 restraints weight = 48524.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.110851 restraints weight = 26674.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.112722 restraints weight = 15515.501| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29684 Z= 0.131 Angle : 0.591 17.975 40537 Z= 0.307 Chirality : 0.045 0.390 4687 Planarity : 0.004 0.051 5188 Dihedral : 5.024 55.311 4834 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.41 % Favored : 94.48 % Rotamer: Outliers : 3.33 % Allowed : 16.53 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.13), residues: 3717 helix: 2.18 (0.21), residues: 634 sheet: -0.04 (0.16), residues: 973 loop : -1.40 (0.12), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 64 HIS 0.005 0.001 HIS C 69 PHE 0.021 0.001 PHE C 201 TYR 0.024 0.001 TYR N 93 ARG 0.010 0.000 ARG B 567 Details of bonding type rmsd hydrogen bonds : bond 0.04887 ( 1110) hydrogen bonds : angle 5.28258 ( 3009) SS BOND : bond 0.00439 ( 45) SS BOND : angle 2.51911 ( 90) covalent geometry : bond 0.00303 (29639) covalent geometry : angle 0.57938 (40447) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 220 time to evaluate : 2.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ASP cc_start: 0.9017 (t0) cc_final: 0.8725 (t70) REVERT: C 202 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7310 (mttp) REVERT: C 238 PHE cc_start: 0.6819 (OUTLIER) cc_final: 0.6580 (p90) REVERT: C 405 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.8016 (p0) REVERT: C 960 ASN cc_start: 0.8501 (t0) cc_final: 0.7879 (t0) REVERT: C 1029 MET cc_start: 0.9104 (tpp) cc_final: 0.8654 (ttm) REVERT: C 1094 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8307 (m) REVERT: B 129 LYS cc_start: 0.8389 (mmtt) cc_final: 0.8174 (mmtt) REVERT: B 190 ARG cc_start: 0.7998 (mtt-85) cc_final: 0.7339 (mtt90) REVERT: B 202 LYS cc_start: 0.8188 (mttp) cc_final: 0.7461 (mppt) REVERT: B 226 LEU cc_start: 0.7774 (tp) cc_final: 0.7529 (tt) REVERT: B 298 GLU cc_start: 0.8576 (tt0) cc_final: 0.8297 (tp30) REVERT: B 378 LYS cc_start: 0.8150 (ptpp) cc_final: 0.7887 (ptmt) REVERT: B 383 SER cc_start: 0.8385 (m) cc_final: 0.8003 (p) REVERT: B 399 SER cc_start: 0.8624 (OUTLIER) cc_final: 0.8158 (t) REVERT: B 403 ARG cc_start: 0.8757 (ttm-80) cc_final: 0.8358 (tpp80) REVERT: B 440 LYS cc_start: 0.7063 (ttpp) cc_final: 0.6799 (tttm) REVERT: B 493 GLN cc_start: 0.8063 (pt0) cc_final: 0.7767 (pt0) REVERT: B 902 MET cc_start: 0.9216 (tpt) cc_final: 0.8875 (tpt) REVERT: B 904 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.7203 (m-10) REVERT: B 964 LYS cc_start: 0.9092 (tptt) cc_final: 0.8886 (tptt) REVERT: B 1017 GLU cc_start: 0.8321 (tp30) cc_final: 0.7941 (tm-30) REVERT: B 1094 VAL cc_start: 0.9177 (OUTLIER) cc_final: 0.8851 (m) REVERT: A 88 ASP cc_start: 0.8231 (t0) cc_final: 0.7972 (m-30) REVERT: A 239 GLN cc_start: 0.7345 (mp10) cc_final: 0.6429 (mp10) REVERT: A 957 GLN cc_start: 0.8543 (tm-30) cc_final: 0.8213 (tm-30) REVERT: A 1096 VAL cc_start: 0.9295 (OUTLIER) cc_final: 0.9059 (m) REVERT: N 55 ASN cc_start: 0.8411 (t0) cc_final: 0.8107 (p0) REVERT: O 67 ARG cc_start: 0.7385 (mtm180) cc_final: 0.6943 (mtm-85) REVERT: O 78 PHE cc_start: 0.7677 (m-10) cc_final: 0.7364 (m-10) REVERT: K 34 MET cc_start: 0.6791 (pmm) cc_final: 0.6468 (pmm) outliers start: 100 outliers final: 68 residues processed: 303 average time/residue: 0.3616 time to fit residues: 183.7062 Evaluate side-chains 292 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 216 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain K residue 56 TYR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 123 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 117 optimal weight: 0.0670 chunk 34 optimal weight: 10.0000 chunk 249 optimal weight: 6.9990 chunk 68 optimal weight: 0.1980 chunk 88 optimal weight: 1.9990 chunk 52 optimal weight: 0.0050 chunk 143 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 273 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 310 optimal weight: 6.9990 overall best weight: 0.3132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN A 801 ASN N 41 HIS ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.186473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.115358 restraints weight = 49791.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.116918 restraints weight = 37707.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.118719 restraints weight = 20263.135| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29684 Z= 0.104 Angle : 0.561 15.364 40537 Z= 0.290 Chirality : 0.044 0.346 4687 Planarity : 0.004 0.052 5188 Dihedral : 4.660 54.114 4834 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.76 % Favored : 95.13 % Rotamer: Outliers : 2.59 % Allowed : 17.66 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.13), residues: 3717 helix: 2.35 (0.21), residues: 634 sheet: 0.07 (0.16), residues: 972 loop : -1.27 (0.13), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 886 HIS 0.005 0.000 HIS C 69 PHE 0.018 0.001 PHE C 377 TYR 0.023 0.001 TYR N 93 ARG 0.009 0.000 ARG B 567 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 1110) hydrogen bonds : angle 5.09166 ( 3009) SS BOND : bond 0.00536 ( 45) SS BOND : angle 2.18081 ( 90) covalent geometry : bond 0.00217 (29639) covalent geometry : angle 0.55172 (40447) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 244 time to evaluate : 3.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 202 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7123 (mttp) REVERT: C 238 PHE cc_start: 0.6847 (OUTLIER) cc_final: 0.6590 (p90) REVERT: C 405 ASN cc_start: 0.8502 (OUTLIER) cc_final: 0.7999 (p0) REVERT: C 960 ASN cc_start: 0.8454 (t0) cc_final: 0.7807 (t0) REVERT: C 1029 MET cc_start: 0.9012 (tpp) cc_final: 0.8586 (ttm) REVERT: B 190 ARG cc_start: 0.7983 (mtt-85) cc_final: 0.7342 (mtt90) REVERT: B 191 GLU cc_start: 0.8465 (mt-10) cc_final: 0.7548 (mt-10) REVERT: B 202 LYS cc_start: 0.8109 (mttp) cc_final: 0.7360 (mppt) REVERT: B 226 LEU cc_start: 0.7545 (tp) cc_final: 0.7201 (tt) REVERT: B 378 LYS cc_start: 0.8188 (ptpp) cc_final: 0.7938 (ptmt) REVERT: B 383 SER cc_start: 0.8192 (m) cc_final: 0.7870 (p) REVERT: B 403 ARG cc_start: 0.8753 (ttm-80) cc_final: 0.8380 (tpp80) REVERT: B 493 GLN cc_start: 0.8202 (pt0) cc_final: 0.7906 (pt0) REVERT: B 904 TYR cc_start: 0.8089 (OUTLIER) cc_final: 0.7142 (m-10) REVERT: B 1017 GLU cc_start: 0.8244 (tp30) cc_final: 0.7920 (tm-30) REVERT: B 1094 VAL cc_start: 0.9026 (OUTLIER) cc_final: 0.8791 (m) REVERT: A 88 ASP cc_start: 0.8285 (t0) cc_final: 0.8044 (m-30) REVERT: A 239 GLN cc_start: 0.7284 (mp10) cc_final: 0.6661 (mp10) REVERT: A 957 GLN cc_start: 0.8527 (tm-30) cc_final: 0.8167 (tm-30) REVERT: O 22 CYS cc_start: 0.5601 (t) cc_final: 0.4860 (t) REVERT: O 67 ARG cc_start: 0.7390 (mtm180) cc_final: 0.6914 (mtm-85) REVERT: O 78 PHE cc_start: 0.7678 (m-10) cc_final: 0.7371 (m-10) REVERT: I 49 MET cc_start: 0.6726 (ppp) cc_final: 0.6492 (ppp) REVERT: K 34 MET cc_start: 0.6698 (pmm) cc_final: 0.6429 (pmm) REVERT: K 111 ARG cc_start: 0.4311 (mtm-85) cc_final: 0.3955 (mtp180) outliers start: 78 outliers final: 53 residues processed: 306 average time/residue: 0.3648 time to fit residues: 186.7807 Evaluate side-chains 278 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 220 time to evaluate : 3.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain K residue 56 TYR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 123 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 19 optimal weight: 30.0000 chunk 299 optimal weight: 3.9990 chunk 223 optimal weight: 40.0000 chunk 33 optimal weight: 9.9990 chunk 253 optimal weight: 0.4980 chunk 169 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 298 optimal weight: 0.9990 chunk 230 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 199 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A 992 GLN A1134 ASN N 40 GLN N 41 HIS ** O 74 ASN ** 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 = 0.4307 r_free = 0.4307 target = 0.176382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.107507 restraints weight = 49703.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.106534 restraints weight = 30416.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.105182 restraints weight = 25302.131| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29684 Z= 0.136 Angle : 0.580 14.529 40537 Z= 0.300 Chirality : 0.044 0.319 4687 Planarity : 0.004 0.052 5188 Dihedral : 4.681 55.989 4834 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.27 % Favored : 94.62 % Rotamer: Outliers : 2.73 % Allowed : 18.20 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.32 (0.14), residues: 3717 helix: 2.33 (0.21), residues: 632 sheet: 0.16 (0.16), residues: 966 loop : -1.24 (0.13), residues: 2119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 64 HIS 0.004 0.001 HIS C 69 PHE 0.025 0.001 PHE B 374 TYR 0.020 0.001 TYR A1067 ARG 0.008 0.000 ARG B 567 Details of bonding type rmsd hydrogen bonds : bond 0.04720 ( 1110) hydrogen bonds : angle 5.10012 ( 3009) SS BOND : bond 0.00372 ( 45) SS BOND : angle 2.22408 ( 90) covalent geometry : bond 0.00320 (29639) covalent geometry : angle 0.57118 (40447) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 221 time to evaluate : 3.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 202 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7220 (mttp) REVERT: C 238 PHE cc_start: 0.6887 (OUTLIER) cc_final: 0.6667 (p90) REVERT: C 357 ARG cc_start: 0.8177 (tpt90) cc_final: 0.7964 (tpt90) REVERT: C 386 LYS cc_start: 0.9149 (mmmt) cc_final: 0.8927 (pttp) REVERT: C 405 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8029 (p0) REVERT: C 960 ASN cc_start: 0.8476 (t0) cc_final: 0.7836 (t0) REVERT: C 1029 MET cc_start: 0.9014 (tpp) cc_final: 0.8667 (ttm) REVERT: B 190 ARG cc_start: 0.7938 (mtt-85) cc_final: 0.7252 (mtt90) REVERT: B 202 LYS cc_start: 0.8202 (mttp) cc_final: 0.7483 (mppt) REVERT: B 226 LEU cc_start: 0.7638 (tp) cc_final: 0.7291 (tt) REVERT: B 383 SER cc_start: 0.8195 (m) cc_final: 0.7827 (p) REVERT: B 399 SER cc_start: 0.8630 (OUTLIER) cc_final: 0.8192 (t) REVERT: B 403 ARG cc_start: 0.8746 (ttm-80) cc_final: 0.8433 (ttm-80) REVERT: B 493 GLN cc_start: 0.8064 (pt0) cc_final: 0.7774 (pt0) REVERT: B 904 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.6965 (m-10) REVERT: B 1017 GLU cc_start: 0.8419 (tp30) cc_final: 0.8023 (tm-30) REVERT: B 1094 VAL cc_start: 0.8968 (OUTLIER) cc_final: 0.8701 (m) REVERT: A 239 GLN cc_start: 0.7403 (mp10) cc_final: 0.6495 (mp10) REVERT: A 934 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8767 (tt) REVERT: A 957 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8266 (tm-30) REVERT: A 1050 MET cc_start: 0.7822 (mtm) cc_final: 0.7377 (ptm) REVERT: N 49 MET cc_start: 0.6138 (mmm) cc_final: 0.5729 (mmp) REVERT: O 22 CYS cc_start: 0.5847 (t) cc_final: 0.5195 (t) REVERT: O 67 ARG cc_start: 0.7402 (mtm180) cc_final: 0.6927 (mtm-85) REVERT: K 34 MET cc_start: 0.6612 (pmm) cc_final: 0.6367 (pmm) REVERT: K 111 ARG cc_start: 0.3971 (mtm-85) cc_final: 0.3672 (mtp180) outliers start: 82 outliers final: 66 residues processed: 289 average time/residue: 0.3686 time to fit residues: 181.4252 Evaluate side-chains 285 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 212 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain K residue 56 TYR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 123 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 194 optimal weight: 0.5980 chunk 28 optimal weight: 7.9990 chunk 250 optimal weight: 0.6980 chunk 228 optimal weight: 0.4980 chunk 159 optimal weight: 1.9990 chunk 37 optimal weight: 0.0980 chunk 117 optimal weight: 0.0170 chunk 356 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 296 optimal weight: 1.9990 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 218 GLN C 405 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN N 41 HIS ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.179676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.111227 restraints weight = 49077.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.110764 restraints weight = 28513.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.109478 restraints weight = 21204.969| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29684 Z= 0.102 Angle : 0.567 17.373 40537 Z= 0.291 Chirality : 0.044 0.322 4687 Planarity : 0.004 0.053 5188 Dihedral : 4.488 53.662 4834 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.68 % Favored : 95.21 % Rotamer: Outliers : 2.53 % Allowed : 18.56 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.14 (0.14), residues: 3717 helix: 2.48 (0.21), residues: 629 sheet: 0.24 (0.16), residues: 981 loop : -1.11 (0.13), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.004 0.000 HIS C 69 PHE 0.023 0.001 PHE C 201 TYR 0.023 0.001 TYR B 170 ARG 0.007 0.000 ARG B 567 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 1110) hydrogen bonds : angle 4.94588 ( 3009) SS BOND : bond 0.00318 ( 45) SS BOND : angle 2.21959 ( 90) covalent geometry : bond 0.00219 (29639) covalent geometry : angle 0.55831 (40447) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 228 time to evaluate : 2.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 202 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7164 (mttp) REVERT: C 238 PHE cc_start: 0.6796 (OUTLIER) cc_final: 0.6557 (p90) REVERT: C 357 ARG cc_start: 0.8164 (tpt90) cc_final: 0.7896 (tpt90) REVERT: C 386 LYS cc_start: 0.9123 (mmmt) cc_final: 0.8891 (pttp) REVERT: C 465 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6583 (pt0) REVERT: C 881 THR cc_start: 0.8597 (OUTLIER) cc_final: 0.8378 (t) REVERT: C 904 TYR cc_start: 0.7786 (OUTLIER) cc_final: 0.7547 (m-80) REVERT: C 960 ASN cc_start: 0.8472 (t0) cc_final: 0.7810 (t0) REVERT: C 1029 MET cc_start: 0.8943 (tpp) cc_final: 0.8588 (ttm) REVERT: B 190 ARG cc_start: 0.7930 (mtt-85) cc_final: 0.7349 (mtt90) REVERT: B 202 LYS cc_start: 0.8099 (mttp) cc_final: 0.7380 (mppt) REVERT: B 226 LEU cc_start: 0.7616 (tp) cc_final: 0.7264 (tt) REVERT: B 269 TYR cc_start: 0.7185 (m-10) cc_final: 0.6768 (m-10) REVERT: B 383 SER cc_start: 0.8114 (m) cc_final: 0.7774 (p) REVERT: B 399 SER cc_start: 0.8589 (OUTLIER) cc_final: 0.8137 (t) REVERT: B 403 ARG cc_start: 0.8736 (ttm-80) cc_final: 0.8384 (ttm-80) REVERT: B 493 GLN cc_start: 0.8113 (pt0) cc_final: 0.7792 (pt0) REVERT: B 904 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.7777 (m-80) REVERT: B 1017 GLU cc_start: 0.8347 (tp30) cc_final: 0.7994 (tm-30) REVERT: A 239 GLN cc_start: 0.7123 (mp10) cc_final: 0.6568 (mp10) REVERT: A 957 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8178 (tm-30) REVERT: N 44 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8103 (tppt) REVERT: N 49 MET cc_start: 0.6681 (mmm) cc_final: 0.6034 (mmp) REVERT: N 98 THR cc_start: 0.6221 (p) cc_final: 0.5668 (t) REVERT: O 22 CYS cc_start: 0.5746 (t) cc_final: 0.5034 (t) REVERT: O 34 MET cc_start: 0.7199 (mmm) cc_final: 0.6951 (mmm) REVERT: O 67 ARG cc_start: 0.7457 (mtm180) cc_final: 0.7000 (mtm-85) REVERT: K 34 MET cc_start: 0.6661 (pmm) cc_final: 0.6422 (pmm) REVERT: K 111 ARG cc_start: 0.4037 (mtm-85) cc_final: 0.3757 (mtp180) outliers start: 76 outliers final: 59 residues processed: 288 average time/residue: 0.3735 time to fit residues: 182.5169 Evaluate side-chains 280 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 213 time to evaluate : 3.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain K residue 56 TYR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 123 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 323 optimal weight: 0.0770 chunk 354 optimal weight: 30.0000 chunk 191 optimal weight: 1.9990 chunk 362 optimal weight: 9.9990 chunk 281 optimal weight: 1.9990 chunk 221 optimal weight: 3.9990 chunk 256 optimal weight: 1.9990 chunk 190 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 341 optimal weight: 0.0570 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 HIS ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.178638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.109446 restraints weight = 49363.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.108951 restraints weight = 30152.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.108045 restraints weight = 22862.331| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29684 Z= 0.108 Angle : 0.562 10.806 40537 Z= 0.289 Chirality : 0.044 0.341 4687 Planarity : 0.004 0.050 5188 Dihedral : 4.372 54.998 4834 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.95 % Favored : 94.94 % Rotamer: Outliers : 2.50 % Allowed : 18.73 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.08 (0.14), residues: 3717 helix: 2.47 (0.21), residues: 629 sheet: 0.30 (0.16), residues: 986 loop : -1.05 (0.13), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 64 HIS 0.004 0.000 HIS C 69 PHE 0.019 0.001 PHE O 78 TYR 0.023 0.001 TYR A 170 ARG 0.007 0.000 ARG B 567 Details of bonding type rmsd hydrogen bonds : bond 0.04206 ( 1110) hydrogen bonds : angle 4.90176 ( 3009) SS BOND : bond 0.00324 ( 45) SS BOND : angle 2.10321 ( 90) covalent geometry : bond 0.00240 (29639) covalent geometry : angle 0.55413 (40447) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 215 time to evaluate : 3.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 202 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7204 (mttp) REVERT: C 238 PHE cc_start: 0.6851 (OUTLIER) cc_final: 0.6630 (p90) REVERT: C 357 ARG cc_start: 0.8178 (tpt90) cc_final: 0.7952 (tpt90) REVERT: C 386 LYS cc_start: 0.9141 (mmmt) cc_final: 0.8911 (pttp) REVERT: C 465 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6611 (pt0) REVERT: C 881 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8397 (t) REVERT: C 904 TYR cc_start: 0.7810 (OUTLIER) cc_final: 0.7569 (m-80) REVERT: C 960 ASN cc_start: 0.8476 (t0) cc_final: 0.7829 (t0) REVERT: C 1029 MET cc_start: 0.8962 (tpp) cc_final: 0.8584 (ttm) REVERT: B 190 ARG cc_start: 0.7958 (mtt-85) cc_final: 0.7352 (mtt90) REVERT: B 202 LYS cc_start: 0.8082 (mttp) cc_final: 0.7366 (mppt) REVERT: B 383 SER cc_start: 0.8091 (m) cc_final: 0.7741 (p) REVERT: B 399 SER cc_start: 0.8592 (OUTLIER) cc_final: 0.8159 (t) REVERT: B 403 ARG cc_start: 0.8723 (ttm-80) cc_final: 0.8419 (ttm-80) REVERT: B 493 GLN cc_start: 0.8140 (pt0) cc_final: 0.7811 (pt0) REVERT: B 501 TYR cc_start: 0.8141 (m-10) cc_final: 0.7514 (m-80) REVERT: B 904 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.7729 (m-80) REVERT: B 1017 GLU cc_start: 0.8326 (tp30) cc_final: 0.7944 (tm-30) REVERT: A 239 GLN cc_start: 0.7268 (mp10) cc_final: 0.6380 (mp10) REVERT: A 904 TYR cc_start: 0.8119 (m-10) cc_final: 0.7619 (m-10) REVERT: A 957 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8192 (tm-30) REVERT: N 44 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.8044 (tppt) REVERT: N 49 MET cc_start: 0.6755 (mmm) cc_final: 0.6082 (mmp) REVERT: N 98 THR cc_start: 0.6034 (p) cc_final: 0.5466 (t) REVERT: O 22 CYS cc_start: 0.5445 (t) cc_final: 0.4836 (t) REVERT: O 34 MET cc_start: 0.7216 (mmm) cc_final: 0.6962 (mmm) REVERT: K 28 MET cc_start: 0.5594 (ppp) cc_final: 0.5242 (ppp) REVERT: K 34 MET cc_start: 0.6658 (pmm) cc_final: 0.6423 (pmm) REVERT: K 111 ARG cc_start: 0.4054 (mtm-85) cc_final: 0.3794 (mtp180) outliers start: 75 outliers final: 62 residues processed: 275 average time/residue: 0.3673 time to fit residues: 172.1064 Evaluate side-chains 276 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 206 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 123 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 111 optimal weight: 6.9990 chunk 260 optimal weight: 0.9990 chunk 275 optimal weight: 0.0970 chunk 108 optimal weight: 0.8980 chunk 284 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 85 optimal weight: 0.0970 chunk 209 optimal weight: 4.9990 chunk 291 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 218 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 HIS ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.178043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.110372 restraints weight = 49639.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.108529 restraints weight = 30804.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.107815 restraints weight = 24567.954| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 29684 Z= 0.106 Angle : 0.561 14.182 40537 Z= 0.288 Chirality : 0.043 0.306 4687 Planarity : 0.004 0.052 5188 Dihedral : 4.321 54.371 4834 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.74 % Favored : 95.16 % Rotamer: Outliers : 2.46 % Allowed : 18.96 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.01 (0.14), residues: 3717 helix: 2.50 (0.21), residues: 629 sheet: 0.33 (0.16), residues: 989 loop : -1.00 (0.13), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 64 HIS 0.004 0.000 HIS C 69 PHE 0.038 0.001 PHE O 78 TYR 0.024 0.001 TYR K 56 ARG 0.007 0.000 ARG B 567 Details of bonding type rmsd hydrogen bonds : bond 0.04126 ( 1110) hydrogen bonds : angle 4.84044 ( 3009) SS BOND : bond 0.00317 ( 45) SS BOND : angle 2.13892 ( 90) covalent geometry : bond 0.00234 (29639) covalent geometry : angle 0.55261 (40447) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10232.06 seconds wall clock time: 181 minutes 27.45 seconds (10887.45 seconds total)