Starting phenix.real_space_refine on Fri Jun 20 04:26:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tla_25985/06_2025/7tla_25985.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tla_25985/06_2025/7tla_25985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tla_25985/06_2025/7tla_25985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tla_25985/06_2025/7tla_25985.map" model { file = "/net/cci-nas-00/data/ceres_data/7tla_25985/06_2025/7tla_25985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tla_25985/06_2025/7tla_25985.cif" } resolution = 3.13 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= 0.003 sd= 0.080 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 105 5.16 5 C 14738 2.51 5 N 3827 2.21 5 O 4382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23052 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7602 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "B" Number of atoms: 7757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7757 Classifications: {'peptide': 992} Link IDs: {'PTRANS': 50, 'TRANS': 941} Chain breaks: 10 Chain: "C" Number of atoms: 7693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 7693 Classifications: {'peptide': 984} Link IDs: {'PTRANS': 48, 'TRANS': 935} Chain breaks: 11 Time building chain proxies: 13.32, per 1000 atoms: 0.58 Number of scatterers: 23052 At special positions: 0 Unit cell: (131.44, 130.38, 170.66, 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 105 16.00 O 4382 8.00 N 3827 7.00 C 14738 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS B 985 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A 985 " - pdb=" SG CYS C 383 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.99 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.00 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=2.05 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS C 985 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.01 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.00 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.01 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.01 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: 5.11 Conformation dependent library (CDL) restraints added in 2.7 seconds 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5542 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 49 sheets defined 28.0% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.201A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.093A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.781A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.607A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.791A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.613A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.652A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.678A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.753A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.172A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.058A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.108A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.582A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 737 through 743 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 removed outlier: 3.650A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.604A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.604A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.820A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.688A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.804A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.671A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.530A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.988A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.085A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.626A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) 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 755 removed outlier: 3.937A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.672A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.893A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 838 removed outlier: 4.332A pdb=" N GLN C 836 " --> pdb=" O GLY C 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.601A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.714A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.164A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.028A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.646A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.431A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.431A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.870A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.643A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.081A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.137A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.137A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.763A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.415A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.726A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.132A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.504A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.201A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.669A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.407A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.745A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.765A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.109A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG B 102 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE B 119 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.724A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.214A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.214A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.899A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD3, first strand: chain 'B' and resid 542 through 543 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.671A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.551A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.129A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.394A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.654A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.468A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.231A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.774A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.499A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.298A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.805A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.521A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.803A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.803A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.540A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) 1062 hydrogen bonds defined for protein. 2877 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: 11.82 Time building geometry restraints manager: 6.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6040 1.33 - 1.45: 4479 1.45 - 1.58: 12917 1.58 - 1.70: 0 1.70 - 1.82: 129 Bond restraints: 23565 Sorted by residual: bond pdb=" CA PRO A 862 " pdb=" C PRO A 862 " ideal model delta sigma weight residual 1.517 1.540 -0.023 6.70e-03 2.23e+04 1.16e+01 bond pdb=" CA PRO C 862 " pdb=" C PRO C 862 " ideal model delta sigma weight residual 1.517 1.540 -0.023 6.70e-03 2.23e+04 1.15e+01 bond pdb=" CA PRO B 862 " pdb=" C PRO B 862 " ideal model delta sigma weight residual 1.517 1.540 -0.023 6.70e-03 2.23e+04 1.14e+01 bond pdb=" CZ ARG B1039 " pdb=" NH2 ARG B1039 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.61e+00 bond pdb=" CZ ARG A1039 " pdb=" NH2 ARG A1039 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 9.11e+00 ... (remaining 23560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 23647 1.94 - 3.88: 7505 3.88 - 5.81: 836 5.81 - 7.75: 66 7.75 - 9.69: 5 Bond angle restraints: 32059 Sorted by residual: angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 118.76 -8.06 1.22e+00 6.72e-01 4.36e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 118.03 -7.33 1.22e+00 6.72e-01 3.61e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 117.73 -7.03 1.22e+00 6.72e-01 3.32e+01 angle pdb=" CA ASP B 796 " pdb=" CB ASP B 796 " pdb=" CG ASP B 796 " ideal model delta sigma weight residual 112.60 117.99 -5.39 1.00e+00 1.00e+00 2.90e+01 angle pdb=" CB HIS C 519 " pdb=" CG HIS C 519 " pdb=" CD2 HIS C 519 " ideal model delta sigma weight residual 131.20 124.34 6.86 1.30e+00 5.92e-01 2.78e+01 ... (remaining 32054 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.13: 13059 18.13 - 36.25: 792 36.25 - 54.38: 127 54.38 - 72.50: 46 72.50 - 90.63: 32 Dihedral angle restraints: 14056 sinusoidal: 5473 harmonic: 8583 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -165.35 79.35 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -160.97 74.97 1 1.00e+01 1.00e-02 7.11e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 153.55 -60.55 1 1.00e+01 1.00e-02 4.88e+01 ... (remaining 14053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2191 0.079 - 0.159: 1231 0.159 - 0.238: 199 0.238 - 0.317: 40 0.317 - 0.397: 10 Chirality restraints: 3671 Sorted by residual: chirality pdb=" CA PRO C 986 " pdb=" N PRO C 986 " pdb=" C PRO C 986 " pdb=" CB PRO C 986 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA ASP A 571 " pdb=" N ASP A 571 " pdb=" C ASP A 571 " pdb=" CB ASP A 571 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CA ALA B 123 " pdb=" N ALA B 123 " pdb=" C ALA B 123 " pdb=" CB ALA B 123 " both_signs ideal model delta sigma weight residual False 2.48 2.10 0.38 2.00e-01 2.50e+01 3.66e+00 ... (remaining 3668 not shown) Planarity restraints: 4144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 495 " -0.153 2.00e-02 2.50e+03 8.42e-02 1.42e+02 pdb=" CG TYR A 495 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A 495 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 TYR A 495 " 0.076 2.00e-02 2.50e+03 pdb=" CE1 TYR A 495 " 0.054 2.00e-02 2.50e+03 pdb=" CE2 TYR A 495 " 0.040 2.00e-02 2.50e+03 pdb=" CZ TYR A 495 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 495 " -0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 707 " -0.113 2.00e-02 2.50e+03 6.81e-02 9.26e+01 pdb=" CG TYR C 707 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR C 707 " 0.062 2.00e-02 2.50e+03 pdb=" CD2 TYR C 707 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR C 707 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR C 707 " 0.065 2.00e-02 2.50e+03 pdb=" CZ TYR C 707 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR C 707 " -0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 423 " -0.126 2.00e-02 2.50e+03 6.70e-02 8.97e+01 pdb=" CG TYR B 423 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR B 423 " 0.064 2.00e-02 2.50e+03 pdb=" CD2 TYR B 423 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 TYR B 423 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR B 423 " 0.037 2.00e-02 2.50e+03 pdb=" CZ TYR B 423 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 423 " -0.097 2.00e-02 2.50e+03 ... (remaining 4141 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 11424 3.00 - 3.47: 22523 3.47 - 3.95: 38851 3.95 - 4.42: 43488 4.42 - 4.90: 74194 Nonbonded interactions: 190480 Sorted by model distance: nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.522 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.524 3.040 nonbonded pdb=" OE1 GLU B 516 " pdb=" OH TYR C 200 " model vdw 2.525 3.040 nonbonded pdb=" OE1 GLU A 298 " pdb=" OG SER A 316 " model vdw 2.532 3.040 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.543 3.040 ... (remaining 190475 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 620 or resid 641 through 1147)) selection = (chain 'C' and (resid 27 through 827 or resid 854 through 1147)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 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: 0.010 Extract box with map and model: 0.880 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 55.100 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.100 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5969 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 : 0.012 0.042 23604 Z= 0.723 Angle : 1.761 9.688 32137 Z= 1.194 Chirality : 0.092 0.397 3671 Planarity : 0.014 0.198 4144 Dihedral : 13.367 90.625 8397 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 0.09 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.01 % Favored : 93.71 % Rotamer: Outliers : 1.12 % Allowed : 2.83 % Favored : 96.05 % Cbeta Deviations : 0.11 % 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: -1.09 (0.14), residues: 2878 helix: -0.85 (0.16), residues: 692 sheet: 0.27 (0.21), residues: 581 loop : -1.02 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.101 0.021 TRP A 104 HIS 0.010 0.003 HIS A1083 PHE 0.073 0.012 PHE B 718 TYR 0.153 0.020 TYR A 495 ARG 0.010 0.001 ARG B1019 Details of bonding type rmsd hydrogen bonds : bond 0.14213 ( 1034) hydrogen bonds : angle 8.33519 ( 2877) SS BOND : bond 0.01479 ( 39) SS BOND : angle 2.15938 ( 78) covalent geometry : bond 0.01234 (23565) covalent geometry : angle 1.76018 (32059) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 375 time to evaluate : 2.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8017 (p0) cc_final: 0.7654 (p0) REVERT: A 200 TYR cc_start: 0.6918 (m-80) cc_final: 0.6231 (m-80) REVERT: A 237 ARG cc_start: 0.6626 (mtt90) cc_final: 0.6169 (mtp180) REVERT: A 239 GLN cc_start: 0.6163 (tt0) cc_final: 0.5872 (tt0) REVERT: A 269 TYR cc_start: 0.7322 (m-80) cc_final: 0.6925 (m-80) REVERT: A 366 SER cc_start: 0.9100 (OUTLIER) cc_final: 0.8870 (p) REVERT: A 442 ASP cc_start: 0.7236 (m-30) cc_final: 0.6978 (m-30) REVERT: A 495 TYR cc_start: 0.6711 (m-80) cc_final: 0.5920 (m-80) REVERT: A 528 LYS cc_start: 0.8254 (tttt) cc_final: 0.8004 (tttm) REVERT: A 529 LYS cc_start: 0.8476 (mttt) cc_final: 0.7640 (mmtt) REVERT: A 558 LYS cc_start: 0.7706 (tttt) cc_final: 0.7117 (mmmt) REVERT: A 614 ASP cc_start: 0.7250 (t70) cc_final: 0.7046 (m-30) REVERT: A 646 ARG cc_start: 0.8127 (mtm180) cc_final: 0.7730 (mtp180) REVERT: A 654 GLU cc_start: 0.6965 (tt0) cc_final: 0.6503 (tp30) REVERT: A 675 GLN cc_start: 0.6524 (mt0) cc_final: 0.5447 (pp30) REVERT: A 776 LYS cc_start: 0.6686 (tttt) cc_final: 0.6437 (tttp) REVERT: A 780 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6660 (mt-10) REVERT: A 786 LYS cc_start: 0.7875 (pttt) cc_final: 0.7473 (pttm) REVERT: A 790 LYS cc_start: 0.7519 (pttt) cc_final: 0.7220 (pttp) REVERT: A 902 MET cc_start: 0.7202 (mmt) cc_final: 0.6846 (mmm) REVERT: A 950 ASP cc_start: 0.6486 (t70) cc_final: 0.6197 (m-30) REVERT: A 957 GLN cc_start: 0.6211 (tp-100) cc_final: 0.5854 (tt0) REVERT: A 995 ARG cc_start: 0.6774 (mtt180) cc_final: 0.6565 (mtp180) REVERT: A 1002 GLN cc_start: 0.6647 (tt0) cc_final: 0.6145 (tp40) REVERT: A 1045 LYS cc_start: 0.7435 (ttpp) cc_final: 0.7229 (mmmt) REVERT: B 29 THR cc_start: 0.7176 (t) cc_final: 0.6930 (t) REVERT: B 81 ASN cc_start: 0.7296 (p0) cc_final: 0.6136 (p0) REVERT: B 118 LEU cc_start: 0.7158 (tp) cc_final: 0.6515 (mt) REVERT: B 128 ILE cc_start: 0.5270 (mt) cc_final: 0.4824 (mt) REVERT: B 198 ASP cc_start: 0.7159 (m-30) cc_final: 0.6777 (p0) REVERT: B 200 TYR cc_start: 0.7156 (m-80) cc_final: 0.6840 (m-80) REVERT: B 231 ILE cc_start: 0.7186 (pt) cc_final: 0.6947 (pt) REVERT: B 307 THR cc_start: 0.8595 (m) cc_final: 0.8153 (t) REVERT: B 309 GLU cc_start: 0.6169 (mp0) cc_final: 0.5905 (mp0) REVERT: B 332 ILE cc_start: 0.5674 (tt) cc_final: 0.5445 (tt) REVERT: B 334 ASN cc_start: 0.6803 (m-40) cc_final: 0.6575 (m110) REVERT: B 335 LEU cc_start: 0.8263 (mt) cc_final: 0.7829 (tt) REVERT: B 351 TYR cc_start: 0.6857 (p90) cc_final: 0.6585 (p90) REVERT: B 518 LEU cc_start: 0.6412 (mt) cc_final: 0.6166 (pp) REVERT: B 529 LYS cc_start: 0.7683 (mttt) cc_final: 0.6927 (mmmm) REVERT: B 556 ASN cc_start: 0.7098 (p0) cc_final: 0.6582 (m110) REVERT: B 661 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7216 (mm-30) REVERT: B 723 THR cc_start: 0.6866 (t) cc_final: 0.6603 (p) REVERT: B 776 LYS cc_start: 0.6495 (tttt) cc_final: 0.5981 (tttm) REVERT: B 786 LYS cc_start: 0.8241 (pttt) cc_final: 0.7979 (pttm) REVERT: B 902 MET cc_start: 0.7492 (mmm) cc_final: 0.6631 (tpt) REVERT: B 950 ASP cc_start: 0.6513 (t70) cc_final: 0.6291 (m-30) REVERT: B 990 GLU cc_start: 0.6481 (mt-10) cc_final: 0.6051 (tt0) REVERT: B 1003 SER cc_start: 0.6932 (t) cc_final: 0.6603 (m) REVERT: B 1045 LYS cc_start: 0.8209 (ttpp) cc_final: 0.7649 (tmtt) REVERT: B 1094 VAL cc_start: 0.7541 (OUTLIER) cc_final: 0.7138 (m) REVERT: B 1114 ILE cc_start: 0.8155 (mm) cc_final: 0.7941 (mm) REVERT: C 32 PHE cc_start: 0.6766 (m-80) cc_final: 0.6164 (m-80) REVERT: C 63 THR cc_start: 0.7142 (m) cc_final: 0.6933 (p) REVERT: C 133 PHE cc_start: 0.6145 (m-80) cc_final: 0.5349 (t80) REVERT: C 239 GLN cc_start: 0.7452 (tt0) cc_final: 0.7102 (tt0) REVERT: C 269 TYR cc_start: 0.7632 (m-80) cc_final: 0.7249 (m-10) REVERT: C 304 LYS cc_start: 0.7556 (mmtm) cc_final: 0.7350 (mmtm) REVERT: C 335 LEU cc_start: 0.7996 (mt) cc_final: 0.7561 (tt) REVERT: C 380 TYR cc_start: 0.6529 (m-80) cc_final: 0.6036 (m-10) REVERT: C 396 TYR cc_start: 0.5062 (m-80) cc_final: 0.4546 (m-10) REVERT: C 558 LYS cc_start: 0.7654 (tttt) cc_final: 0.7363 (mmmt) REVERT: C 568 ASP cc_start: 0.6838 (t0) cc_final: 0.6627 (m-30) REVERT: C 574 ASP cc_start: 0.6281 (t0) cc_final: 0.6080 (t0) REVERT: C 614 ASP cc_start: 0.7515 (t0) cc_final: 0.7180 (m-30) REVERT: C 780 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6300 (mm-30) REVERT: C 786 LYS cc_start: 0.8273 (pttt) cc_final: 0.7824 (ptpp) REVERT: C 902 MET cc_start: 0.7696 (mmt) cc_final: 0.7350 (tpt) REVERT: C 964 LYS cc_start: 0.7200 (mttt) cc_final: 0.6870 (mmtt) REVERT: C 1005 GLN cc_start: 0.7086 (mt0) cc_final: 0.6635 (mm-40) outliers start: 29 outliers final: 9 residues processed: 402 average time/residue: 0.3560 time to fit residues: 220.5847 Evaluate side-chains 227 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 216 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 0.8980 chunk 222 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 230 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 266 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 751 ASN B 314 GLN B 394 ASN B 540 ASN B 955 ASN B 965 GLN C 388 ASN C 613 GLN C 751 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.149033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.099676 restraints weight = 33595.886| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.36 r_work: 0.3081 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23604 Z= 0.147 Angle : 0.618 10.875 32137 Z= 0.330 Chirality : 0.047 0.197 3671 Planarity : 0.004 0.037 4144 Dihedral : 6.068 66.936 3151 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.92 % Favored : 96.98 % Rotamer: Outliers : 1.63 % Allowed : 6.04 % Favored : 92.33 % 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: -0.11 (0.15), residues: 2878 helix: 1.24 (0.20), residues: 687 sheet: 0.04 (0.18), residues: 724 loop : -0.73 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 64 HIS 0.004 0.001 HIS B 519 PHE 0.026 0.002 PHE B 168 TYR 0.019 0.002 TYR A 170 ARG 0.009 0.001 ARG B 102 Details of bonding type rmsd hydrogen bonds : bond 0.04403 ( 1034) hydrogen bonds : angle 6.10640 ( 2877) SS BOND : bond 0.00833 ( 39) SS BOND : angle 1.51903 ( 78) covalent geometry : bond 0.00317 (23565) covalent geometry : angle 0.61392 (32059) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 258 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.7773 (mt) cc_final: 0.7567 (mp) REVERT: A 230 PRO cc_start: 0.8144 (Cg_endo) cc_final: 0.7735 (Cg_exo) REVERT: A 237 ARG cc_start: 0.7592 (mtt90) cc_final: 0.7257 (mtm-85) REVERT: A 239 GLN cc_start: 0.7784 (tt0) cc_final: 0.7579 (tt0) REVERT: A 529 LYS cc_start: 0.8586 (mttt) cc_final: 0.8331 (mmtt) REVERT: A 558 LYS cc_start: 0.8817 (tttt) cc_final: 0.8474 (mmmt) REVERT: A 619 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6818 (mp0) REVERT: A 675 GLN cc_start: 0.7911 (mt0) cc_final: 0.7396 (pp30) REVERT: A 780 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8397 (mm-30) REVERT: A 790 LYS cc_start: 0.8508 (pttt) cc_final: 0.8267 (pttp) REVERT: A 804 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8264 (mp10) REVERT: A 811 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.6515 (tmtt) REVERT: A 957 GLN cc_start: 0.8381 (tp-100) cc_final: 0.8145 (tt0) REVERT: A 1050 MET cc_start: 0.9332 (ptm) cc_final: 0.9038 (ptp) REVERT: A 1107 ARG cc_start: 0.8483 (mtm-85) cc_final: 0.8278 (mtt90) REVERT: B 81 ASN cc_start: 0.7874 (p0) cc_final: 0.7127 (p0) REVERT: B 117 LEU cc_start: 0.7506 (mp) cc_final: 0.7201 (mt) REVERT: B 118 LEU cc_start: 0.7905 (tp) cc_final: 0.7460 (mm) REVERT: B 140 PHE cc_start: 0.7823 (p90) cc_final: 0.7512 (p90) REVERT: B 307 THR cc_start: 0.9255 (m) cc_final: 0.9004 (t) REVERT: B 335 LEU cc_start: 0.8504 (mt) cc_final: 0.8095 (tp) REVERT: B 387 LEU cc_start: 0.7812 (mt) cc_final: 0.7587 (mt) REVERT: B 492 LEU cc_start: 0.7421 (pt) cc_final: 0.7107 (mt) REVERT: B 529 LYS cc_start: 0.8126 (mttt) cc_final: 0.7493 (mmmm) REVERT: B 568 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7384 (m-30) REVERT: B 574 ASP cc_start: 0.8016 (t70) cc_final: 0.7173 (t0) REVERT: B 776 LYS cc_start: 0.8929 (tttt) cc_final: 0.8723 (ttpt) REVERT: B 950 ASP cc_start: 0.8483 (t70) cc_final: 0.8216 (m-30) REVERT: B 990 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7695 (tt0) REVERT: B 1003 SER cc_start: 0.9032 (t) cc_final: 0.8723 (m) REVERT: C 32 PHE cc_start: 0.7472 (m-80) cc_final: 0.7254 (m-80) REVERT: C 133 PHE cc_start: 0.6145 (m-80) cc_final: 0.5399 (t80) REVERT: C 239 GLN cc_start: 0.8190 (tt0) cc_final: 0.7749 (tm-30) REVERT: C 241 LEU cc_start: 0.8113 (mt) cc_final: 0.7702 (mp) REVERT: C 304 LYS cc_start: 0.8860 (mmtm) cc_final: 0.8543 (mmtm) REVERT: C 335 LEU cc_start: 0.8317 (mt) cc_final: 0.7476 (tt) REVERT: C 380 TYR cc_start: 0.7296 (m-80) cc_final: 0.7060 (m-80) REVERT: C 425 LEU cc_start: 0.4270 (OUTLIER) cc_final: 0.4003 (pp) REVERT: C 780 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8196 (mm-30) REVERT: C 964 LYS cc_start: 0.8983 (mttt) cc_final: 0.8669 (mmtt) REVERT: C 990 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7423 (tm-30) outliers start: 42 outliers final: 15 residues processed: 287 average time/residue: 0.3511 time to fit residues: 156.9032 Evaluate side-chains 212 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 859 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 179 optimal weight: 0.9980 chunk 227 optimal weight: 2.9990 chunk 216 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 chunk 257 optimal weight: 0.8980 chunk 292 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 194 optimal weight: 0.0030 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN B 506 GLN B 969 ASN C 394 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.147432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.103692 restraints weight = 33300.015| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.20 r_work: 0.3079 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 23604 Z= 0.142 Angle : 0.559 7.840 32137 Z= 0.295 Chirality : 0.045 0.183 3671 Planarity : 0.004 0.046 4144 Dihedral : 5.442 64.179 3142 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.63 % Allowed : 8.10 % Favored : 90.28 % 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: -0.00 (0.15), residues: 2878 helix: 1.53 (0.20), residues: 689 sheet: 0.08 (0.18), residues: 675 loop : -0.74 (0.15), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 353 HIS 0.004 0.001 HIS A 519 PHE 0.024 0.001 PHE B 400 TYR 0.019 0.001 TYR B1067 ARG 0.004 0.000 ARG C 577 Details of bonding type rmsd hydrogen bonds : bond 0.04059 ( 1034) hydrogen bonds : angle 5.70125 ( 2877) SS BOND : bond 0.00296 ( 39) SS BOND : angle 1.41569 ( 78) covalent geometry : bond 0.00326 (23565) covalent geometry : angle 0.55494 (32059) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 215 time to evaluate : 2.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7612 (mtt90) cc_final: 0.7191 (mtm-85) REVERT: A 269 TYR cc_start: 0.8607 (m-10) cc_final: 0.8385 (m-10) REVERT: A 529 LYS cc_start: 0.8623 (mttt) cc_final: 0.8342 (mmtt) REVERT: A 558 LYS cc_start: 0.8832 (tttt) cc_final: 0.8433 (mmmt) REVERT: A 619 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: A 661 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8206 (mm-30) REVERT: A 675 GLN cc_start: 0.7838 (mt0) cc_final: 0.7436 (pp30) REVERT: A 780 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8338 (mm-30) REVERT: A 790 LYS cc_start: 0.8545 (pttt) cc_final: 0.8331 (pttp) REVERT: A 811 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.6641 (tmtt) REVERT: A 957 GLN cc_start: 0.8305 (tp-100) cc_final: 0.8040 (tt0) REVERT: A 1073 LYS cc_start: 0.8918 (tttt) cc_final: 0.8611 (ttmm) REVERT: A 1107 ARG cc_start: 0.8495 (mtm-85) cc_final: 0.8228 (mtt90) REVERT: B 81 ASN cc_start: 0.8032 (p0) cc_final: 0.7253 (p0) REVERT: B 118 LEU cc_start: 0.7799 (tp) cc_final: 0.7388 (mm) REVERT: B 140 PHE cc_start: 0.7826 (p90) cc_final: 0.7560 (p90) REVERT: B 307 THR cc_start: 0.9217 (m) cc_final: 0.8920 (t) REVERT: B 400 PHE cc_start: 0.8670 (p90) cc_final: 0.8326 (p90) REVERT: B 441 LEU cc_start: 0.8654 (mm) cc_final: 0.8372 (mt) REVERT: B 492 LEU cc_start: 0.7314 (pt) cc_final: 0.7067 (mt) REVERT: B 568 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7711 (m-30) REVERT: B 574 ASP cc_start: 0.8126 (t70) cc_final: 0.7793 (t70) REVERT: B 776 LYS cc_start: 0.8967 (tttt) cc_final: 0.8735 (ttpt) REVERT: B 950 ASP cc_start: 0.8522 (t70) cc_final: 0.8110 (m-30) REVERT: B 990 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7492 (tt0) REVERT: B 1003 SER cc_start: 0.9006 (t) cc_final: 0.8729 (m) REVERT: C 32 PHE cc_start: 0.7533 (m-80) cc_final: 0.7044 (m-80) REVERT: C 133 PHE cc_start: 0.6106 (m-80) cc_final: 0.5421 (t80) REVERT: C 239 GLN cc_start: 0.8167 (tt0) cc_final: 0.7756 (tm-30) REVERT: C 241 LEU cc_start: 0.8142 (mt) cc_final: 0.7789 (mp) REVERT: C 304 LYS cc_start: 0.8844 (mmtm) cc_final: 0.8565 (mmtm) REVERT: C 335 LEU cc_start: 0.8075 (mt) cc_final: 0.7514 (tt) REVERT: C 380 TYR cc_start: 0.7329 (m-80) cc_final: 0.7125 (m-80) REVERT: C 387 LEU cc_start: 0.8729 (mp) cc_final: 0.8508 (mt) REVERT: C 425 LEU cc_start: 0.4084 (OUTLIER) cc_final: 0.3816 (pp) REVERT: C 427 ASP cc_start: 0.7337 (m-30) cc_final: 0.7054 (t0) REVERT: C 586 ASP cc_start: 0.8243 (m-30) cc_final: 0.7911 (m-30) REVERT: C 780 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8176 (mm-30) REVERT: C 827 THR cc_start: 0.8399 (t) cc_final: 0.8128 (p) REVERT: C 990 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7392 (tm-30) outliers start: 42 outliers final: 25 residues processed: 247 average time/residue: 0.3272 time to fit residues: 130.1705 Evaluate side-chains 218 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 859 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 37 optimal weight: 9.9990 chunk 279 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 237 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN B 52 GLN B 360 ASN B 613 GLN B 935 GLN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.144675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.101376 restraints weight = 33936.756| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.34 r_work: 0.3013 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 23604 Z= 0.269 Angle : 0.623 8.692 32137 Z= 0.326 Chirality : 0.048 0.203 3671 Planarity : 0.004 0.052 4144 Dihedral : 5.526 61.053 3142 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.98 % Allowed : 9.57 % Favored : 88.45 % 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: -0.27 (0.15), residues: 2878 helix: 1.27 (0.20), residues: 693 sheet: -0.08 (0.18), residues: 679 loop : -0.90 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 353 HIS 0.006 0.001 HIS A 519 PHE 0.016 0.002 PHE A 43 TYR 0.022 0.002 TYR C1067 ARG 0.004 0.001 ARG B 102 Details of bonding type rmsd hydrogen bonds : bond 0.04404 ( 1034) hydrogen bonds : angle 5.85145 ( 2877) SS BOND : bond 0.00412 ( 39) SS BOND : angle 1.76071 ( 78) covalent geometry : bond 0.00644 (23565) covalent geometry : angle 0.61760 (32059) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 191 time to evaluate : 2.616 Fit side-chains revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7665 (mtt90) cc_final: 0.7213 (mtm-85) REVERT: A 529 LYS cc_start: 0.8705 (mttt) cc_final: 0.8377 (mmtt) REVERT: A 546 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7958 (tp) REVERT: A 558 LYS cc_start: 0.8908 (tttt) cc_final: 0.8501 (mmmt) REVERT: A 619 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6899 (mp0) REVERT: A 675 GLN cc_start: 0.7967 (mt0) cc_final: 0.7478 (pp30) REVERT: A 790 LYS cc_start: 0.8701 (pttt) cc_final: 0.8363 (pttp) REVERT: A 804 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8150 (mp10) REVERT: A 811 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.6832 (tmtt) REVERT: A 957 GLN cc_start: 0.8387 (tp-100) cc_final: 0.8116 (tt0) REVERT: A 1073 LYS cc_start: 0.8893 (tttt) cc_final: 0.8616 (ttmm) REVERT: A 1107 ARG cc_start: 0.8417 (mtm-85) cc_final: 0.8189 (mtt180) REVERT: B 118 LEU cc_start: 0.7895 (tp) cc_final: 0.7578 (mm) REVERT: B 190 ARG cc_start: 0.8265 (mtm-85) cc_final: 0.8036 (mtt-85) REVERT: B 307 THR cc_start: 0.9196 (m) cc_final: 0.8923 (t) REVERT: B 400 PHE cc_start: 0.8541 (p90) cc_final: 0.8165 (p90) REVERT: B 554 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7790 (pt0) REVERT: B 574 ASP cc_start: 0.8302 (t70) cc_final: 0.8047 (t0) REVERT: B 776 LYS cc_start: 0.8967 (tttt) cc_final: 0.8643 (ttpt) REVERT: B 950 ASP cc_start: 0.8591 (t70) cc_final: 0.8277 (m-30) REVERT: B 990 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7611 (tt0) REVERT: B 1003 SER cc_start: 0.9059 (t) cc_final: 0.8744 (m) REVERT: C 32 PHE cc_start: 0.7713 (m-80) cc_final: 0.7169 (m-80) REVERT: C 132 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7703 (mt-10) REVERT: C 133 PHE cc_start: 0.6145 (m-80) cc_final: 0.5479 (t80) REVERT: C 239 GLN cc_start: 0.8182 (tt0) cc_final: 0.7885 (tt0) REVERT: C 281 GLU cc_start: 0.6802 (pm20) cc_final: 0.6358 (pm20) REVERT: C 335 LEU cc_start: 0.8171 (mt) cc_final: 0.7459 (tt) REVERT: C 425 LEU cc_start: 0.4340 (OUTLIER) cc_final: 0.4082 (pp) REVERT: C 427 ASP cc_start: 0.7414 (m-30) cc_final: 0.7083 (t0) REVERT: C 586 ASP cc_start: 0.8212 (m-30) cc_final: 0.7891 (m-30) REVERT: C 990 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7406 (tm-30) outliers start: 51 outliers final: 36 residues processed: 233 average time/residue: 0.3187 time to fit residues: 121.1497 Evaluate side-chains 215 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 159 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 221 optimal weight: 8.9990 chunk 163 optimal weight: 0.9990 chunk 289 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 chunk 123 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 264 optimal weight: 0.9980 chunk 235 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.147836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.098457 restraints weight = 33504.418| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.36 r_work: 0.3058 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23604 Z= 0.121 Angle : 0.517 6.980 32137 Z= 0.272 Chirality : 0.044 0.175 3671 Planarity : 0.004 0.050 4144 Dihedral : 5.107 60.931 3142 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.86 % Allowed : 10.46 % Favored : 87.68 % 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 (0.15), residues: 2878 helix: 1.66 (0.20), residues: 696 sheet: 0.03 (0.18), residues: 660 loop : -0.80 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 353 HIS 0.002 0.001 HIS B 49 PHE 0.028 0.001 PHE C 515 TYR 0.019 0.001 TYR B 351 ARG 0.004 0.000 ARG A 905 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 1034) hydrogen bonds : angle 5.38864 ( 2877) SS BOND : bond 0.00308 ( 39) SS BOND : angle 1.32487 ( 78) covalent geometry : bond 0.00268 (23565) covalent geometry : angle 0.51313 (32059) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.6848 (m-80) cc_final: 0.6279 (m-80) REVERT: A 237 ARG cc_start: 0.7673 (mtt90) cc_final: 0.7255 (mtm-85) REVERT: A 269 TYR cc_start: 0.8544 (m-10) cc_final: 0.8246 (m-10) REVERT: A 529 LYS cc_start: 0.8616 (mttt) cc_final: 0.8313 (mmtt) REVERT: A 546 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7892 (tp) REVERT: A 558 LYS cc_start: 0.8881 (tttt) cc_final: 0.8487 (mmmt) REVERT: A 675 GLN cc_start: 0.7926 (mt0) cc_final: 0.7494 (pp30) REVERT: A 780 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8482 (mm-30) REVERT: A 790 LYS cc_start: 0.8614 (pttt) cc_final: 0.8360 (pttp) REVERT: A 804 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8198 (mp10) REVERT: A 957 GLN cc_start: 0.8359 (tp-100) cc_final: 0.8094 (tt0) REVERT: A 1073 LYS cc_start: 0.8871 (tttt) cc_final: 0.8616 (ttmm) REVERT: A 1107 ARG cc_start: 0.8368 (mtm-85) cc_final: 0.8158 (mtt180) REVERT: B 118 LEU cc_start: 0.7809 (tp) cc_final: 0.7482 (mm) REVERT: B 241 LEU cc_start: 0.8211 (mt) cc_final: 0.7991 (mp) REVERT: B 271 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8615 (mp10) REVERT: B 320 VAL cc_start: 0.8283 (OUTLIER) cc_final: 0.8082 (m) REVERT: B 332 ILE cc_start: 0.6571 (OUTLIER) cc_final: 0.6331 (tt) REVERT: B 364 ASP cc_start: 0.8376 (t0) cc_final: 0.8156 (t0) REVERT: B 400 PHE cc_start: 0.8505 (p90) cc_final: 0.8250 (p90) REVERT: B 441 LEU cc_start: 0.8736 (mm) cc_final: 0.8464 (mt) REVERT: B 528 LYS cc_start: 0.8166 (tppp) cc_final: 0.7897 (mmmm) REVERT: B 554 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7716 (pt0) REVERT: B 574 ASP cc_start: 0.8247 (t70) cc_final: 0.7897 (t0) REVERT: B 950 ASP cc_start: 0.8549 (t70) cc_final: 0.8192 (m-30) REVERT: B 990 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7496 (tt0) REVERT: B 1003 SER cc_start: 0.8986 (t) cc_final: 0.8750 (m) REVERT: C 32 PHE cc_start: 0.7562 (m-80) cc_final: 0.7158 (m-80) REVERT: C 63 THR cc_start: 0.8398 (m) cc_final: 0.8079 (p) REVERT: C 133 PHE cc_start: 0.6079 (m-80) cc_final: 0.5557 (t80) REVERT: C 239 GLN cc_start: 0.8034 (tt0) cc_final: 0.7684 (tt0) REVERT: C 281 GLU cc_start: 0.6771 (pm20) cc_final: 0.6344 (pm20) REVERT: C 335 LEU cc_start: 0.8213 (mt) cc_final: 0.7385 (tt) REVERT: C 353 TRP cc_start: 0.5555 (p-90) cc_final: 0.4598 (p-90) REVERT: C 425 LEU cc_start: 0.4229 (OUTLIER) cc_final: 0.3980 (pp) REVERT: C 427 ASP cc_start: 0.7376 (m-30) cc_final: 0.7004 (t0) REVERT: C 586 ASP cc_start: 0.8228 (m-30) cc_final: 0.7910 (m-30) REVERT: C 814 LYS cc_start: 0.8444 (mttt) cc_final: 0.8058 (mmtt) outliers start: 48 outliers final: 30 residues processed: 251 average time/residue: 0.3320 time to fit residues: 134.6715 Evaluate side-chains 215 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 145 optimal weight: 0.5980 chunk 97 optimal weight: 10.0000 chunk 222 optimal weight: 20.0000 chunk 194 optimal weight: 0.3980 chunk 223 optimal weight: 6.9990 chunk 221 optimal weight: 7.9990 chunk 100 optimal weight: 0.4980 chunk 292 optimal weight: 2.9990 chunk 4 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 240 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.147530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.103622 restraints weight = 33230.944| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.17 r_work: 0.3072 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23604 Z= 0.124 Angle : 0.519 10.247 32137 Z= 0.270 Chirality : 0.044 0.178 3671 Planarity : 0.004 0.078 4144 Dihedral : 4.957 59.638 3142 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.17 % Allowed : 10.73 % Favored : 87.10 % 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 (0.15), residues: 2878 helix: 1.77 (0.20), residues: 696 sheet: 0.10 (0.18), residues: 653 loop : -0.77 (0.15), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 436 HIS 0.008 0.001 HIS C 519 PHE 0.017 0.001 PHE B 342 TYR 0.020 0.001 TYR B 351 ARG 0.007 0.000 ARG B 190 Details of bonding type rmsd hydrogen bonds : bond 0.03571 ( 1034) hydrogen bonds : angle 5.30143 ( 2877) SS BOND : bond 0.00263 ( 39) SS BOND : angle 1.40377 ( 78) covalent geometry : bond 0.00283 (23565) covalent geometry : angle 0.51537 (32059) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 197 time to evaluate : 2.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7658 (mtt90) cc_final: 0.7198 (mtm-85) REVERT: A 269 TYR cc_start: 0.8552 (m-10) cc_final: 0.8236 (m-10) REVERT: A 493 GLN cc_start: 0.7262 (mm-40) cc_final: 0.6988 (mm-40) REVERT: A 529 LYS cc_start: 0.8634 (mttt) cc_final: 0.8278 (mmtt) REVERT: A 558 LYS cc_start: 0.8878 (tttt) cc_final: 0.8372 (mmmt) REVERT: A 675 GLN cc_start: 0.8061 (mt0) cc_final: 0.7794 (mt0) REVERT: A 780 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8439 (mm-30) REVERT: A 790 LYS cc_start: 0.8657 (pttt) cc_final: 0.8397 (pttp) REVERT: A 804 GLN cc_start: 0.8554 (mm-40) cc_final: 0.8165 (mp10) REVERT: A 811 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.6657 (mttt) REVERT: A 957 GLN cc_start: 0.8330 (tp-100) cc_final: 0.8046 (tt0) REVERT: A 1073 LYS cc_start: 0.8840 (tttt) cc_final: 0.8584 (ttmm) REVERT: A 1107 ARG cc_start: 0.8378 (mtm-85) cc_final: 0.8152 (mtt180) REVERT: B 118 LEU cc_start: 0.7769 (tp) cc_final: 0.7419 (mm) REVERT: B 271 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8566 (mp10) REVERT: B 320 VAL cc_start: 0.8266 (OUTLIER) cc_final: 0.8064 (m) REVERT: B 332 ILE cc_start: 0.6520 (OUTLIER) cc_final: 0.6277 (tt) REVERT: B 364 ASP cc_start: 0.8391 (t0) cc_final: 0.8175 (t0) REVERT: B 400 PHE cc_start: 0.8447 (p90) cc_final: 0.8180 (p90) REVERT: B 441 LEU cc_start: 0.8742 (mm) cc_final: 0.8430 (mt) REVERT: B 554 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7699 (pt0) REVERT: B 574 ASP cc_start: 0.8175 (t70) cc_final: 0.7814 (t0) REVERT: B 950 ASP cc_start: 0.8526 (t70) cc_final: 0.8146 (m-30) REVERT: B 979 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7725 (t0) REVERT: B 990 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7444 (tt0) REVERT: B 1003 SER cc_start: 0.8981 (t) cc_final: 0.8714 (m) REVERT: C 32 PHE cc_start: 0.7535 (m-80) cc_final: 0.7134 (m-80) REVERT: C 63 THR cc_start: 0.8364 (m) cc_final: 0.8061 (p) REVERT: C 117 LEU cc_start: 0.7825 (tp) cc_final: 0.7168 (mm) REVERT: C 118 LEU cc_start: 0.8208 (tp) cc_final: 0.8007 (tt) REVERT: C 130 VAL cc_start: 0.8494 (m) cc_final: 0.8171 (t) REVERT: C 133 PHE cc_start: 0.6010 (m-80) cc_final: 0.5478 (t80) REVERT: C 205 SER cc_start: 0.8772 (p) cc_final: 0.8305 (t) REVERT: C 281 GLU cc_start: 0.6852 (pm20) cc_final: 0.6426 (pm20) REVERT: C 335 LEU cc_start: 0.8246 (mt) cc_final: 0.7537 (tt) REVERT: C 353 TRP cc_start: 0.5330 (p-90) cc_final: 0.4425 (p-90) REVERT: C 425 LEU cc_start: 0.4179 (OUTLIER) cc_final: 0.3969 (pp) REVERT: C 427 ASP cc_start: 0.7459 (m-30) cc_final: 0.7103 (t0) REVERT: C 586 ASP cc_start: 0.8163 (m-30) cc_final: 0.7881 (m-30) REVERT: C 814 LYS cc_start: 0.8375 (mttt) cc_final: 0.7998 (mmmt) REVERT: C 990 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7251 (tt0) REVERT: C 1072 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8349 (mp0) outliers start: 56 outliers final: 39 residues processed: 242 average time/residue: 0.3237 time to fit residues: 128.2525 Evaluate side-chains 230 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 184 time to evaluate : 2.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 285 optimal weight: 0.7980 chunk 293 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 222 optimal weight: 20.0000 chunk 90 optimal weight: 3.9990 chunk 281 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 219 optimal weight: 9.9990 chunk 203 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 242 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.145072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.101403 restraints weight = 33458.514| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.23 r_work: 0.3023 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23604 Z= 0.214 Angle : 0.559 7.732 32137 Z= 0.293 Chirality : 0.046 0.175 3671 Planarity : 0.004 0.065 4144 Dihedral : 5.118 59.053 3142 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.29 % Allowed : 11.08 % Favored : 86.63 % 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: -0.07 (0.15), residues: 2878 helix: 1.62 (0.20), residues: 695 sheet: 0.02 (0.18), residues: 679 loop : -0.86 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 436 HIS 0.006 0.001 HIS C 519 PHE 0.016 0.002 PHE B 342 TYR 0.019 0.002 TYR A 904 ARG 0.006 0.000 ARG B 190 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 1034) hydrogen bonds : angle 5.49339 ( 2877) SS BOND : bond 0.00369 ( 39) SS BOND : angle 1.47117 ( 78) covalent geometry : bond 0.00508 (23565) covalent geometry : angle 0.55514 (32059) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 188 time to evaluate : 3.063 Fit side-chains revert: symmetry clash REVERT: A 106 PHE cc_start: 0.6959 (m-80) cc_final: 0.6341 (m-80) REVERT: A 237 ARG cc_start: 0.7661 (mtt90) cc_final: 0.7192 (mtm-85) REVERT: A 269 TYR cc_start: 0.8554 (m-10) cc_final: 0.8278 (m-10) REVERT: A 493 GLN cc_start: 0.7233 (mm-40) cc_final: 0.6964 (mm-40) REVERT: A 529 LYS cc_start: 0.8600 (mttt) cc_final: 0.8322 (mmtt) REVERT: A 558 LYS cc_start: 0.8888 (tttt) cc_final: 0.8370 (mmmt) REVERT: A 675 GLN cc_start: 0.8069 (mt0) cc_final: 0.7817 (mt0) REVERT: A 790 LYS cc_start: 0.8731 (pttt) cc_final: 0.8396 (pttp) REVERT: A 804 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8163 (mp10) REVERT: A 811 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.6586 (mttt) REVERT: A 957 GLN cc_start: 0.8365 (tp-100) cc_final: 0.8058 (tt0) REVERT: A 1073 LYS cc_start: 0.8826 (tttt) cc_final: 0.8572 (ttmm) REVERT: A 1107 ARG cc_start: 0.8425 (mtm-85) cc_final: 0.8195 (mtt180) REVERT: B 118 LEU cc_start: 0.7815 (tp) cc_final: 0.7515 (mm) REVERT: B 200 TYR cc_start: 0.7984 (m-80) cc_final: 0.7658 (m-80) REVERT: B 271 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8524 (mp10) REVERT: B 332 ILE cc_start: 0.6491 (OUTLIER) cc_final: 0.6271 (tt) REVERT: B 400 PHE cc_start: 0.8474 (p90) cc_final: 0.8180 (p90) REVERT: B 441 LEU cc_start: 0.8768 (mm) cc_final: 0.8448 (mt) REVERT: B 528 LYS cc_start: 0.8158 (tppp) cc_final: 0.7871 (mmmm) REVERT: B 554 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7751 (pt0) REVERT: B 574 ASP cc_start: 0.8235 (t70) cc_final: 0.7895 (t0) REVERT: B 950 ASP cc_start: 0.8573 (t70) cc_final: 0.8191 (m-30) REVERT: B 979 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7761 (t0) REVERT: B 990 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7478 (tt0) REVERT: B 1003 SER cc_start: 0.9060 (t) cc_final: 0.8751 (m) REVERT: C 32 PHE cc_start: 0.7633 (m-80) cc_final: 0.7187 (m-80) REVERT: C 117 LEU cc_start: 0.7819 (tp) cc_final: 0.7203 (mm) REVERT: C 130 VAL cc_start: 0.8487 (m) cc_final: 0.8278 (t) REVERT: C 132 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7659 (mt-10) REVERT: C 133 PHE cc_start: 0.6047 (m-80) cc_final: 0.5491 (t80) REVERT: C 205 SER cc_start: 0.8758 (p) cc_final: 0.8298 (t) REVERT: C 231 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8364 (pt) REVERT: C 281 GLU cc_start: 0.6781 (pm20) cc_final: 0.6380 (pm20) REVERT: C 427 ASP cc_start: 0.7521 (m-30) cc_final: 0.7151 (t0) REVERT: C 586 ASP cc_start: 0.8108 (m-30) cc_final: 0.7863 (m-30) REVERT: C 690 GLN cc_start: 0.7663 (mt0) cc_final: 0.7382 (mm-40) REVERT: C 814 LYS cc_start: 0.8475 (mttt) cc_final: 0.8183 (mmmt) REVERT: C 1072 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8352 (mp0) outliers start: 59 outliers final: 47 residues processed: 232 average time/residue: 0.5078 time to fit residues: 187.7222 Evaluate side-chains 227 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 174 time to evaluate : 3.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 55 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 chunk 190 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 258 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 283 optimal weight: 4.9990 chunk 281 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 234 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.145725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.101903 restraints weight = 33394.137| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.22 r_work: 0.3035 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 23604 Z= 0.183 Angle : 0.549 10.362 32137 Z= 0.285 Chirality : 0.045 0.171 3671 Planarity : 0.004 0.056 4144 Dihedral : 5.051 58.214 3142 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.32 % Allowed : 11.16 % Favored : 86.52 % 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: -0.04 (0.15), residues: 2878 helix: 1.72 (0.20), residues: 685 sheet: 0.01 (0.18), residues: 681 loop : -0.85 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 436 HIS 0.006 0.001 HIS C 519 PHE 0.016 0.001 PHE A 565 TYR 0.019 0.001 TYR B 351 ARG 0.005 0.000 ARG B 190 Details of bonding type rmsd hydrogen bonds : bond 0.03793 ( 1034) hydrogen bonds : angle 5.43481 ( 2877) SS BOND : bond 0.00332 ( 39) SS BOND : angle 1.62439 ( 78) covalent geometry : bond 0.00434 (23565) covalent geometry : angle 0.54385 (32059) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 183 time to evaluate : 2.518 Fit side-chains revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7725 (mtt90) cc_final: 0.7230 (mtm-85) REVERT: A 269 TYR cc_start: 0.8560 (m-10) cc_final: 0.8232 (m-10) REVERT: A 493 GLN cc_start: 0.7336 (mm-40) cc_final: 0.7122 (mm-40) REVERT: A 529 LYS cc_start: 0.8582 (mttt) cc_final: 0.8267 (mmtt) REVERT: A 558 LYS cc_start: 0.8932 (tttt) cc_final: 0.8423 (mmmt) REVERT: A 675 GLN cc_start: 0.8083 (mt0) cc_final: 0.7853 (mt0) REVERT: A 780 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8453 (mm-30) REVERT: A 790 LYS cc_start: 0.8720 (pttt) cc_final: 0.8399 (pttp) REVERT: A 804 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8191 (mp10) REVERT: A 811 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.6552 (mttt) REVERT: A 957 GLN cc_start: 0.8381 (tp-100) cc_final: 0.8087 (tt0) REVERT: A 1073 LYS cc_start: 0.8885 (tttt) cc_final: 0.8621 (ttmm) REVERT: A 1107 ARG cc_start: 0.8403 (mtm-85) cc_final: 0.8192 (mtt180) REVERT: B 118 LEU cc_start: 0.7796 (tp) cc_final: 0.7474 (mm) REVERT: B 200 TYR cc_start: 0.7955 (m-80) cc_final: 0.7671 (m-80) REVERT: B 231 ILE cc_start: 0.8279 (pt) cc_final: 0.8068 (mm) REVERT: B 271 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8596 (mp10) REVERT: B 332 ILE cc_start: 0.6507 (OUTLIER) cc_final: 0.6285 (tt) REVERT: B 364 ASP cc_start: 0.8430 (t0) cc_final: 0.8039 (t0) REVERT: B 400 PHE cc_start: 0.8419 (p90) cc_final: 0.8101 (p90) REVERT: B 441 LEU cc_start: 0.8786 (mm) cc_final: 0.8450 (mt) REVERT: B 554 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7785 (pt0) REVERT: B 574 ASP cc_start: 0.8259 (t70) cc_final: 0.7934 (t0) REVERT: B 950 ASP cc_start: 0.8574 (t70) cc_final: 0.8241 (m-30) REVERT: B 979 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7806 (t0) REVERT: B 990 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7514 (tt0) REVERT: B 1003 SER cc_start: 0.9046 (t) cc_final: 0.8770 (m) REVERT: C 32 PHE cc_start: 0.7655 (m-80) cc_final: 0.7210 (m-80) REVERT: C 117 LEU cc_start: 0.7816 (tp) cc_final: 0.7177 (mm) REVERT: C 118 LEU cc_start: 0.7865 (tt) cc_final: 0.7654 (tp) REVERT: C 132 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7650 (mt-10) REVERT: C 133 PHE cc_start: 0.6050 (m-80) cc_final: 0.5496 (t80) REVERT: C 205 SER cc_start: 0.8766 (p) cc_final: 0.8322 (t) REVERT: C 231 ILE cc_start: 0.8662 (mt) cc_final: 0.8427 (pt) REVERT: C 281 GLU cc_start: 0.6882 (pm20) cc_final: 0.6501 (pm20) REVERT: C 335 LEU cc_start: 0.8282 (mm) cc_final: 0.7543 (tt) REVERT: C 398 ASP cc_start: 0.8525 (m-30) cc_final: 0.8074 (m-30) REVERT: C 427 ASP cc_start: 0.7499 (m-30) cc_final: 0.7170 (t0) REVERT: C 586 ASP cc_start: 0.8128 (m-30) cc_final: 0.7910 (m-30) REVERT: C 690 GLN cc_start: 0.7728 (mt0) cc_final: 0.7426 (mm-40) REVERT: C 814 LYS cc_start: 0.8473 (mttt) cc_final: 0.8142 (mmmt) REVERT: C 990 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7231 (tt0) REVERT: C 1072 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8366 (mp0) outliers start: 60 outliers final: 47 residues processed: 231 average time/residue: 0.3201 time to fit residues: 120.9053 Evaluate side-chains 233 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 181 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 190 optimal weight: 0.5980 chunk 194 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 251 optimal weight: 0.0970 chunk 172 optimal weight: 1.9990 chunk 166 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 GLN C 388 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.147879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.105391 restraints weight = 33385.970| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.42 r_work: 0.3055 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 23604 Z= 0.121 Angle : 0.518 10.315 32137 Z= 0.268 Chirality : 0.044 0.159 3671 Planarity : 0.004 0.051 4144 Dihedral : 4.879 58.035 3142 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.09 % Allowed : 11.24 % Favored : 86.67 % 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: 0.13 (0.15), residues: 2878 helix: 1.91 (0.20), residues: 680 sheet: 0.11 (0.18), residues: 664 loop : -0.76 (0.16), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 436 HIS 0.005 0.001 HIS C 519 PHE 0.012 0.001 PHE C 400 TYR 0.018 0.001 TYR B1067 ARG 0.004 0.000 ARG B 190 Details of bonding type rmsd hydrogen bonds : bond 0.03489 ( 1034) hydrogen bonds : angle 5.24893 ( 2877) SS BOND : bond 0.00259 ( 39) SS BOND : angle 1.80778 ( 78) covalent geometry : bond 0.00278 (23565) covalent geometry : angle 0.51075 (32059) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 197 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7719 (mtt90) cc_final: 0.7234 (mtm-85) REVERT: A 239 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7431 (tp-100) REVERT: A 269 TYR cc_start: 0.8552 (m-10) cc_final: 0.8222 (m-10) REVERT: A 334 ASN cc_start: 0.7303 (OUTLIER) cc_final: 0.7043 (p0) REVERT: A 493 GLN cc_start: 0.7373 (mm-40) cc_final: 0.7152 (mm-40) REVERT: A 529 LYS cc_start: 0.8580 (mttt) cc_final: 0.8245 (mmtt) REVERT: A 558 LYS cc_start: 0.8933 (tttt) cc_final: 0.8403 (mmmt) REVERT: A 675 GLN cc_start: 0.8072 (mt0) cc_final: 0.7867 (mt0) REVERT: A 780 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8483 (mm-30) REVERT: A 790 LYS cc_start: 0.8708 (pttt) cc_final: 0.8380 (pttp) REVERT: A 804 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8190 (mp10) REVERT: A 957 GLN cc_start: 0.8348 (tp-100) cc_final: 0.8060 (tt0) REVERT: A 1073 LYS cc_start: 0.8853 (tttt) cc_final: 0.8611 (ttmm) REVERT: A 1107 ARG cc_start: 0.8414 (mtm-85) cc_final: 0.8198 (mtt90) REVERT: B 118 LEU cc_start: 0.7775 (tp) cc_final: 0.7443 (mm) REVERT: B 200 TYR cc_start: 0.7830 (m-80) cc_final: 0.7605 (m-80) REVERT: B 271 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8570 (mp10) REVERT: B 332 ILE cc_start: 0.6397 (OUTLIER) cc_final: 0.6172 (tt) REVERT: B 364 ASP cc_start: 0.8384 (t0) cc_final: 0.8001 (t0) REVERT: B 400 PHE cc_start: 0.8370 (p90) cc_final: 0.8044 (p90) REVERT: B 440 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.7986 (p0) REVERT: B 441 LEU cc_start: 0.8755 (mm) cc_final: 0.8440 (mt) REVERT: B 528 LYS cc_start: 0.8103 (tppp) cc_final: 0.7846 (mmmm) REVERT: B 568 ASP cc_start: 0.8037 (m-30) cc_final: 0.7509 (m-30) REVERT: B 574 ASP cc_start: 0.8226 (t70) cc_final: 0.7756 (t0) REVERT: B 950 ASP cc_start: 0.8555 (t70) cc_final: 0.8132 (m-30) REVERT: B 979 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7675 (t0) REVERT: B 990 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7467 (tt0) REVERT: B 1003 SER cc_start: 0.8990 (t) cc_final: 0.8724 (m) REVERT: C 32 PHE cc_start: 0.7539 (m-80) cc_final: 0.7160 (m-80) REVERT: C 63 THR cc_start: 0.8348 (m) cc_final: 0.8061 (p) REVERT: C 117 LEU cc_start: 0.7841 (tp) cc_final: 0.7270 (mp) REVERT: C 132 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7598 (mt-10) REVERT: C 192 PHE cc_start: 0.7749 (m-80) cc_final: 0.7411 (m-80) REVERT: C 205 SER cc_start: 0.8728 (p) cc_final: 0.8503 (t) REVERT: C 207 HIS cc_start: 0.7072 (m170) cc_final: 0.6552 (m170) REVERT: C 239 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7226 (tm-30) REVERT: C 281 GLU cc_start: 0.6955 (pm20) cc_final: 0.6564 (pm20) REVERT: C 335 LEU cc_start: 0.8268 (mm) cc_final: 0.7516 (tt) REVERT: C 398 ASP cc_start: 0.8514 (m-30) cc_final: 0.8079 (m-30) REVERT: C 690 GLN cc_start: 0.7721 (mt0) cc_final: 0.7435 (mm-40) REVERT: C 814 LYS cc_start: 0.8318 (mttt) cc_final: 0.8000 (mmmt) REVERT: C 990 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7232 (tt0) REVERT: C 1072 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8357 (mp0) outliers start: 54 outliers final: 42 residues processed: 237 average time/residue: 0.3113 time to fit residues: 120.8614 Evaluate side-chains 236 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 186 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 266 optimal weight: 0.0010 chunk 14 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 291 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 230 optimal weight: 10.0000 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.147851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.103933 restraints weight = 33543.410| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.30 r_work: 0.3073 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 23604 Z= 0.162 Angle : 0.734 59.198 32137 Z= 0.419 Chirality : 0.044 0.382 3671 Planarity : 0.005 0.150 4144 Dihedral : 4.869 58.130 3142 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.90 % Allowed : 11.82 % Favored : 86.28 % Cbeta Deviations : 0.07 % 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: 0.14 (0.15), residues: 2878 helix: 1.93 (0.20), residues: 680 sheet: 0.10 (0.18), residues: 664 loop : -0.76 (0.16), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 436 HIS 0.004 0.001 HIS C 519 PHE 0.012 0.001 PHE C 400 TYR 0.017 0.001 TYR B1067 ARG 0.003 0.000 ARG B 190 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 1034) hydrogen bonds : angle 5.24847 ( 2877) SS BOND : bond 0.00314 ( 39) SS BOND : angle 1.78050 ( 78) covalent geometry : bond 0.00361 (23565) covalent geometry : angle 0.73010 (32059) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 184 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7679 (mtt90) cc_final: 0.7204 (mtm-85) REVERT: A 269 TYR cc_start: 0.8517 (m-10) cc_final: 0.8191 (m-10) REVERT: A 334 ASN cc_start: 0.7266 (OUTLIER) cc_final: 0.7008 (p0) REVERT: A 493 GLN cc_start: 0.7371 (mm-40) cc_final: 0.7147 (mm-40) REVERT: A 529 LYS cc_start: 0.8516 (mttt) cc_final: 0.8224 (mmtt) REVERT: A 558 LYS cc_start: 0.8897 (tttt) cc_final: 0.8373 (mmmt) REVERT: A 675 GLN cc_start: 0.8040 (mt0) cc_final: 0.7832 (mt0) REVERT: A 780 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8407 (mm-30) REVERT: A 790 LYS cc_start: 0.8695 (pttt) cc_final: 0.8357 (pttp) REVERT: A 804 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8145 (mp10) REVERT: A 957 GLN cc_start: 0.8311 (tp-100) cc_final: 0.8013 (tt0) REVERT: A 1073 LYS cc_start: 0.8810 (tttt) cc_final: 0.8562 (ttmm) REVERT: A 1107 ARG cc_start: 0.8405 (mtm-85) cc_final: 0.8176 (mtt90) REVERT: B 118 LEU cc_start: 0.7728 (tp) cc_final: 0.7403 (mm) REVERT: B 200 TYR cc_start: 0.7817 (m-80) cc_final: 0.7601 (m-80) REVERT: B 271 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8524 (mp10) REVERT: B 332 ILE cc_start: 0.6405 (OUTLIER) cc_final: 0.6179 (tt) REVERT: B 364 ASP cc_start: 0.8363 (t0) cc_final: 0.7979 (t0) REVERT: B 400 PHE cc_start: 0.8381 (p90) cc_final: 0.8056 (p90) REVERT: B 440 ASN cc_start: 0.8337 (OUTLIER) cc_final: 0.7962 (p0) REVERT: B 441 LEU cc_start: 0.8753 (mm) cc_final: 0.8437 (mt) REVERT: B 528 LYS cc_start: 0.8084 (tppp) cc_final: 0.7827 (mmmm) REVERT: B 568 ASP cc_start: 0.8002 (m-30) cc_final: 0.7460 (m-30) REVERT: B 574 ASP cc_start: 0.8202 (t70) cc_final: 0.7724 (t0) REVERT: B 950 ASP cc_start: 0.8503 (t70) cc_final: 0.8077 (m-30) REVERT: B 979 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7616 (t0) REVERT: B 990 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7408 (tt0) REVERT: B 1003 SER cc_start: 0.8964 (t) cc_final: 0.8683 (m) REVERT: C 32 PHE cc_start: 0.7529 (m-80) cc_final: 0.7148 (m-80) REVERT: C 63 THR cc_start: 0.8359 (m) cc_final: 0.8066 (p) REVERT: C 117 LEU cc_start: 0.7867 (tp) cc_final: 0.7290 (mp) REVERT: C 192 PHE cc_start: 0.7705 (m-80) cc_final: 0.7363 (m-80) REVERT: C 205 SER cc_start: 0.8720 (p) cc_final: 0.8489 (t) REVERT: C 207 HIS cc_start: 0.7046 (m170) cc_final: 0.6535 (m170) REVERT: C 239 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7507 (tp-100) REVERT: C 281 GLU cc_start: 0.6896 (pm20) cc_final: 0.6507 (pm20) REVERT: C 335 LEU cc_start: 0.8270 (mm) cc_final: 0.7517 (tt) REVERT: C 398 ASP cc_start: 0.8506 (m-30) cc_final: 0.8100 (m-30) REVERT: C 690 GLN cc_start: 0.7680 (mt0) cc_final: 0.7421 (mm-40) REVERT: C 814 LYS cc_start: 0.8266 (mttt) cc_final: 0.7960 (mmmt) REVERT: C 990 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7192 (tt0) REVERT: C 1072 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8294 (mp0) outliers start: 49 outliers final: 42 residues processed: 222 average time/residue: 0.3368 time to fit residues: 122.8485 Evaluate side-chains 230 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 181 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 68 optimal weight: 1.9990 chunk 218 optimal weight: 0.5980 chunk 96 optimal weight: 8.9990 chunk 258 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 98 optimal weight: 0.5980 chunk 222 optimal weight: 10.0000 chunk 220 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.147910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.104074 restraints weight = 33545.723| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.29 r_work: 0.3068 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.239 23604 Z= 0.181 Angle : 0.644 35.647 32137 Z= 0.354 Chirality : 0.044 0.382 3671 Planarity : 0.005 0.150 4144 Dihedral : 4.869 58.130 3142 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.86 % Allowed : 11.89 % Favored : 86.25 % Cbeta Deviations : 0.07 % 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: 0.14 (0.15), residues: 2878 helix: 1.93 (0.20), residues: 680 sheet: 0.10 (0.18), residues: 664 loop : -0.76 (0.16), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 436 HIS 0.004 0.001 HIS C 519 PHE 0.012 0.001 PHE C 400 TYR 0.017 0.001 TYR B1067 ARG 0.003 0.000 ARG B 190 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 1034) hydrogen bonds : angle 5.24847 ( 2877) SS BOND : bond 0.00314 ( 39) SS BOND : angle 1.78050 ( 78) covalent geometry : bond 0.00396 (23565) covalent geometry : angle 0.63877 (32059) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13633.54 seconds wall clock time: 235 minutes 54.71 seconds (14154.71 seconds total)