Starting phenix.real_space_refine on Thu May 29 03:03:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8keh_37157/05_2025/8keh_37157.cif Found real_map, /net/cci-nas-00/data/ceres_data/8keh_37157/05_2025/8keh_37157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8keh_37157/05_2025/8keh_37157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8keh_37157/05_2025/8keh_37157.map" model { file = "/net/cci-nas-00/data/ceres_data/8keh_37157/05_2025/8keh_37157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8keh_37157/05_2025/8keh_37157.cif" } resolution = 3.21 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= 0.006 sd= 0.040 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 137 5.16 5 C 20107 2.51 5 N 5266 2.21 5 O 6065 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 137 residue(s): 0.49s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 31575 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 8331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8331 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 57, 'TRANS': 1007} Chain breaks: 3 Chain: "B" Number of atoms: 8331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8331 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 57, 'TRANS': 1007} Chain breaks: 3 Chain: "A" Number of atoms: 8331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8331 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 57, 'TRANS': 1007} Chain breaks: 3 Chain: "F" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1653 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 12, 'TRANS': 200} Chain: "G" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1638 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "D" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1653 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 12, 'TRANS': 200} Chain: "E" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1638 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Time building chain proxies: 17.29, per 1000 atoms: 0.55 Number of scatterers: 31575 At special positions: 0 Unit cell: (153.78, 164.964, 224.612, 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 137 16.00 O 6065 8.00 N 5266 7.00 C 20107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.07 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.01 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 132 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.12 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.06 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.10 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.05 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 136 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 147 " - pdb=" SG CYS G 203 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 203 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.19 Conformation dependent library (CDL) restraints added in 4.3 seconds 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7590 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 66 sheets defined 17.3% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.36 Creating SS restraints... Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.819A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.527A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.806A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.513A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 941 removed outlier: 4.146A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.695A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.014A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.807A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.514A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 783 Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 907 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.757A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.695A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.528A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.662A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 removed outlier: 3.561A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.806A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 4.163A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.591A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 783 removed outlier: 3.641A pdb=" N ARG A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 941 removed outlier: 4.173A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.937A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.545A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.825A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 129 removed outlier: 3.699A pdb=" N SER F 129 " --> pdb=" O GLU F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 191 Processing helix chain 'G' and resid 194 through 196 No H-bonds generated for 'chain 'G' and resid 194 through 196' Processing helix chain 'D' and resid 126 through 130 Processing helix chain 'D' and resid 184 through 191 removed outlier: 3.603A pdb=" N HIS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 165 No H-bonds generated for 'chain 'E' and resid 163 through 165' Processing helix chain 'E' and resid 194 through 196 No H-bonds generated for 'chain 'E' and resid 194 through 196' Processing sheet with id=AA1, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AA2, first strand: chain 'C' and resid 49 through 52 removed outlier: 7.142A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'C' and resid 66 through 67 removed outlier: 3.626A pdb=" N TYR C 265 " --> pdb=" O PHE C 66 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 91 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE C 194 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 205 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AA7, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AA8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.949A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.599A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'C' and resid 542 through 543 removed outlier: 3.631A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.940A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 701 through 703 removed outlier: 6.043A pdb=" N ALA C 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.373A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.373A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.306A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 788 through 789 removed outlier: 6.001A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 49 through 56 removed outlier: 3.608A pdb=" N ASP B 54 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 66 through 67 removed outlier: 3.556A pdb=" N TYR B 265 " --> pdb=" O PHE B 66 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'B' and resid 85 through 86 removed outlier: 3.545A pdb=" N LEU B 85 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 90 through 93 removed outlier: 3.622A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B 205 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 129 through 130 removed outlier: 3.567A pdb=" N ILE B 129 " --> pdb=" O TYR B 170 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 316 removed outlier: 6.975A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.673A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.933A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 728 removed outlier: 7.205A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD6, first strand: chain 'A' and resid 49 through 56 removed outlier: 3.715A pdb=" N PHE A 56 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AD8, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AD9, first strand: chain 'A' and resid 91 through 95 removed outlier: 3.658A pdb=" N PHE A 194 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER A 205 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 102 through 108 removed outlier: 3.617A pdb=" N GLY A 104 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AE3, first strand: chain 'A' and resid 311 through 316 removed outlier: 3.543A pdb=" N VAL A 597 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.641A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.500A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 553 through 554 Processing sheet with id=AE7, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.840A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.714A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.714A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.264A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.517A pdb=" N PHE A1121 " --> pdb=" O PHE A1089 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.524A pdb=" N LEU F 13 " --> pdb=" O GLU F 107 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR F 87 " --> pdb=" O TYR F 36 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLN F 37 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LEU F 46 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 19 through 22 removed outlier: 3.886A pdb=" N ALA F 19 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU F 21 " --> pdb=" O LEU F 73 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER F 67 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR F 72 " --> pdb=" O SER F 65 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER F 65 " --> pdb=" O THR F 72 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 116 through 120 removed outlier: 6.039A pdb=" N TYR F 175 " --> pdb=" O ASN F 140 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 147 through 149 removed outlier: 3.760A pdb=" N LYS F 147 " --> pdb=" O THR F 199 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR F 199 " --> pdb=" O LYS F 147 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.522A pdb=" N VAL G 18 " --> pdb=" O LEU G 83 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU G 83 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR G 80 " --> pdb=" O THR G 71 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR G 71 " --> pdb=" O TYR G 80 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.702A pdb=" N GLU G 10 " --> pdb=" O THR G 119 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET G 34 " --> pdb=" O ILE G 51 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 127 through 131 removed outlier: 3.551A pdb=" N GLY G 146 " --> pdb=" O LEU G 131 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU G 185 " --> pdb=" O VAL G 149 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP G 151 " --> pdb=" O TYR G 183 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TYR G 183 " --> pdb=" O ASP G 151 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 127 through 131 removed outlier: 3.551A pdb=" N GLY G 146 " --> pdb=" O LEU G 131 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU G 185 " --> pdb=" O VAL G 149 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP G 151 " --> pdb=" O TYR G 183 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TYR G 183 " --> pdb=" O ASP G 151 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 160 through 161 removed outlier: 4.630A pdb=" N TYR G 201 " --> pdb=" O VAL G 218 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.514A pdb=" N LEU D 13 " --> pdb=" O GLU D 107 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 19 through 22 removed outlier: 3.879A pdb=" N ALA D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU D 21 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D 67 " --> pdb=" O ASP D 70 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER D 65 " --> pdb=" O THR D 72 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 45 through 49 removed outlier: 5.450A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 116 through 120 removed outlier: 3.955A pdb=" N VAL D 135 " --> pdb=" O PHE D 120 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N TYR D 175 " --> pdb=" O ASN D 140 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 155 through 157 removed outlier: 4.413A pdb=" N TRP D 150 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS D 147 " --> pdb=" O THR D 199 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR D 199 " --> pdb=" O LYS D 147 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR D 194 " --> pdb=" O PHE D 211 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.717A pdb=" N LEU E 83 " --> pdb=" O VAL E 18 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 9 through 12 removed outlier: 3.827A pdb=" N MET E 34 " --> pdb=" O ILE E 51 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 127 through 131 removed outlier: 3.616A pdb=" N GLY E 146 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP E 151 " --> pdb=" O TYR E 183 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N TYR E 183 " --> pdb=" O ASP E 151 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 127 through 131 removed outlier: 3.616A pdb=" N GLY E 146 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP E 151 " --> pdb=" O TYR E 183 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N TYR E 183 " --> pdb=" O ASP E 151 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 160 through 161 removed outlier: 4.691A pdb=" N TYR E 201 " --> pdb=" O VAL E 218 " (cutoff:3.500A) 1002 hydrogen bonds defined for protein. 2706 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: 12.86 Time building geometry restraints manager: 9.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 5166 1.30 - 1.43: 8696 1.43 - 1.56: 18297 1.56 - 1.69: 0 1.69 - 1.82: 177 Bond restraints: 32336 Sorted by residual: bond pdb=" C CYS A 743 " pdb=" O CYS A 743 " ideal model delta sigma weight residual 1.235 1.165 0.070 1.28e-02 6.10e+03 3.03e+01 bond pdb=" CA SER B 32 " pdb=" CB SER B 32 " ideal model delta sigma weight residual 1.527 1.457 0.070 1.36e-02 5.41e+03 2.63e+01 bond pdb=" CA SER A 305 " pdb=" CB SER A 305 " ideal model delta sigma weight residual 1.535 1.468 0.067 1.32e-02 5.74e+03 2.55e+01 bond pdb=" CA SER C 51 " pdb=" CB SER C 51 " ideal model delta sigma weight residual 1.531 1.459 0.072 1.52e-02 4.33e+03 2.24e+01 bond pdb=" CA SER C 673 " pdb=" CB SER C 673 " ideal model delta sigma weight residual 1.532 1.461 0.071 1.56e-02 4.11e+03 2.04e+01 ... (remaining 32331 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 41850 2.52 - 5.03: 1864 5.03 - 7.55: 248 7.55 - 10.07: 46 10.07 - 12.59: 6 Bond angle restraints: 44014 Sorted by residual: angle pdb=" N LEU C1145 " pdb=" CA LEU C1145 " pdb=" C LEU C1145 " ideal model delta sigma weight residual 112.97 103.15 9.82 1.06e+00 8.90e-01 8.58e+01 angle pdb=" N ILE B 909 " pdb=" CA ILE B 909 " pdb=" C ILE B 909 " ideal model delta sigma weight residual 113.43 104.57 8.86 1.09e+00 8.42e-01 6.60e+01 angle pdb=" N ASP A1146 " pdb=" CA ASP A1146 " pdb=" C ASP A1146 " ideal model delta sigma weight residual 113.23 103.26 9.97 1.24e+00 6.50e-01 6.47e+01 angle pdb=" CA PHE A 44 " pdb=" CB PHE A 44 " pdb=" CG PHE A 44 " ideal model delta sigma weight residual 113.80 121.35 -7.55 1.00e+00 1.00e+00 5.70e+01 angle pdb=" C THR A 125 " pdb=" CA THR A 125 " pdb=" CB THR A 125 " ideal model delta sigma weight residual 111.26 123.85 -12.59 1.67e+00 3.59e-01 5.68e+01 ... (remaining 44009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 17863 17.96 - 35.91: 917 35.91 - 53.87: 398 53.87 - 71.82: 122 71.82 - 89.78: 12 Dihedral angle restraints: 19312 sinusoidal: 7497 harmonic: 11815 Sorted by residual: dihedral pdb=" C THR A 125 " pdb=" N THR A 125 " pdb=" CA THR A 125 " pdb=" CB THR A 125 " ideal model delta harmonic sigma weight residual -122.00 -143.59 21.59 0 2.50e+00 1.60e-01 7.46e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -155.13 69.13 1 1.00e+01 1.00e-02 6.18e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -149.40 63.40 1 1.00e+01 1.00e-02 5.30e+01 ... (remaining 19309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 4651 0.146 - 0.293: 253 0.293 - 0.439: 50 0.439 - 0.585: 5 0.585 - 0.731: 1 Chirality restraints: 4960 Sorted by residual: chirality pdb=" CA THR A 125 " pdb=" N THR A 125 " pdb=" C THR A 125 " pdb=" CB THR A 125 " both_signs ideal model delta sigma weight residual False 2.53 1.79 0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CA TYR B 756 " pdb=" N TYR B 756 " pdb=" C TYR B 756 " pdb=" CB TYR B 756 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.22e+00 chirality pdb=" CA THR B 96 " pdb=" N THR B 96 " pdb=" C THR B 96 " pdb=" CB THR B 96 " both_signs ideal model delta sigma weight residual False 2.53 3.01 -0.48 2.00e-01 2.50e+01 5.84e+00 ... (remaining 4957 not shown) Planarity restraints: 5697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 193 " -0.026 2.00e-02 2.50e+03 5.32e-02 2.84e+01 pdb=" C VAL C 193 " 0.092 2.00e-02 2.50e+03 pdb=" O VAL C 193 " -0.035 2.00e-02 2.50e+03 pdb=" N PHE C 194 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C1137 " 0.024 2.00e-02 2.50e+03 4.73e-02 2.23e+01 pdb=" C VAL C1137 " -0.082 2.00e-02 2.50e+03 pdb=" O VAL C1137 " 0.030 2.00e-02 2.50e+03 pdb=" N TYR C1138 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 558 " 0.022 2.00e-02 2.50e+03 4.42e-02 1.96e+01 pdb=" C LYS C 558 " -0.077 2.00e-02 2.50e+03 pdb=" O LYS C 558 " 0.028 2.00e-02 2.50e+03 pdb=" N PHE C 559 " 0.026 2.00e-02 2.50e+03 ... (remaining 5694 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2674 2.74 - 3.28: 30156 3.28 - 3.82: 52275 3.82 - 4.36: 61096 4.36 - 4.90: 104054 Nonbonded interactions: 250255 Sorted by model distance: nonbonded pdb=" OG SER A 884 " pdb=" OG1 THR A 887 " model vdw 2.200 3.040 nonbonded pdb=" OG SER B 884 " pdb=" OG1 THR B 887 " model vdw 2.202 3.040 nonbonded pdb=" OG SER C 884 " pdb=" OG1 THR C 887 " model vdw 2.213 3.040 nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.230 3.040 nonbonded pdb=" OH TYR B 741 " pdb=" O LEU B 962 " model vdw 2.255 3.040 ... (remaining 250250 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } 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: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.260 Check model and map are aligned: 0.230 Set scattering table: 0.270 Process input model: 68.960 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 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 : 0.006 0.094 32379 Z= 0.431 Angle : 1.093 12.586 44100 Z= 0.741 Chirality : 0.076 0.731 4960 Planarity : 0.005 0.060 5697 Dihedral : 13.547 89.778 11593 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 1.32 % Allowed : 8.15 % Favored : 90.53 % Rotamer: Outliers : 11.50 % Allowed : 8.84 % Favored : 79.66 % Cbeta Deviations : 0.90 % 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: -3.71 (0.11), residues: 4025 helix: -0.03 (0.20), residues: 626 sheet: -2.16 (0.15), residues: 919 loop : -3.45 (0.10), residues: 2480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 65 HIS 0.008 0.001 HIS C 50 PHE 0.031 0.001 PHE C 541 TYR 0.046 0.001 TYR A 39 ARG 0.003 0.000 ARG B 328 Details of bonding type rmsd hydrogen bonds : bond 0.23347 ( 954) hydrogen bonds : angle 9.08453 ( 2706) SS BOND : bond 0.02092 ( 43) SS BOND : angle 1.95842 ( 86) covalent geometry : bond 0.00603 (32336) covalent geometry : angle 1.09100 (44014) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 407 poor density : 325 time to evaluate : 3.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 530 SER cc_start: 0.6866 (OUTLIER) cc_final: 0.5739 (t) REVERT: C 676 THR cc_start: 0.8471 (OUTLIER) cc_final: 0.7433 (m) REVERT: B 80 PHE cc_start: 0.3031 (OUTLIER) cc_final: 0.2433 (p90) REVERT: B 511 VAL cc_start: 0.4092 (OUTLIER) cc_final: 0.3887 (t) REVERT: A 84 VAL cc_start: 0.7986 (OUTLIER) cc_final: 0.7734 (p) REVERT: A 457 ARG cc_start: -0.3125 (OUTLIER) cc_final: -0.4477 (mtt180) REVERT: A 676 THR cc_start: 0.8222 (OUTLIER) cc_final: 0.7911 (m) REVERT: A 855 PHE cc_start: 0.6537 (OUTLIER) cc_final: 0.6288 (m-80) REVERT: F 1 GLU cc_start: 0.3659 (OUTLIER) cc_final: 0.3021 (tt0) REVERT: F 10 THR cc_start: 0.4465 (OUTLIER) cc_final: 0.4196 (p) REVERT: E 20 VAL cc_start: 0.0833 (OUTLIER) cc_final: 0.0421 (t) REVERT: E 155 GLU cc_start: 0.2286 (OUTLIER) cc_final: 0.1549 (tp30) outliers start: 407 outliers final: 64 residues processed: 679 average time/residue: 0.4655 time to fit residues: 490.6666 Evaluate side-chains 206 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 130 time to evaluate : 3.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 155 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 339 optimal weight: 30.0000 chunk 304 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 315 optimal weight: 0.8980 chunk 121 optimal weight: 20.0000 chunk 191 optimal weight: 6.9990 chunk 234 optimal weight: 8.9990 chunk 365 optimal weight: 50.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 ASN C 146 GLN C 173 GLN C 474 GLN C 563 GLN C 613 GLN C 644 GLN C 675 GLN C 853 GLN C 901 GLN C 913 GLN C 914 ASN C 949 GLN C 965 GLN C1002 GLN C1011 GLN C1048 HIS C1119 ASN B 53 GLN B 173 GLN B 409 GLN B 414 GLN B 450 ASN B 487 ASN B 542 ASN B 613 GLN B 784 GLN B 856 ASN B 901 GLN B 913 GLN B 949 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1010 GLN B1011 GLN B1048 HIS B1119 ASN B1125 ASN A 70 HIS ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 317 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A 542 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 784 GLN A 853 GLN A 901 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A 935 GLN A1002 GLN A1011 GLN A1048 HIS A1054 GLN A1106 GLN A1119 ASN A1125 ASN F 38 GLN F 42 GLN F 53 ASN F 102 GLN F 126 GLN F 168 GLN G 107 ASN D 38 GLN D 42 GLN D 53 ASN D 102 GLN D 149 GLN D 168 GLN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN Total number of N/Q/H flips: 70 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.113558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.065797 restraints weight = 124391.243| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 6.27 r_work: 0.3076 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 32379 Z= 0.205 Angle : 0.665 12.288 44100 Z= 0.342 Chirality : 0.045 0.209 4960 Planarity : 0.005 0.051 5697 Dihedral : 6.672 64.315 4485 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.23 % Favored : 92.62 % Rotamer: Outliers : 4.41 % Allowed : 13.14 % Favored : 82.46 % 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: -2.87 (0.12), residues: 4025 helix: 1.04 (0.21), residues: 637 sheet: -1.69 (0.15), residues: 1024 loop : -3.02 (0.11), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 65 HIS 0.007 0.001 HIS C1064 PHE 0.030 0.002 PHE B 93 TYR 0.033 0.001 TYR G 33 ARG 0.007 0.001 ARG B 567 Details of bonding type rmsd hydrogen bonds : bond 0.04251 ( 954) hydrogen bonds : angle 6.19002 ( 2706) SS BOND : bond 0.00362 ( 43) SS BOND : angle 1.06650 ( 86) covalent geometry : bond 0.00463 (32336) covalent geometry : angle 0.66401 (44014) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 133 time to evaluate : 3.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 105 TRP cc_start: 0.8219 (m-90) cc_final: 0.7831 (m-90) REVERT: C 175 PHE cc_start: 0.8078 (p90) cc_final: 0.6934 (p90) REVERT: C 177 MET cc_start: 0.7163 (tmm) cc_final: 0.6363 (tmm) REVERT: C 571 ASP cc_start: 0.9161 (m-30) cc_final: 0.8719 (t0) REVERT: C 676 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.8971 (m) REVERT: C 697 MET cc_start: 0.9061 (ptm) cc_final: 0.8831 (ptm) REVERT: C 900 MET cc_start: 0.8887 (mtp) cc_final: 0.8608 (mtt) REVERT: C 1017 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8904 (tm-30) REVERT: B 80 PHE cc_start: 0.2939 (OUTLIER) cc_final: 0.2565 (p90) REVERT: B 200 TYR cc_start: 0.8431 (m-80) cc_final: 0.7959 (m-80) REVERT: B 203 ILE cc_start: 0.8754 (mt) cc_final: 0.8451 (tt) REVERT: B 571 ASP cc_start: 0.8158 (t0) cc_final: 0.7850 (t0) REVERT: B 900 MET cc_start: 0.8975 (mtp) cc_final: 0.8712 (mtt) REVERT: A 84 VAL cc_start: 0.8082 (OUTLIER) cc_final: 0.7651 (p) REVERT: A 141 PHE cc_start: 0.5012 (p90) cc_final: 0.4766 (p90) REVERT: A 333 THR cc_start: 0.7758 (OUTLIER) cc_final: 0.7504 (p) REVERT: A 387 LEU cc_start: 0.5524 (OUTLIER) cc_final: 0.5317 (mt) REVERT: A 457 ARG cc_start: -0.1189 (OUTLIER) cc_final: -0.1845 (mtt180) REVERT: A 565 PHE cc_start: 0.8422 (m-80) cc_final: 0.8053 (t80) REVERT: A 577 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8848 (ttm-80) REVERT: A 780 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8390 (mp0) REVERT: A 935 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8439 (tt0) REVERT: G 34 MET cc_start: 0.2405 (tpp) cc_final: 0.1856 (tpp) REVERT: G 37 VAL cc_start: -0.0526 (OUTLIER) cc_final: -0.0832 (t) REVERT: G 70 MET cc_start: 0.5446 (mtt) cc_final: 0.5154 (mtt) REVERT: E 81 MET cc_start: 0.3000 (ttp) cc_final: 0.2768 (ttp) REVERT: E 155 GLU cc_start: 0.5769 (OUTLIER) cc_final: 0.5363 (tp30) outliers start: 156 outliers final: 71 residues processed: 276 average time/residue: 0.4272 time to fit residues: 194.1070 Evaluate side-chains 191 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 109 time to evaluate : 3.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 155 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 397 optimal weight: 40.0000 chunk 233 optimal weight: 20.0000 chunk 170 optimal weight: 9.9990 chunk 298 optimal weight: 2.9990 chunk 357 optimal weight: 50.0000 chunk 23 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 chunk 301 optimal weight: 0.0050 chunk 88 optimal weight: 7.9990 chunk 277 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 overall best weight: 2.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN C1125 ASN B 31 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN F 42 GLN D 42 GLN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.112638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.068087 restraints weight = 124761.301| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 5.07 r_work: 0.3056 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32379 Z= 0.165 Angle : 0.579 11.182 44100 Z= 0.295 Chirality : 0.043 0.205 4960 Planarity : 0.004 0.077 5697 Dihedral : 5.890 59.277 4439 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.98 % Favored : 92.92 % Rotamer: Outliers : 3.22 % Allowed : 13.50 % Favored : 83.28 % 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: -2.40 (0.12), residues: 4025 helix: 1.34 (0.21), residues: 650 sheet: -1.33 (0.16), residues: 992 loop : -2.71 (0.11), residues: 2383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 436 HIS 0.005 0.001 HIS C 339 PHE 0.017 0.001 PHE B 93 TYR 0.017 0.001 TYR F 142 ARG 0.012 0.000 ARG F 110 Details of bonding type rmsd hydrogen bonds : bond 0.03642 ( 954) hydrogen bonds : angle 5.55224 ( 2706) SS BOND : bond 0.00311 ( 43) SS BOND : angle 0.86956 ( 86) covalent geometry : bond 0.00364 (32336) covalent geometry : angle 0.57812 (44014) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 110 time to evaluate : 3.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 175 PHE cc_start: 0.8292 (p90) cc_final: 0.7157 (p90) REVERT: C 571 ASP cc_start: 0.9252 (m-30) cc_final: 0.8724 (t0) REVERT: C 854 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.7176 (mtmm) REVERT: C 1017 GLU cc_start: 0.9179 (tm-30) cc_final: 0.8931 (tm-30) REVERT: B 80 PHE cc_start: 0.2834 (OUTLIER) cc_final: 0.2410 (p90) REVERT: B 100 ASN cc_start: 0.9111 (OUTLIER) cc_final: 0.8845 (t0) REVERT: B 200 TYR cc_start: 0.8671 (m-80) cc_final: 0.8185 (m-80) REVERT: B 246 ARG cc_start: 0.2738 (OUTLIER) cc_final: 0.2021 (ptt180) REVERT: B 571 ASP cc_start: 0.8256 (t0) cc_final: 0.7774 (t0) REVERT: B 869 MET cc_start: 0.9498 (OUTLIER) cc_final: 0.9093 (mtt) REVERT: B 900 MET cc_start: 0.8960 (mtp) cc_final: 0.8706 (mtt) REVERT: B 969 LYS cc_start: 0.8967 (mtmm) cc_final: 0.8476 (mtmm) REVERT: A 84 VAL cc_start: 0.8201 (OUTLIER) cc_final: 0.7824 (p) REVERT: A 191 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: A 565 PHE cc_start: 0.8391 (m-80) cc_final: 0.8040 (t80) REVERT: A 780 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8256 (mp0) REVERT: A 950 ASP cc_start: 0.9117 (t0) cc_final: 0.8739 (t0) REVERT: G 34 MET cc_start: 0.2250 (tpp) cc_final: 0.1890 (tpp) REVERT: G 37 VAL cc_start: -0.0835 (OUTLIER) cc_final: -0.1126 (t) REVERT: E 155 GLU cc_start: 0.5540 (OUTLIER) cc_final: 0.4871 (tp30) outliers start: 114 outliers final: 67 residues processed: 215 average time/residue: 0.4500 time to fit residues: 159.1755 Evaluate side-chains 178 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 101 time to evaluate : 3.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 155 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 371 optimal weight: 40.0000 chunk 15 optimal weight: 9.9990 chunk 401 optimal weight: 50.0000 chunk 309 optimal weight: 0.9980 chunk 272 optimal weight: 7.9990 chunk 218 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 41 optimal weight: 50.0000 chunk 252 optimal weight: 50.0000 chunk 227 optimal weight: 20.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 HIS C 100 ASN C 439 ASN C 606 ASN C 644 GLN C 913 GLN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 GLN ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN F 42 GLN F 168 GLN G 32 HIS E 32 HIS E 52 ASN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.109159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.063656 restraints weight = 125576.630| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 5.48 r_work: 0.2987 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 32379 Z= 0.284 Angle : 0.637 12.294 44100 Z= 0.327 Chirality : 0.045 0.226 4960 Planarity : 0.004 0.059 5697 Dihedral : 5.644 59.818 4423 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.73 % Favored : 92.15 % Rotamer: Outliers : 3.50 % Allowed : 13.36 % Favored : 83.14 % 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: -2.24 (0.13), residues: 4025 helix: 1.29 (0.21), residues: 653 sheet: -1.26 (0.16), residues: 1007 loop : -2.54 (0.11), residues: 2365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 436 HIS 0.007 0.001 HIS B1083 PHE 0.020 0.002 PHE A 823 TYR 0.017 0.001 TYR B 707 ARG 0.006 0.001 ARG A 815 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 954) hydrogen bonds : angle 5.57003 ( 2706) SS BOND : bond 0.00347 ( 43) SS BOND : angle 0.79925 ( 86) covalent geometry : bond 0.00638 (32336) covalent geometry : angle 0.63685 (44014) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 105 time to evaluate : 4.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 HIS cc_start: 0.6810 (OUTLIER) cc_final: 0.6593 (p90) REVERT: C 175 PHE cc_start: 0.8330 (p90) cc_final: 0.7124 (p90) REVERT: C 387 LEU cc_start: 0.8563 (mt) cc_final: 0.8307 (mm) REVERT: C 388 ASN cc_start: 0.7781 (m-40) cc_final: 0.7577 (m-40) REVERT: C 571 ASP cc_start: 0.9222 (m-30) cc_final: 0.8758 (t0) REVERT: C 697 MET cc_start: 0.8937 (ptm) cc_final: 0.8727 (ptm) REVERT: C 854 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.7222 (mtmm) REVERT: C 900 MET cc_start: 0.9209 (mtp) cc_final: 0.8918 (mtt) REVERT: C 1017 GLU cc_start: 0.9196 (tm-30) cc_final: 0.8928 (tm-30) REVERT: B 80 PHE cc_start: 0.2760 (OUTLIER) cc_final: 0.2399 (p90) REVERT: B 100 ASN cc_start: 0.9144 (OUTLIER) cc_final: 0.8855 (t0) REVERT: B 136 PHE cc_start: 0.9076 (OUTLIER) cc_final: 0.8423 (p90) REVERT: B 153 MET cc_start: 0.4718 (ppp) cc_final: 0.4494 (ppp) REVERT: B 200 TYR cc_start: 0.8911 (m-80) cc_final: 0.8453 (m-80) REVERT: B 229 LEU cc_start: 0.9287 (mm) cc_final: 0.8754 (tp) REVERT: B 246 ARG cc_start: 0.2866 (OUTLIER) cc_final: 0.2198 (ptt180) REVERT: B 571 ASP cc_start: 0.8596 (t0) cc_final: 0.8186 (t0) REVERT: B 869 MET cc_start: 0.9505 (OUTLIER) cc_final: 0.9047 (mtt) REVERT: A 84 VAL cc_start: 0.8251 (OUTLIER) cc_final: 0.7916 (p) REVERT: A 177 MET cc_start: 0.7774 (ppp) cc_final: 0.7529 (ppp) REVERT: A 191 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: A 457 ARG cc_start: -0.1535 (OUTLIER) cc_final: -0.2515 (mtt180) REVERT: A 563 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8573 (mt0) REVERT: A 565 PHE cc_start: 0.8475 (m-80) cc_final: 0.8043 (t80) REVERT: A 950 ASP cc_start: 0.9187 (t0) cc_final: 0.8873 (t0) REVERT: G 34 MET cc_start: 0.2520 (tpp) cc_final: 0.2138 (tpp) REVERT: G 37 VAL cc_start: -0.0532 (OUTLIER) cc_final: -0.0853 (t) REVERT: E 34 MET cc_start: 0.4856 (tmm) cc_final: 0.4547 (tpp) REVERT: E 155 GLU cc_start: 0.5225 (OUTLIER) cc_final: 0.4386 (tp30) outliers start: 124 outliers final: 70 residues processed: 220 average time/residue: 0.4325 time to fit residues: 157.4664 Evaluate side-chains 180 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 97 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 155 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 338 optimal weight: 2.9990 chunk 255 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 335 optimal weight: 50.0000 chunk 273 optimal weight: 3.9990 chunk 247 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 311 optimal weight: 0.8980 chunk 204 optimal weight: 0.8980 chunk 184 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN D 42 GLN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.110691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.065976 restraints weight = 124960.312| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 5.36 r_work: 0.3043 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32379 Z= 0.113 Angle : 0.538 10.996 44100 Z= 0.271 Chirality : 0.042 0.171 4960 Planarity : 0.004 0.055 5697 Dihedral : 5.127 58.827 4408 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.48 % Favored : 93.39 % Rotamer: Outliers : 2.66 % Allowed : 14.55 % Favored : 82.80 % 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: -1.93 (0.13), residues: 4025 helix: 1.70 (0.21), residues: 653 sheet: -1.03 (0.16), residues: 1015 loop : -2.40 (0.12), residues: 2357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 436 HIS 0.006 0.001 HIS C 339 PHE 0.022 0.001 PHE C 141 TYR 0.013 0.001 TYR B 707 ARG 0.003 0.000 ARG C1019 Details of bonding type rmsd hydrogen bonds : bond 0.03392 ( 954) hydrogen bonds : angle 5.20831 ( 2706) SS BOND : bond 0.00192 ( 43) SS BOND : angle 0.60220 ( 86) covalent geometry : bond 0.00254 (32336) covalent geometry : angle 0.53823 (44014) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 108 time to evaluate : 3.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 HIS cc_start: 0.6825 (OUTLIER) cc_final: 0.6620 (p90) REVERT: C 136 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.7940 (p90) REVERT: C 175 PHE cc_start: 0.8443 (p90) cc_final: 0.7242 (p90) REVERT: C 249 LEU cc_start: -0.3541 (OUTLIER) cc_final: -0.3796 (mt) REVERT: C 387 LEU cc_start: 0.8581 (mt) cc_final: 0.8364 (mm) REVERT: C 388 ASN cc_start: 0.7942 (m-40) cc_final: 0.7611 (m-40) REVERT: C 571 ASP cc_start: 0.9227 (m-30) cc_final: 0.8740 (t0) REVERT: C 854 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.7261 (mtmm) REVERT: C 900 MET cc_start: 0.9091 (mtp) cc_final: 0.8750 (mtt) REVERT: C 1017 GLU cc_start: 0.9184 (tm-30) cc_final: 0.8953 (tm-30) REVERT: B 80 PHE cc_start: 0.2975 (OUTLIER) cc_final: 0.2588 (p90) REVERT: B 100 ASN cc_start: 0.9203 (OUTLIER) cc_final: 0.8907 (t0) REVERT: B 136 PHE cc_start: 0.9200 (OUTLIER) cc_final: 0.8577 (p90) REVERT: B 200 TYR cc_start: 0.8881 (m-80) cc_final: 0.8406 (m-80) REVERT: B 229 LEU cc_start: 0.9318 (mm) cc_final: 0.8776 (tp) REVERT: B 246 ARG cc_start: 0.2934 (OUTLIER) cc_final: 0.2327 (ptt180) REVERT: B 571 ASP cc_start: 0.8594 (t0) cc_final: 0.8125 (t0) REVERT: B 969 LYS cc_start: 0.8990 (mtmm) cc_final: 0.8670 (mtmm) REVERT: A 177 MET cc_start: 0.7823 (ppp) cc_final: 0.7522 (ppp) REVERT: A 191 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7785 (mp0) REVERT: A 457 ARG cc_start: -0.0809 (OUTLIER) cc_final: -0.1845 (mtt180) REVERT: A 780 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8200 (mp0) REVERT: A 950 ASP cc_start: 0.9100 (t0) cc_final: 0.8753 (t0) REVERT: G 34 MET cc_start: 0.2360 (tpp) cc_final: 0.2038 (tpp) REVERT: G 37 VAL cc_start: -0.0414 (OUTLIER) cc_final: -0.0718 (t) REVERT: D 97 MET cc_start: 0.8033 (tpt) cc_final: 0.7690 (mmm) REVERT: E 155 GLU cc_start: 0.5535 (OUTLIER) cc_final: 0.4928 (tp30) outliers start: 94 outliers final: 44 residues processed: 194 average time/residue: 0.4195 time to fit residues: 133.9128 Evaluate side-chains 151 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 95 time to evaluate : 3.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 155 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 360 optimal weight: 0.5980 chunk 91 optimal weight: 10.0000 chunk 266 optimal weight: 9.9990 chunk 184 optimal weight: 0.9980 chunk 287 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 279 optimal weight: 3.9990 chunk 350 optimal weight: 50.0000 chunk 333 optimal weight: 0.6980 chunk 262 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1125 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 ASN ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 GLN ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN G 52 ASN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.110477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.065453 restraints weight = 124706.303| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 5.80 r_work: 0.3056 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32379 Z= 0.122 Angle : 0.531 10.194 44100 Z= 0.266 Chirality : 0.042 0.167 4960 Planarity : 0.004 0.064 5697 Dihedral : 4.947 56.987 4400 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.63 % Favored : 93.27 % Rotamer: Outliers : 2.54 % Allowed : 14.97 % Favored : 82.49 % 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: -1.75 (0.13), residues: 4025 helix: 1.87 (0.21), residues: 655 sheet: -0.92 (0.16), residues: 1014 loop : -2.29 (0.12), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 436 HIS 0.005 0.001 HIS C 339 PHE 0.047 0.001 PHE A 157 TYR 0.014 0.001 TYR A 453 ARG 0.003 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.03257 ( 954) hydrogen bonds : angle 5.06634 ( 2706) SS BOND : bond 0.00191 ( 43) SS BOND : angle 0.58930 ( 86) covalent geometry : bond 0.00278 (32336) covalent geometry : angle 0.53068 (44014) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 100 time to evaluate : 3.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 HIS cc_start: 0.6785 (OUTLIER) cc_final: 0.6557 (p90) REVERT: C 136 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.7694 (p90) REVERT: C 175 PHE cc_start: 0.8387 (p90) cc_final: 0.7219 (p90) REVERT: C 249 LEU cc_start: -0.3034 (OUTLIER) cc_final: -0.3329 (mt) REVERT: C 571 ASP cc_start: 0.9206 (m-30) cc_final: 0.8711 (t0) REVERT: C 854 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.7271 (mtmm) REVERT: C 900 MET cc_start: 0.9058 (mtp) cc_final: 0.8716 (mtt) REVERT: C 1017 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8929 (tm-30) REVERT: B 80 PHE cc_start: 0.3060 (OUTLIER) cc_final: 0.2648 (p90) REVERT: B 100 ASN cc_start: 0.9198 (OUTLIER) cc_final: 0.8929 (t0) REVERT: B 136 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8442 (p90) REVERT: B 200 TYR cc_start: 0.8862 (m-80) cc_final: 0.8378 (m-80) REVERT: B 229 LEU cc_start: 0.9295 (mm) cc_final: 0.8769 (tp) REVERT: B 246 ARG cc_start: 0.2893 (OUTLIER) cc_final: 0.2338 (ptt180) REVERT: B 571 ASP cc_start: 0.8530 (t0) cc_final: 0.8064 (t0) REVERT: B 869 MET cc_start: 0.9450 (OUTLIER) cc_final: 0.8958 (mtt) REVERT: B 969 LYS cc_start: 0.8986 (mtmm) cc_final: 0.8654 (mtmm) REVERT: A 170 TYR cc_start: 0.8730 (t80) cc_final: 0.8436 (t80) REVERT: A 177 MET cc_start: 0.7908 (ppp) cc_final: 0.7592 (ppp) REVERT: A 191 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7856 (mp0) REVERT: A 249 LEU cc_start: -0.2541 (OUTLIER) cc_final: -0.3109 (tp) REVERT: A 950 ASP cc_start: 0.9084 (t0) cc_final: 0.8738 (t0) REVERT: G 34 MET cc_start: 0.2347 (tpp) cc_final: 0.2047 (tpp) REVERT: G 37 VAL cc_start: -0.0438 (OUTLIER) cc_final: -0.0742 (t) outliers start: 90 outliers final: 51 residues processed: 181 average time/residue: 0.4246 time to fit residues: 126.5371 Evaluate side-chains 157 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 94 time to evaluate : 3.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 68 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 98 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 278 optimal weight: 0.9990 chunk 259 optimal weight: 40.0000 chunk 35 optimal weight: 7.9990 chunk 39 optimal weight: 40.0000 chunk 323 optimal weight: 0.3980 chunk 252 optimal weight: 40.0000 chunk 322 optimal weight: 50.0000 chunk 129 optimal weight: 8.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 409 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN D 42 GLN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.109898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.062917 restraints weight = 125676.563| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 5.85 r_work: 0.2987 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 32379 Z= 0.217 Angle : 0.578 11.726 44100 Z= 0.293 Chirality : 0.043 0.164 4960 Planarity : 0.004 0.061 5697 Dihedral : 4.994 56.981 4397 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.30 % Favored : 92.60 % Rotamer: Outliers : 2.57 % Allowed : 14.66 % Favored : 82.77 % 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: -1.69 (0.13), residues: 4025 helix: 1.69 (0.21), residues: 665 sheet: -0.90 (0.16), residues: 1001 loop : -2.16 (0.12), residues: 2359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 65 HIS 0.006 0.001 HIS B1083 PHE 0.023 0.001 PHE C 141 TYR 0.019 0.001 TYR B 707 ARG 0.005 0.000 ARG A 815 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 954) hydrogen bonds : angle 5.19068 ( 2706) SS BOND : bond 0.00251 ( 43) SS BOND : angle 0.60032 ( 86) covalent geometry : bond 0.00485 (32336) covalent geometry : angle 0.57778 (44014) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 97 time to evaluate : 3.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 HIS cc_start: 0.6846 (OUTLIER) cc_final: 0.6636 (p90) REVERT: C 136 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8042 (p90) REVERT: C 175 PHE cc_start: 0.8339 (p90) cc_final: 0.7161 (p90) REVERT: C 177 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.6791 (tmm) REVERT: C 571 ASP cc_start: 0.9247 (m-30) cc_final: 0.8793 (t0) REVERT: C 854 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.7238 (mtmm) REVERT: C 900 MET cc_start: 0.9213 (mtp) cc_final: 0.8931 (mtt) REVERT: C 1017 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8899 (tm-30) REVERT: B 80 PHE cc_start: 0.2879 (OUTLIER) cc_final: 0.2445 (p90) REVERT: B 100 ASN cc_start: 0.9221 (OUTLIER) cc_final: 0.8895 (t0) REVERT: B 200 TYR cc_start: 0.8962 (m-80) cc_final: 0.8469 (m-80) REVERT: B 246 ARG cc_start: 0.3222 (OUTLIER) cc_final: 0.2554 (ptt180) REVERT: B 571 ASP cc_start: 0.8767 (t0) cc_final: 0.8376 (t0) REVERT: B 869 MET cc_start: 0.9490 (OUTLIER) cc_final: 0.9035 (mtt) REVERT: A 191 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: A 249 LEU cc_start: -0.2351 (OUTLIER) cc_final: -0.3084 (tp) REVERT: A 574 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8790 (t0) REVERT: A 950 ASP cc_start: 0.9169 (t0) cc_final: 0.8838 (t0) REVERT: G 34 MET cc_start: 0.2404 (tpp) cc_final: 0.2153 (tpp) REVERT: G 37 VAL cc_start: -0.0510 (OUTLIER) cc_final: -0.0727 (t) REVERT: D 24 ARG cc_start: 0.7757 (mtm-85) cc_final: 0.7525 (mtm-85) REVERT: D 42 GLN cc_start: 0.6287 (OUTLIER) cc_final: 0.6065 (pm20) outliers start: 91 outliers final: 53 residues processed: 181 average time/residue: 0.4234 time to fit residues: 127.0114 Evaluate side-chains 154 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 88 time to evaluate : 3.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 68 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 106 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 260 optimal weight: 50.0000 chunk 123 optimal weight: 9.9990 chunk 204 optimal weight: 2.9990 chunk 374 optimal weight: 50.0000 chunk 352 optimal weight: 40.0000 chunk 248 optimal weight: 8.9990 chunk 299 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 114 optimal weight: 0.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.109340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.064105 restraints weight = 125728.508| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 5.62 r_work: 0.3004 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 32379 Z= 0.167 Angle : 0.550 11.287 44100 Z= 0.277 Chirality : 0.042 0.163 4960 Planarity : 0.004 0.076 5697 Dihedral : 4.902 57.386 4396 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.76 % Favored : 93.14 % Rotamer: Outliers : 2.34 % Allowed : 15.03 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.13), residues: 4025 helix: 1.84 (0.21), residues: 658 sheet: -0.84 (0.16), residues: 1011 loop : -2.11 (0.12), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 65 HIS 0.005 0.001 HIS B1083 PHE 0.033 0.001 PHE A 157 TYR 0.017 0.001 TYR B 707 ARG 0.004 0.000 ARG C 246 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 954) hydrogen bonds : angle 5.08652 ( 2706) SS BOND : bond 0.00211 ( 43) SS BOND : angle 0.55496 ( 86) covalent geometry : bond 0.00381 (32336) covalent geometry : angle 0.55021 (44014) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 92 time to evaluate : 3.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 HIS cc_start: 0.6953 (OUTLIER) cc_final: 0.6747 (p90) REVERT: C 136 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8118 (p90) REVERT: C 175 PHE cc_start: 0.8405 (p90) cc_final: 0.7250 (p90) REVERT: C 177 MET cc_start: 0.7616 (tmm) cc_final: 0.6843 (tmm) REVERT: C 571 ASP cc_start: 0.9252 (m-30) cc_final: 0.8820 (t0) REVERT: C 854 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7218 (mtmm) REVERT: C 900 MET cc_start: 0.9140 (mtp) cc_final: 0.8857 (mtt) REVERT: C 1017 GLU cc_start: 0.9168 (tm-30) cc_final: 0.8917 (tm-30) REVERT: B 80 PHE cc_start: 0.2878 (OUTLIER) cc_final: 0.2510 (p90) REVERT: B 100 ASN cc_start: 0.9224 (OUTLIER) cc_final: 0.8860 (t0) REVERT: B 136 PHE cc_start: 0.9203 (OUTLIER) cc_final: 0.8612 (p90) REVERT: B 200 TYR cc_start: 0.8921 (m-80) cc_final: 0.8415 (m-80) REVERT: B 571 ASP cc_start: 0.8806 (t0) cc_final: 0.8427 (t0) REVERT: B 869 MET cc_start: 0.9465 (OUTLIER) cc_final: 0.9000 (mtt) REVERT: A 177 MET cc_start: 0.7849 (ppp) cc_final: 0.7590 (ppp) REVERT: A 191 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: A 249 LEU cc_start: -0.2540 (OUTLIER) cc_final: -0.3250 (tp) REVERT: A 457 ARG cc_start: -0.0982 (OUTLIER) cc_final: -0.2010 (mtt180) REVERT: A 950 ASP cc_start: 0.9159 (t0) cc_final: 0.8813 (t0) REVERT: G 34 MET cc_start: 0.2140 (tpp) cc_final: 0.1857 (tpp) REVERT: G 37 VAL cc_start: -0.0459 (OUTLIER) cc_final: -0.0736 (t) REVERT: D 24 ARG cc_start: 0.7731 (mtm-85) cc_final: 0.7489 (mtm-85) outliers start: 83 outliers final: 58 residues processed: 168 average time/residue: 0.4624 time to fit residues: 130.2116 Evaluate side-chains 158 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 89 time to evaluate : 3.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain E residue 33 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 397 optimal weight: 0.2980 chunk 281 optimal weight: 8.9990 chunk 175 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 321 optimal weight: 6.9990 chunk 214 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 344 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 127 optimal weight: 20.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 914 ASN A 70 HIS ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN F 42 GLN D 42 GLN D 168 GLN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.110316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.063972 restraints weight = 125451.477| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 6.37 r_work: 0.3012 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32379 Z= 0.160 Angle : 0.552 11.393 44100 Z= 0.277 Chirality : 0.042 0.162 4960 Planarity : 0.004 0.076 5697 Dihedral : 4.804 59.452 4393 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.11 % Favored : 92.80 % Rotamer: Outliers : 2.32 % Allowed : 15.17 % Favored : 82.51 % 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: -1.49 (0.13), residues: 4025 helix: 1.92 (0.21), residues: 657 sheet: -0.80 (0.16), residues: 1003 loop : -2.03 (0.12), residues: 2365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A 258 HIS 0.007 0.001 HIS A 70 PHE 0.025 0.001 PHE C 141 TYR 0.016 0.001 TYR B 707 ARG 0.007 0.000 ARG A 246 Details of bonding type rmsd hydrogen bonds : bond 0.03349 ( 954) hydrogen bonds : angle 5.01978 ( 2706) SS BOND : bond 0.00198 ( 43) SS BOND : angle 0.53671 ( 86) covalent geometry : bond 0.00361 (32336) covalent geometry : angle 0.55251 (44014) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 96 time to evaluate : 3.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 HIS cc_start: 0.7032 (OUTLIER) cc_final: 0.6818 (p90) REVERT: C 136 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8142 (p90) REVERT: C 175 PHE cc_start: 0.8481 (p90) cc_final: 0.7317 (p90) REVERT: C 177 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.6835 (tmm) REVERT: C 571 ASP cc_start: 0.9186 (m-30) cc_final: 0.8820 (t0) REVERT: C 854 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.7174 (mtmm) REVERT: C 900 MET cc_start: 0.9128 (mtp) cc_final: 0.8838 (mtt) REVERT: C 1017 GLU cc_start: 0.9142 (tm-30) cc_final: 0.8912 (tm-30) REVERT: B 80 PHE cc_start: 0.2963 (OUTLIER) cc_final: 0.2616 (p90) REVERT: B 100 ASN cc_start: 0.9263 (OUTLIER) cc_final: 0.8877 (t0) REVERT: B 136 PHE cc_start: 0.9193 (OUTLIER) cc_final: 0.8582 (p90) REVERT: B 200 TYR cc_start: 0.8940 (m-80) cc_final: 0.8437 (m-80) REVERT: B 571 ASP cc_start: 0.8786 (t0) cc_final: 0.8403 (t0) REVERT: B 869 MET cc_start: 0.9448 (OUTLIER) cc_final: 0.8980 (mtt) REVERT: A 177 MET cc_start: 0.7763 (ppp) cc_final: 0.7509 (ppp) REVERT: A 191 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: A 249 LEU cc_start: -0.2220 (OUTLIER) cc_final: -0.3162 (tp) REVERT: A 574 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.8639 (t0) REVERT: A 950 ASP cc_start: 0.9094 (t0) cc_final: 0.8753 (t0) REVERT: G 34 MET cc_start: 0.2022 (tpp) cc_final: 0.1761 (tpp) REVERT: G 37 VAL cc_start: -0.0345 (OUTLIER) cc_final: -0.0550 (t) REVERT: D 24 ARG cc_start: 0.7858 (mtm-85) cc_final: 0.7656 (mtm-85) outliers start: 82 outliers final: 61 residues processed: 171 average time/residue: 0.4410 time to fit residues: 123.3112 Evaluate side-chains 164 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 91 time to evaluate : 3.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain E residue 33 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 117 optimal weight: 20.0000 chunk 279 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 228 optimal weight: 8.9990 chunk 285 optimal weight: 1.9990 chunk 187 optimal weight: 0.5980 chunk 349 optimal weight: 50.0000 chunk 260 optimal weight: 8.9990 chunk 12 optimal weight: 0.0020 chunk 121 optimal weight: 20.0000 overall best weight: 1.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN A 448 ASN A 450 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN D 42 GLN E 52 ASN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.110744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.064483 restraints weight = 125796.853| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 6.51 r_work: 0.3027 rms_B_bonded: 5.12 restraints_weight: 2.0000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32379 Z= 0.122 Angle : 0.533 12.046 44100 Z= 0.265 Chirality : 0.042 0.165 4960 Planarity : 0.004 0.076 5697 Dihedral : 4.654 57.629 4392 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.58 % Favored : 93.32 % Rotamer: Outliers : 1.89 % Allowed : 15.54 % Favored : 82.57 % 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: -1.38 (0.13), residues: 4025 helix: 2.08 (0.21), residues: 651 sheet: -0.79 (0.16), residues: 1020 loop : -1.95 (0.12), residues: 2354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 65 HIS 0.004 0.001 HIS C 339 PHE 0.045 0.001 PHE A 157 TYR 0.013 0.001 TYR B 707 ARG 0.004 0.000 ARG E 87 Details of bonding type rmsd hydrogen bonds : bond 0.03169 ( 954) hydrogen bonds : angle 4.87804 ( 2706) SS BOND : bond 0.00169 ( 43) SS BOND : angle 0.51569 ( 86) covalent geometry : bond 0.00278 (32336) covalent geometry : angle 0.53326 (44014) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 92 time to evaluate : 3.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 136 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.7985 (p90) REVERT: C 153 MET cc_start: 0.5324 (ppp) cc_final: 0.5117 (ppp) REVERT: C 175 PHE cc_start: 0.8420 (p90) cc_final: 0.7238 (p90) REVERT: C 177 MET cc_start: 0.7565 (tmm) cc_final: 0.6806 (tmm) REVERT: C 571 ASP cc_start: 0.9197 (m-30) cc_final: 0.8853 (t0) REVERT: C 854 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.7210 (mtmm) REVERT: C 1017 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8889 (tm-30) REVERT: B 80 PHE cc_start: 0.3179 (OUTLIER) cc_final: 0.2851 (p90) REVERT: B 136 PHE cc_start: 0.9237 (OUTLIER) cc_final: 0.8614 (p90) REVERT: B 200 TYR cc_start: 0.8904 (m-80) cc_final: 0.8433 (m-80) REVERT: B 571 ASP cc_start: 0.8773 (t0) cc_final: 0.8411 (t0) REVERT: B 869 MET cc_start: 0.9430 (OUTLIER) cc_final: 0.8967 (mtt) REVERT: A 177 MET cc_start: 0.7879 (ppp) cc_final: 0.7609 (ppp) REVERT: A 191 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.7900 (mp0) REVERT: A 457 ARG cc_start: -0.0976 (OUTLIER) cc_final: -0.1958 (mtt180) REVERT: A 574 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.8506 (t0) REVERT: A 585 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9296 (pp) REVERT: A 950 ASP cc_start: 0.9061 (t0) cc_final: 0.8718 (t0) REVERT: G 34 MET cc_start: 0.2115 (tpp) cc_final: 0.1884 (tpp) REVERT: G 37 VAL cc_start: -0.0300 (OUTLIER) cc_final: -0.0593 (t) REVERT: D 24 ARG cc_start: 0.7828 (mtm-85) cc_final: 0.7622 (mtm-85) outliers start: 67 outliers final: 49 residues processed: 156 average time/residue: 0.4578 time to fit residues: 118.1125 Evaluate side-chains 149 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 90 time to evaluate : 3.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 68 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 385 optimal weight: 0.1980 chunk 350 optimal weight: 50.0000 chunk 113 optimal weight: 1.9990 chunk 347 optimal weight: 0.3980 chunk 346 optimal weight: 20.0000 chunk 367 optimal weight: 9.9990 chunk 308 optimal weight: 4.9990 chunk 268 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.110788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.065012 restraints weight = 125383.026| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 5.86 r_work: 0.3028 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.139 32379 Z= 0.148 Angle : 0.665 59.005 44100 Z= 0.355 Chirality : 0.042 0.456 4960 Planarity : 0.004 0.071 5697 Dihedral : 4.641 57.578 4391 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.58 % Favored : 93.32 % Rotamer: Outliers : 1.84 % Allowed : 15.59 % Favored : 82.57 % Cbeta Deviations : 0.03 % 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: -1.37 (0.13), residues: 4025 helix: 2.09 (0.21), residues: 651 sheet: -0.79 (0.16), residues: 1021 loop : -1.94 (0.12), residues: 2353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 65 HIS 0.005 0.001 HIS C 339 PHE 0.033 0.001 PHE A 157 TYR 0.012 0.001 TYR B 707 ARG 0.004 0.000 ARG F 54 Details of bonding type rmsd hydrogen bonds : bond 0.03166 ( 954) hydrogen bonds : angle 4.87833 ( 2706) SS BOND : bond 0.00166 ( 43) SS BOND : angle 0.50281 ( 86) covalent geometry : bond 0.00328 (32336) covalent geometry : angle 0.66577 (44014) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28557.92 seconds wall clock time: 492 minutes 24.45 seconds (29544.45 seconds total)