Starting phenix.real_space_refine on Mon Sep 30 01:26:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxi_32180/09_2024/7vxi_32180.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxi_32180/09_2024/7vxi_32180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxi_32180/09_2024/7vxi_32180.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxi_32180/09_2024/7vxi_32180.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxi_32180/09_2024/7vxi_32180.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxi_32180/09_2024/7vxi_32180.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.114 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 113 5.16 5 C 15677 2.51 5 N 4111 2.21 5 O 4669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24570 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8310 Classifications: {'peptide': 1062} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1009} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 7950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7950 Classifications: {'peptide': 1020} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 50, 'TRANS': 969} Chain breaks: 6 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 8310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8310 Classifications: {'peptide': 1062} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1009} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 14.08, per 1000 atoms: 0.57 Number of scatterers: 24570 At special positions: 0 Unit cell: (158.485, 158.485, 180.345, 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 113 16.00 O 4669 8.00 N 4111 7.00 C 15677 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 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 B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 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 C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " 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=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.62 Conformation dependent library (CDL) restraints added in 3.3 seconds 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5888 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 49 sheets defined 24.2% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.61 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.503A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 4.412A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.549A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.761A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.767A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.621A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.702A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.972A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.769A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 941 removed outlier: 5.726A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.923A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.142A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.687A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.636A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 390 removed outlier: 3.851A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.336A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 623 Proline residue: B 621 - end of helix Processing helix chain 'B' and resid 739 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.605A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.835A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.608A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 856 removed outlier: 3.637A pdb=" N PHE B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.199A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.668A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 5.971A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.154A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.993A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1140 through 1148 removed outlier: 3.990A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.597A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 385 through 390 removed outlier: 4.428A pdb=" N ASP C 389 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 removed outlier: 4.028A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.747A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.638A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.544A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA C 783 " --> pdb=" O GLN C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.847A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.505A pdb=" N THR C 874 " --> pdb=" O ILE C 870 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.012A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.833A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 941 removed outlier: 3.502A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.041A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.158A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.923A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.098A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.529A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.599A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.074A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.622A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.363A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 3.606A pdb=" N ALA A 348 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 401 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349 removed outlier: 3.606A pdb=" N ALA A 348 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 401 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.396A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.160A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.431A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.112A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.566A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AC3, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.243A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.542A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.591A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B 156 " --> pdb=" O ASP B 142 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR B 144 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LYS B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.328A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.867A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.648A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B 156 " --> pdb=" O ASP B 142 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR B 144 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LYS B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.184A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL B 595 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.734A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.100A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.713A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.537A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.016A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.275A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.066A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.596A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.049A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.537A pdb=" N ARG C 237 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 118 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.630A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.001A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.942A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.195A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.731A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.597A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF4, first strand: chain 'C' and resid 1094 through 1097 968 hydrogen bonds defined for protein. 2697 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: 10.91 Time building geometry restraints manager: 7.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7948 1.35 - 1.47: 6161 1.47 - 1.59: 10883 1.59 - 1.71: 0 1.71 - 1.83: 143 Bond restraints: 25135 Sorted by residual: bond pdb=" C CYS A 336 " pdb=" N PRO A 337 " ideal model delta sigma weight residual 1.334 1.439 -0.105 2.34e-02 1.83e+03 2.03e+01 bond pdb=" C LEU A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 1.334 1.422 -0.088 2.34e-02 1.83e+03 1.41e+01 bond pdb=" C LEU C 229 " pdb=" N PRO C 230 " ideal model delta sigma weight residual 1.334 1.416 -0.082 2.34e-02 1.83e+03 1.24e+01 bond pdb=" C LYS C 424 " pdb=" N LEU C 425 " ideal model delta sigma weight residual 1.331 1.387 -0.056 2.07e-02 2.33e+03 7.26e+00 bond pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 1.517 1.541 -0.024 9.30e-03 1.16e+04 6.81e+00 ... (remaining 25130 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 32720 1.04 - 2.07: 1189 2.07 - 3.11: 182 3.11 - 4.14: 98 4.14 - 5.18: 7 Bond angle restraints: 34196 Sorted by residual: angle pdb=" C ASP A 215 " pdb=" CA ASP A 215 " pdb=" CB ASP A 215 " ideal model delta sigma weight residual 116.63 111.59 5.04 1.16e+00 7.43e-01 1.89e+01 angle pdb=" C PRO B 986 " pdb=" N PRO B 987 " pdb=" CA PRO B 987 " ideal model delta sigma weight residual 118.85 122.36 -3.51 1.09e+00 8.42e-01 1.04e+01 angle pdb=" C PHE B 32 " pdb=" CA PHE B 32 " pdb=" CB PHE B 32 " ideal model delta sigma weight residual 116.34 111.95 4.39 1.40e+00 5.10e-01 9.82e+00 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 114.31 -3.61 1.22e+00 6.72e-01 8.77e+00 angle pdb=" O LEU A 24 " pdb=" C LEU A 24 " pdb=" N PRO A 25 " ideal model delta sigma weight residual 121.88 123.88 -2.00 7.10e-01 1.98e+00 7.92e+00 ... (remaining 34191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 14670 16.60 - 33.21: 222 33.21 - 49.81: 79 49.81 - 66.42: 12 66.42 - 83.02: 5 Dihedral angle restraints: 14988 sinusoidal: 5841 harmonic: 9147 Sorted by residual: dihedral pdb=" CA THR B 19 " pdb=" C THR B 19 " pdb=" N THR B 20 " pdb=" CA THR B 20 " ideal model delta harmonic sigma weight residual 180.00 150.58 29.42 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA HIS B 66 " pdb=" C HIS B 66 " pdb=" N ALA B 67 " pdb=" CA ALA B 67 " ideal model delta harmonic sigma weight residual 180.00 155.46 24.54 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA ALA B 352 " pdb=" C ALA B 352 " pdb=" N TRP B 353 " pdb=" CA TRP B 353 " ideal model delta harmonic sigma weight residual -180.00 -156.70 -23.30 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 14985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2564 0.032 - 0.063: 833 0.063 - 0.095: 195 0.095 - 0.127: 261 0.127 - 0.158: 25 Chirality restraints: 3878 Sorted by residual: chirality pdb=" CA ILE A 68 " pdb=" N ILE A 68 " pdb=" C ILE A 68 " pdb=" CB ILE A 68 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CA ILE C 896 " pdb=" N ILE C 896 " pdb=" C ILE C 896 " pdb=" CB ILE C 896 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE B 664 " pdb=" N ILE B 664 " pdb=" C ILE B 664 " pdb=" CB ILE B 664 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 3875 not shown) Planarity restraints: 4436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 24 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.05e+00 pdb=" C LEU C 24 " -0.049 2.00e-02 2.50e+03 pdb=" O LEU C 24 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO C 25 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 24 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C LEU A 24 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU A 24 " 0.015 2.00e-02 2.50e+03 pdb=" N PRO A 25 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 985 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.95e+00 pdb=" C ASP B 985 " -0.039 2.00e-02 2.50e+03 pdb=" O ASP B 985 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO B 986 " 0.013 2.00e-02 2.50e+03 ... (remaining 4433 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 431 2.68 - 3.23: 23442 3.23 - 3.79: 35558 3.79 - 4.34: 51187 4.34 - 4.90: 83401 Nonbonded interactions: 194019 Sorted by model distance: nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.125 3.040 nonbonded pdb=" OG1 THR B 912 " pdb=" OD1 ASN B 914 " model vdw 2.125 3.040 nonbonded pdb=" OD1 ASN B 422 " pdb=" N TYR B 423 " model vdw 2.126 3.120 nonbonded pdb=" OG1 THR C 33 " pdb=" O GLY C 219 " model vdw 2.150 3.040 nonbonded pdb=" O GLN C 563 " pdb=" NH1 ARG C 577 " model vdw 2.186 3.120 ... (remaining 194014 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 244 or resid 247 through 438 or resid 495 throu \ gh 1147)) selection = (chain 'B' and (resid 14 through 620 or resid 641 through 827 or resid 854 throu \ gh 1147)) selection = (chain 'C' and (resid 14 through 244 or resid 247 through 438 or resid 495 throu \ gh 1147)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.080 Check model and map are aligned: 0.170 Set scattering table: 0.240 Process input model: 57.540 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5844 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 : 0.002 0.105 25135 Z= 0.144 Angle : 0.488 5.176 34196 Z= 0.298 Chirality : 0.043 0.158 3878 Planarity : 0.003 0.046 4436 Dihedral : 7.294 83.023 8989 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.35 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.83 (0.12), residues: 3106 helix: -1.73 (0.17), residues: 649 sheet: -0.49 (0.16), residues: 710 loop : -1.29 (0.12), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 64 HIS 0.006 0.001 HIS B1048 PHE 0.016 0.001 PHE B 133 TYR 0.014 0.001 TYR A 495 ARG 0.004 0.000 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 659 time to evaluate : 2.838 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: A 300 LYS cc_start: 0.7698 (mttt) cc_final: 0.7368 (mtmm) REVERT: A 541 PHE cc_start: 0.6371 (p90) cc_final: 0.5887 (p90) REVERT: A 581 THR cc_start: 0.6716 (m) cc_final: 0.5759 (p) REVERT: A 605 SER cc_start: 0.7805 (t) cc_final: 0.7597 (p) REVERT: A 716 THR cc_start: 0.8076 (p) cc_final: 0.7832 (t) REVERT: A 725 GLU cc_start: 0.6073 (mt-10) cc_final: 0.5841 (mt-10) REVERT: A 863 PRO cc_start: 0.8554 (Cg_endo) cc_final: 0.8326 (Cg_exo) REVERT: A 864 LEU cc_start: 0.7742 (tp) cc_final: 0.7030 (tp) REVERT: A 881 THR cc_start: 0.6459 (p) cc_final: 0.6222 (p) REVERT: A 886 TRP cc_start: 0.7740 (p90) cc_final: 0.7456 (p90) REVERT: A 912 THR cc_start: 0.7875 (m) cc_final: 0.7668 (p) REVERT: A 976 VAL cc_start: 0.7854 (t) cc_final: 0.7621 (t) REVERT: A 1073 LYS cc_start: 0.7192 (tttt) cc_final: 0.6856 (ttpp) REVERT: B 45 SER cc_start: 0.6482 (p) cc_final: 0.6219 (t) REVERT: B 49 HIS cc_start: 0.7378 (t-90) cc_final: 0.7127 (t70) REVERT: B 129 LYS cc_start: 0.6274 (ttmt) cc_final: 0.5944 (tptt) REVERT: B 206 LYS cc_start: 0.6772 (tptt) cc_final: 0.6520 (tptp) REVERT: B 651 ILE cc_start: 0.7642 (pt) cc_final: 0.7193 (mp) REVERT: B 657 ASN cc_start: 0.7615 (m-40) cc_final: 0.7405 (m-40) REVERT: B 747 THR cc_start: 0.7109 (m) cc_final: 0.6323 (p) REVERT: B 780 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6777 (mt-10) REVERT: B 960 ASN cc_start: 0.7572 (t0) cc_final: 0.7088 (m-40) REVERT: B 1011 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7361 (mm110) REVERT: B 1028 LYS cc_start: 0.7288 (mttt) cc_final: 0.6631 (mmtp) REVERT: B 1036 GLN cc_start: 0.8208 (tt0) cc_final: 0.7017 (tt0) REVERT: B 1050 MET cc_start: 0.7636 (ptm) cc_final: 0.7275 (ptm) REVERT: B 1054 GLN cc_start: 0.6757 (mm-40) cc_final: 0.5624 (mt0) REVERT: B 1073 LYS cc_start: 0.7439 (mttt) cc_final: 0.7174 (mttt) REVERT: B 1122 VAL cc_start: 0.8306 (t) cc_final: 0.7912 (p) REVERT: C 56 LEU cc_start: 0.8173 (tp) cc_final: 0.7926 (tt) REVERT: C 59 PHE cc_start: 0.7135 (m-10) cc_final: 0.6875 (m-80) REVERT: C 92 PHE cc_start: 0.5727 (t80) cc_final: 0.5469 (t80) REVERT: C 177 MET cc_start: 0.3610 (tpp) cc_final: 0.3212 (tpp) REVERT: C 398 ASP cc_start: 0.5315 (m-30) cc_final: 0.4996 (m-30) REVERT: C 399 SER cc_start: 0.7076 (m) cc_final: 0.6255 (p) REVERT: C 400 PHE cc_start: 0.5507 (p90) cc_final: 0.5091 (p90) REVERT: C 615 VAL cc_start: 0.7278 (m) cc_final: 0.6957 (t) REVERT: C 775 ASP cc_start: 0.7492 (m-30) cc_final: 0.7117 (m-30) REVERT: C 780 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6830 (mt-10) REVERT: C 819 GLU cc_start: 0.7231 (mt-10) cc_final: 0.7014 (mt-10) REVERT: C 869 MET cc_start: 0.7435 (mtt) cc_final: 0.7201 (mtt) REVERT: C 884 SER cc_start: 0.7977 (m) cc_final: 0.7765 (m) REVERT: C 886 TRP cc_start: 0.8476 (p90) cc_final: 0.8175 (p90) REVERT: C 936 ASP cc_start: 0.7394 (m-30) cc_final: 0.7146 (m-30) REVERT: C 1033 VAL cc_start: 0.7754 (t) cc_final: 0.7509 (t) REVERT: C 1119 ASN cc_start: 0.6229 (m-40) cc_final: 0.5965 (p0) outliers start: 0 outliers final: 0 residues processed: 659 average time/residue: 0.3881 time to fit residues: 386.9825 Evaluate side-chains 506 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 506 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 265 optimal weight: 3.9990 chunk 237 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 81 optimal weight: 0.0770 chunk 160 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 246 optimal weight: 0.0470 chunk 95 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 285 optimal weight: 0.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1119 ASN B 519 HIS B 675 GLN B 751 ASN B 762 GLN B 872 GLN B 901 GLN B1005 GLN C 239 GLN C 388 ASN C 544 ASN C 644 GLN C 655 HIS C 764 ASN C 856 ASN C 901 GLN C 955 ASN C1002 GLN C1071 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6115 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25135 Z= 0.207 Angle : 0.573 7.487 34196 Z= 0.310 Chirality : 0.046 0.188 3878 Planarity : 0.004 0.064 4436 Dihedral : 4.116 19.318 3365 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.12 % Favored : 97.81 % Rotamer: Outliers : 1.68 % Allowed : 5.94 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.13), residues: 3106 helix: 0.89 (0.21), residues: 663 sheet: 0.03 (0.17), residues: 677 loop : -0.95 (0.13), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 64 HIS 0.006 0.001 HIS C1064 PHE 0.022 0.002 PHE A 238 TYR 0.019 0.002 TYR B 265 ARG 0.006 0.001 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 544 time to evaluate : 2.864 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: A 190 ARG cc_start: 0.7191 (mmt180) cc_final: 0.6785 (mtp85) REVERT: A 205 SER cc_start: 0.7597 (t) cc_final: 0.7390 (m) REVERT: A 300 LYS cc_start: 0.7939 (mttt) cc_final: 0.7449 (mmtp) REVERT: A 310 LYS cc_start: 0.7961 (ptmt) cc_final: 0.7717 (ptmm) REVERT: A 541 PHE cc_start: 0.6300 (p90) cc_final: 0.5978 (p90) REVERT: A 605 SER cc_start: 0.7878 (t) cc_final: 0.7539 (m) REVERT: A 716 THR cc_start: 0.8288 (p) cc_final: 0.8035 (t) REVERT: A 725 GLU cc_start: 0.6502 (mt-10) cc_final: 0.6298 (mt-10) REVERT: A 748 GLU cc_start: 0.6545 (mm-30) cc_final: 0.6211 (mm-30) REVERT: A 772 VAL cc_start: 0.7817 (t) cc_final: 0.7527 (p) REVERT: A 782 PHE cc_start: 0.7644 (m-80) cc_final: 0.7339 (m-80) REVERT: A 855 PHE cc_start: 0.5768 (m-80) cc_final: 0.5524 (m-80) REVERT: A 864 LEU cc_start: 0.8044 (tp) cc_final: 0.7438 (tt) REVERT: A 886 TRP cc_start: 0.7823 (p90) cc_final: 0.7600 (p90) REVERT: A 934 ILE cc_start: 0.7495 (OUTLIER) cc_final: 0.7283 (tp) REVERT: A 957 GLN cc_start: 0.7141 (tm-30) cc_final: 0.6701 (tm-30) REVERT: A 976 VAL cc_start: 0.7276 (t) cc_final: 0.7065 (t) REVERT: A 1002 GLN cc_start: 0.7073 (OUTLIER) cc_final: 0.6598 (mp10) REVERT: A 1013 ILE cc_start: 0.7499 (mm) cc_final: 0.7234 (mt) REVERT: A 1057 PRO cc_start: 0.8257 (Cg_exo) cc_final: 0.8016 (Cg_endo) REVERT: B 33 THR cc_start: 0.6416 (p) cc_final: 0.5380 (m) REVERT: B 44 ARG cc_start: 0.7012 (mtm-85) cc_final: 0.6656 (mtm-85) REVERT: B 53 ASP cc_start: 0.6198 (t0) cc_final: 0.5929 (t0) REVERT: B 129 LYS cc_start: 0.6637 (ttmt) cc_final: 0.6329 (tptt) REVERT: B 153 MET cc_start: -0.1703 (ttp) cc_final: -0.2342 (ttp) REVERT: B 300 LYS cc_start: 0.7500 (ptpt) cc_final: 0.6800 (ptpt) REVERT: B 313 TYR cc_start: 0.8132 (m-80) cc_final: 0.7816 (m-80) REVERT: B 531 THR cc_start: 0.6980 (OUTLIER) cc_final: 0.6425 (m) REVERT: B 577 ARG cc_start: 0.6277 (mtp180) cc_final: 0.6043 (mtp180) REVERT: B 657 ASN cc_start: 0.7616 (m-40) cc_final: 0.7402 (m-40) REVERT: B 660 TYR cc_start: 0.7377 (m-80) cc_final: 0.7006 (m-80) REVERT: B 904 TYR cc_start: 0.5576 (t80) cc_final: 0.5371 (t80) REVERT: B 917 TYR cc_start: 0.5342 (m-10) cc_final: 0.4399 (m-80) REVERT: B 983 ARG cc_start: 0.7296 (ttm-80) cc_final: 0.6926 (ttm-80) REVERT: B 1028 LYS cc_start: 0.7758 (mttt) cc_final: 0.7522 (mttm) REVERT: B 1122 VAL cc_start: 0.8423 (t) cc_final: 0.8179 (p) REVERT: C 92 PHE cc_start: 0.6061 (t80) cc_final: 0.5765 (t80) REVERT: C 177 MET cc_start: 0.3737 (tpp) cc_final: 0.3371 (tpp) REVERT: C 310 LYS cc_start: 0.7753 (ptmm) cc_final: 0.7476 (ptmm) REVERT: C 382 VAL cc_start: 0.8640 (p) cc_final: 0.8428 (t) REVERT: C 386 LYS cc_start: 0.7516 (mmtt) cc_final: 0.7179 (mmmm) REVERT: C 396 TYR cc_start: 0.5406 (m-80) cc_final: 0.3849 (m-80) REVERT: C 398 ASP cc_start: 0.5690 (m-30) cc_final: 0.5355 (t70) REVERT: C 400 PHE cc_start: 0.5395 (p90) cc_final: 0.5145 (p90) REVERT: C 531 THR cc_start: 0.7870 (p) cc_final: 0.7626 (t) REVERT: C 655 HIS cc_start: 0.7365 (OUTLIER) cc_final: 0.7085 (t70) REVERT: C 663 ASP cc_start: 0.6936 (m-30) cc_final: 0.6644 (m-30) REVERT: C 776 LYS cc_start: 0.7924 (mtpp) cc_final: 0.7655 (ttpt) REVERT: C 800 PHE cc_start: 0.6240 (m-10) cc_final: 0.5875 (m-10) REVERT: C 819 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6978 (mt-10) REVERT: C 823 PHE cc_start: 0.6234 (m-10) cc_final: 0.5608 (m-80) REVERT: C 825 LYS cc_start: 0.7241 (mtpp) cc_final: 0.6908 (mtpp) REVERT: C 856 ASN cc_start: 0.7218 (OUTLIER) cc_final: 0.6694 (m-40) REVERT: C 867 ASP cc_start: 0.7065 (m-30) cc_final: 0.6687 (t0) REVERT: C 884 SER cc_start: 0.8610 (m) cc_final: 0.8098 (p) REVERT: C 886 TRP cc_start: 0.8581 (p90) cc_final: 0.8277 (p90) REVERT: C 936 ASP cc_start: 0.7554 (m-30) cc_final: 0.7115 (m-30) REVERT: C 952 VAL cc_start: 0.7603 (t) cc_final: 0.7301 (m) REVERT: C 1005 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7462 (mm-40) REVERT: C 1010 GLN cc_start: 0.7588 (mm-40) cc_final: 0.7247 (mm-40) outliers start: 46 outliers final: 24 residues processed: 562 average time/residue: 0.4262 time to fit residues: 363.4943 Evaluate side-chains 513 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 484 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 955 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 158 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 237 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 285 optimal weight: 1.9990 chunk 308 optimal weight: 0.8980 chunk 254 optimal weight: 5.9990 chunk 283 optimal weight: 0.0470 chunk 97 optimal weight: 0.3980 chunk 229 optimal weight: 2.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1106 GLN B 755 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 872 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN C 644 GLN C 764 ASN C1002 GLN C1119 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6231 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25135 Z= 0.207 Angle : 0.535 8.986 34196 Z= 0.288 Chirality : 0.044 0.169 3878 Planarity : 0.004 0.044 4436 Dihedral : 4.108 18.654 3365 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.19 % Favored : 97.71 % Rotamer: Outliers : 2.15 % Allowed : 7.65 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.14), residues: 3106 helix: 1.29 (0.21), residues: 675 sheet: 0.45 (0.17), residues: 723 loop : -0.81 (0.13), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 64 HIS 0.022 0.001 HIS C 655 PHE 0.021 0.002 PHE C 782 TYR 0.031 0.001 TYR C 279 ARG 0.007 0.001 ARG B1091 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 503 time to evaluate : 2.642 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: A 298 GLU cc_start: 0.7396 (tt0) cc_final: 0.6765 (mm-30) REVERT: A 300 LYS cc_start: 0.7925 (mttt) cc_final: 0.7464 (mmtp) REVERT: A 303 LEU cc_start: 0.7798 (mp) cc_final: 0.7573 (tt) REVERT: A 541 PHE cc_start: 0.6451 (p90) cc_final: 0.6222 (p90) REVERT: A 605 SER cc_start: 0.8010 (t) cc_final: 0.7603 (m) REVERT: A 716 THR cc_start: 0.8471 (p) cc_final: 0.8135 (t) REVERT: A 823 PHE cc_start: 0.6017 (OUTLIER) cc_final: 0.5547 (m-10) REVERT: A 886 TRP cc_start: 0.8040 (p90) cc_final: 0.7762 (p90) REVERT: A 900 MET cc_start: 0.6641 (OUTLIER) cc_final: 0.6331 (mtm) REVERT: A 934 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7513 (tp) REVERT: A 976 VAL cc_start: 0.7533 (t) cc_final: 0.7305 (t) REVERT: A 983 ARG cc_start: 0.8034 (mtm180) cc_final: 0.7813 (mtm180) REVERT: A 995 ARG cc_start: 0.7615 (mtt180) cc_final: 0.7382 (mtt180) REVERT: A 1002 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.6711 (mp10) REVERT: A 1013 ILE cc_start: 0.7560 (mm) cc_final: 0.7329 (mt) REVERT: A 1084 ASP cc_start: 0.7108 (m-30) cc_final: 0.6908 (m-30) REVERT: B 33 THR cc_start: 0.6509 (p) cc_final: 0.5525 (m) REVERT: B 100 ILE cc_start: 0.6523 (mm) cc_final: 0.6044 (tp) REVERT: B 129 LYS cc_start: 0.6713 (ttmt) cc_final: 0.6399 (tptt) REVERT: B 290 ASP cc_start: 0.6339 (t0) cc_final: 0.6101 (t0) REVERT: B 313 TYR cc_start: 0.8254 (m-80) cc_final: 0.7958 (m-80) REVERT: B 577 ARG cc_start: 0.6269 (mtp180) cc_final: 0.6035 (mtp180) REVERT: B 660 TYR cc_start: 0.7504 (m-80) cc_final: 0.7280 (m-80) REVERT: B 765 ARG cc_start: 0.6946 (ttm-80) cc_final: 0.6745 (ttm170) REVERT: B 804 GLN cc_start: 0.7438 (tp40) cc_final: 0.7205 (mm-40) REVERT: B 817 PHE cc_start: 0.7853 (t80) cc_final: 0.7527 (t80) REVERT: B 859 THR cc_start: 0.7865 (m) cc_final: 0.7544 (p) REVERT: B 904 TYR cc_start: 0.5660 (t80) cc_final: 0.5459 (t80) REVERT: B 918 GLU cc_start: 0.7466 (mp0) cc_final: 0.7080 (mp0) REVERT: B 933 LYS cc_start: 0.8066 (mttt) cc_final: 0.7615 (mtmt) REVERT: B 934 ILE cc_start: 0.8263 (mm) cc_final: 0.8062 (tp) REVERT: B 973 ILE cc_start: 0.8178 (tp) cc_final: 0.7956 (tp) REVERT: B 974 SER cc_start: 0.8292 (t) cc_final: 0.8066 (m) REVERT: B 983 ARG cc_start: 0.7322 (ttm-80) cc_final: 0.6988 (ttm-80) REVERT: B 1038 LYS cc_start: 0.7636 (ptpp) cc_final: 0.7395 (mtmm) REVERT: B 1073 LYS cc_start: 0.7829 (mttt) cc_final: 0.7623 (mptt) REVERT: B 1111 GLU cc_start: 0.6927 (tt0) cc_final: 0.6493 (tt0) REVERT: B 1122 VAL cc_start: 0.8592 (t) cc_final: 0.8311 (p) REVERT: C 92 PHE cc_start: 0.6252 (t80) cc_final: 0.5932 (t80) REVERT: C 206 LYS cc_start: 0.7035 (tptt) cc_final: 0.6819 (tmtt) REVERT: C 355 ARG cc_start: 0.7292 (ttm-80) cc_final: 0.6901 (ttm170) REVERT: C 364 ASP cc_start: 0.6998 (OUTLIER) cc_final: 0.6588 (m-30) REVERT: C 377 PHE cc_start: 0.7406 (t80) cc_final: 0.6830 (t80) REVERT: C 386 LYS cc_start: 0.7632 (mmtt) cc_final: 0.7296 (mmtm) REVERT: C 400 PHE cc_start: 0.5648 (p90) cc_final: 0.5201 (p90) REVERT: C 533 LEU cc_start: 0.7885 (mt) cc_final: 0.7621 (mt) REVERT: C 581 THR cc_start: 0.8069 (t) cc_final: 0.7788 (t) REVERT: C 740 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.7102 (ttp) REVERT: C 773 GLU cc_start: 0.6592 (mm-30) cc_final: 0.6347 (mm-30) REVERT: C 776 LYS cc_start: 0.8131 (mtpp) cc_final: 0.7832 (ttpt) REVERT: C 777 ASN cc_start: 0.7920 (m-40) cc_final: 0.7666 (m-40) REVERT: C 823 PHE cc_start: 0.6342 (m-10) cc_final: 0.5655 (m-80) REVERT: C 867 ASP cc_start: 0.7055 (m-30) cc_final: 0.6854 (t0) REVERT: C 884 SER cc_start: 0.8549 (m) cc_final: 0.8216 (p) REVERT: C 936 ASP cc_start: 0.7548 (m-30) cc_final: 0.7274 (m-30) REVERT: C 952 VAL cc_start: 0.7700 (t) cc_final: 0.7472 (m) REVERT: C 954 GLN cc_start: 0.7674 (mt0) cc_final: 0.7373 (mt0) REVERT: C 990 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: C 1005 GLN cc_start: 0.7621 (mm-40) cc_final: 0.7379 (mm-40) REVERT: C 1029 MET cc_start: 0.8156 (tpp) cc_final: 0.7883 (tpp) REVERT: C 1038 LYS cc_start: 0.8444 (mttt) cc_final: 0.8037 (mmmm) outliers start: 59 outliers final: 33 residues processed: 529 average time/residue: 0.3831 time to fit residues: 308.8047 Evaluate side-chains 516 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 476 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 282 optimal weight: 0.3980 chunk 214 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 191 optimal weight: 0.9990 chunk 286 optimal weight: 1.9990 chunk 303 optimal weight: 0.6980 chunk 149 optimal weight: 20.0000 chunk 271 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 196 ASN A 239 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 762 GLN B 779 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1101 HIS B1106 GLN C 544 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS C 764 ASN C 955 ASN C1002 GLN C1119 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25135 Z= 0.214 Angle : 0.544 11.775 34196 Z= 0.287 Chirality : 0.045 0.326 3878 Planarity : 0.004 0.039 4436 Dihedral : 4.160 18.377 3365 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.45 % Favored : 97.46 % Rotamer: Outliers : 2.40 % Allowed : 8.85 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.14), residues: 3106 helix: 1.49 (0.21), residues: 672 sheet: 0.53 (0.18), residues: 693 loop : -0.83 (0.13), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1102 HIS 0.010 0.001 HIS A 207 PHE 0.020 0.002 PHE A 238 TYR 0.018 0.002 TYR C 279 ARG 0.012 0.001 ARG C 158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 492 time to evaluate : 2.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7823 (mt) REVERT: A 300 LYS cc_start: 0.8022 (mttt) cc_final: 0.7695 (mtmm) REVERT: A 314 GLN cc_start: 0.7342 (tm-30) cc_final: 0.7125 (tm-30) REVERT: A 605 SER cc_start: 0.8091 (t) cc_final: 0.7662 (m) REVERT: A 886 TRP cc_start: 0.8129 (p90) cc_final: 0.7726 (p90) REVERT: A 900 MET cc_start: 0.6734 (OUTLIER) cc_final: 0.6454 (mtt) REVERT: A 933 LYS cc_start: 0.8169 (tttt) cc_final: 0.7961 (ttmt) REVERT: A 974 SER cc_start: 0.7647 (t) cc_final: 0.7315 (p) REVERT: A 976 VAL cc_start: 0.7833 (t) cc_final: 0.7501 (t) REVERT: A 1002 GLN cc_start: 0.7152 (OUTLIER) cc_final: 0.6588 (mp10) REVERT: A 1013 ILE cc_start: 0.7589 (mm) cc_final: 0.7346 (mt) REVERT: A 1019 ARG cc_start: 0.7423 (ttp-170) cc_final: 0.6924 (ttp-110) REVERT: B 129 LYS cc_start: 0.6764 (ttmt) cc_final: 0.6456 (tptt) REVERT: B 239 GLN cc_start: 0.6056 (tt0) cc_final: 0.5592 (tm-30) REVERT: B 313 TYR cc_start: 0.8358 (m-80) cc_final: 0.8049 (m-80) REVERT: B 747 THR cc_start: 0.7071 (p) cc_final: 0.6657 (t) REVERT: B 765 ARG cc_start: 0.7009 (ttm-80) cc_final: 0.6629 (ttp-170) REVERT: B 817 PHE cc_start: 0.7862 (t80) cc_final: 0.7515 (t80) REVERT: B 859 THR cc_start: 0.7859 (m) cc_final: 0.7580 (p) REVERT: B 917 TYR cc_start: 0.6776 (m-10) cc_final: 0.6570 (m-10) REVERT: B 918 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: B 933 LYS cc_start: 0.8054 (mttt) cc_final: 0.7599 (mtmm) REVERT: B 957 GLN cc_start: 0.7351 (tp-100) cc_final: 0.7090 (mm-40) REVERT: B 973 ILE cc_start: 0.8191 (tp) cc_final: 0.7979 (tp) REVERT: B 974 SER cc_start: 0.8388 (t) cc_final: 0.7941 (p) REVERT: B 1122 VAL cc_start: 0.8598 (t) cc_final: 0.8312 (p) REVERT: C 44 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6804 (ptt-90) REVERT: C 92 PHE cc_start: 0.6391 (t80) cc_final: 0.5978 (t80) REVERT: C 129 LYS cc_start: 0.5941 (mttt) cc_final: 0.5643 (mttt) REVERT: C 206 LYS cc_start: 0.6997 (tptt) cc_final: 0.6765 (tmtt) REVERT: C 364 ASP cc_start: 0.6856 (OUTLIER) cc_final: 0.6542 (m-30) REVERT: C 377 PHE cc_start: 0.7416 (t80) cc_final: 0.6987 (t80) REVERT: C 386 LYS cc_start: 0.7721 (mmtt) cc_final: 0.7358 (mmtm) REVERT: C 400 PHE cc_start: 0.5788 (p90) cc_final: 0.5303 (p90) REVERT: C 597 VAL cc_start: 0.8054 (OUTLIER) cc_final: 0.7815 (t) REVERT: C 644 GLN cc_start: 0.7216 (tp40) cc_final: 0.6922 (tp-100) REVERT: C 655 HIS cc_start: 0.7266 (OUTLIER) cc_final: 0.7056 (t70) REVERT: C 663 ASP cc_start: 0.7055 (m-30) cc_final: 0.6710 (m-30) REVERT: C 777 ASN cc_start: 0.7863 (m-40) cc_final: 0.7638 (m-40) REVERT: C 823 PHE cc_start: 0.6412 (m-10) cc_final: 0.5714 (m-80) REVERT: C 856 ASN cc_start: 0.7619 (m110) cc_final: 0.7203 (m-40) REVERT: C 884 SER cc_start: 0.8489 (m) cc_final: 0.8230 (p) REVERT: C 936 ASP cc_start: 0.7553 (m-30) cc_final: 0.7117 (m-30) REVERT: C 945 LEU cc_start: 0.7164 (mm) cc_final: 0.6888 (mp) REVERT: C 990 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6795 (mp0) REVERT: C 1005 GLN cc_start: 0.7602 (mm-40) cc_final: 0.7251 (mt0) REVERT: C 1010 GLN cc_start: 0.7596 (mm-40) cc_final: 0.7381 (mm-40) REVERT: C 1028 LYS cc_start: 0.7987 (mttt) cc_final: 0.7607 (mtpp) REVERT: C 1038 LYS cc_start: 0.8414 (mttt) cc_final: 0.8024 (mmmm) REVERT: C 1072 GLU cc_start: 0.7294 (pm20) cc_final: 0.7007 (pm20) outliers start: 66 outliers final: 36 residues processed: 521 average time/residue: 0.3757 time to fit residues: 301.2653 Evaluate side-chains 508 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 463 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 252 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 4 optimal weight: 0.0670 chunk 225 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 259 optimal weight: 0.8980 chunk 209 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 chunk 272 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 196 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A1048 HIS ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN C 188 ASN C 484 GLN C 544 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C1002 GLN C1119 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 25135 Z= 0.307 Angle : 0.594 11.986 34196 Z= 0.316 Chirality : 0.046 0.174 3878 Planarity : 0.005 0.097 4436 Dihedral : 4.458 19.284 3365 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.06 % Favored : 96.84 % Rotamer: Outliers : 2.66 % Allowed : 9.44 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3106 helix: 1.40 (0.21), residues: 673 sheet: 0.43 (0.18), residues: 763 loop : -0.92 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1102 HIS 0.026 0.002 HIS C 655 PHE 0.027 0.002 PHE B 541 TYR 0.021 0.002 TYR C 380 ARG 0.019 0.001 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 485 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LYS cc_start: 0.8111 (tptm) cc_final: 0.7733 (tppp) REVERT: A 226 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7858 (mt) REVERT: A 300 LYS cc_start: 0.8016 (mttt) cc_final: 0.7682 (mtmm) REVERT: A 583 GLU cc_start: 0.5666 (tp30) cc_final: 0.5409 (tp30) REVERT: A 596 SER cc_start: 0.8481 (m) cc_final: 0.8039 (p) REVERT: A 605 SER cc_start: 0.8237 (t) cc_final: 0.7720 (m) REVERT: A 690 GLN cc_start: 0.6370 (mm110) cc_final: 0.6108 (mm-40) REVERT: A 858 LEU cc_start: 0.8502 (mm) cc_final: 0.8256 (mt) REVERT: A 914 ASN cc_start: 0.7232 (OUTLIER) cc_final: 0.6885 (m-40) REVERT: A 935 GLN cc_start: 0.7784 (tt0) cc_final: 0.7523 (tt0) REVERT: A 976 VAL cc_start: 0.8143 (t) cc_final: 0.7809 (t) REVERT: A 1002 GLN cc_start: 0.7168 (OUTLIER) cc_final: 0.6837 (mp10) REVERT: A 1013 ILE cc_start: 0.7620 (mm) cc_final: 0.7362 (mt) REVERT: A 1050 MET cc_start: 0.8008 (ptt) cc_final: 0.7749 (ptm) REVERT: B 33 THR cc_start: 0.6494 (p) cc_final: 0.5581 (m) REVERT: B 129 LYS cc_start: 0.6828 (ttmt) cc_final: 0.6446 (tptt) REVERT: B 206 LYS cc_start: 0.6832 (tptp) cc_final: 0.6524 (tptp) REVERT: B 239 GLN cc_start: 0.6198 (tt0) cc_final: 0.5740 (tm-30) REVERT: B 304 LYS cc_start: 0.7051 (mttt) cc_final: 0.6787 (mmtm) REVERT: B 313 TYR cc_start: 0.8362 (m-80) cc_final: 0.8080 (m-80) REVERT: B 531 THR cc_start: 0.7017 (OUTLIER) cc_final: 0.6711 (m) REVERT: B 765 ARG cc_start: 0.7087 (ttm-80) cc_final: 0.6743 (ttp-170) REVERT: B 859 THR cc_start: 0.7819 (m) cc_final: 0.7531 (p) REVERT: B 918 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: B 933 LYS cc_start: 0.8073 (mttt) cc_final: 0.7545 (mtmm) REVERT: B 973 ILE cc_start: 0.8197 (tp) cc_final: 0.7972 (tp) REVERT: B 974 SER cc_start: 0.8300 (t) cc_final: 0.7937 (p) REVERT: C 38 TYR cc_start: 0.7590 (m-10) cc_final: 0.5916 (m-10) REVERT: C 44 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7286 (ptt-90) REVERT: C 129 LYS cc_start: 0.6001 (mttt) cc_final: 0.5664 (mttt) REVERT: C 364 ASP cc_start: 0.6903 (OUTLIER) cc_final: 0.6294 (t0) REVERT: C 377 PHE cc_start: 0.7403 (t80) cc_final: 0.7063 (t80) REVERT: C 386 LYS cc_start: 0.7838 (mmtt) cc_final: 0.7450 (tptt) REVERT: C 577 ARG cc_start: 0.5831 (mtp180) cc_final: 0.5428 (ptm160) REVERT: C 597 VAL cc_start: 0.8116 (OUTLIER) cc_final: 0.7898 (t) REVERT: C 644 GLN cc_start: 0.7402 (tp40) cc_final: 0.7090 (tp-100) REVERT: C 663 ASP cc_start: 0.7081 (m-30) cc_final: 0.6811 (m-30) REVERT: C 711 SER cc_start: 0.8024 (p) cc_final: 0.7781 (p) REVERT: C 740 MET cc_start: 0.7452 (ttp) cc_final: 0.7245 (ttp) REVERT: C 824 ASN cc_start: 0.8024 (m-40) cc_final: 0.7646 (m-40) REVERT: C 825 LYS cc_start: 0.7812 (mtpp) cc_final: 0.7593 (mtmt) REVERT: C 856 ASN cc_start: 0.7738 (m110) cc_final: 0.7377 (m-40) REVERT: C 867 ASP cc_start: 0.6871 (OUTLIER) cc_final: 0.6512 (t0) REVERT: C 936 ASP cc_start: 0.7495 (m-30) cc_final: 0.7080 (m-30) REVERT: C 945 LEU cc_start: 0.7271 (mm) cc_final: 0.6993 (mp) REVERT: C 990 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: C 1005 GLN cc_start: 0.7590 (mm-40) cc_final: 0.7359 (mt0) REVERT: C 1072 GLU cc_start: 0.7287 (pm20) cc_final: 0.6970 (pm20) outliers start: 73 outliers final: 43 residues processed: 523 average time/residue: 0.3908 time to fit residues: 311.7999 Evaluate side-chains 524 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 471 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 102 optimal weight: 0.0370 chunk 273 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 303 optimal weight: 0.9990 chunk 252 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 overall best weight: 1.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 196 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 207 HIS B 613 GLN B 762 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C1119 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.5579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 25135 Z= 0.298 Angle : 0.590 12.611 34196 Z= 0.313 Chirality : 0.046 0.172 3878 Planarity : 0.005 0.064 4436 Dihedral : 4.616 25.514 3365 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.22 % Favored : 96.62 % Rotamer: Outliers : 2.70 % Allowed : 11.00 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.14), residues: 3106 helix: 1.39 (0.20), residues: 682 sheet: 0.47 (0.18), residues: 717 loop : -0.96 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 353 HIS 0.006 0.001 HIS C1048 PHE 0.036 0.002 PHE C 541 TYR 0.021 0.002 TYR A 904 ARG 0.009 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 477 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LYS cc_start: 0.8139 (tptm) cc_final: 0.7769 (tppp) REVERT: A 226 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7864 (mt) REVERT: A 240 THR cc_start: 0.6044 (m) cc_final: 0.5273 (p) REVERT: A 300 LYS cc_start: 0.8013 (mttt) cc_final: 0.7783 (mttm) REVERT: A 353 TRP cc_start: 0.4002 (p90) cc_final: 0.3763 (p90) REVERT: A 605 SER cc_start: 0.8184 (t) cc_final: 0.7655 (m) REVERT: A 797 PHE cc_start: 0.8057 (m-10) cc_final: 0.7808 (m-80) REVERT: A 806 LEU cc_start: 0.8041 (mt) cc_final: 0.7828 (mt) REVERT: A 858 LEU cc_start: 0.8528 (mm) cc_final: 0.8283 (mt) REVERT: A 914 ASN cc_start: 0.7232 (OUTLIER) cc_final: 0.6914 (m-40) REVERT: A 933 LYS cc_start: 0.8045 (ttmt) cc_final: 0.7775 (ttmp) REVERT: A 976 VAL cc_start: 0.8145 (t) cc_final: 0.7918 (t) REVERT: A 1013 ILE cc_start: 0.7609 (mm) cc_final: 0.7307 (mt) REVERT: A 1050 MET cc_start: 0.8016 (ptt) cc_final: 0.7772 (ptm) REVERT: A 1130 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7797 (mt) REVERT: B 129 LYS cc_start: 0.6847 (ttmt) cc_final: 0.6395 (tppt) REVERT: B 153 MET cc_start: -0.1633 (ttp) cc_final: -0.2555 (ttp) REVERT: B 313 TYR cc_start: 0.8367 (m-80) cc_final: 0.7997 (m-80) REVERT: B 531 THR cc_start: 0.6962 (OUTLIER) cc_final: 0.6694 (m) REVERT: B 612 TYR cc_start: 0.8129 (m-10) cc_final: 0.7899 (m-10) REVERT: B 725 GLU cc_start: 0.7351 (mt-10) cc_final: 0.7150 (tt0) REVERT: B 765 ARG cc_start: 0.7206 (ttm-80) cc_final: 0.6837 (ttp-170) REVERT: B 776 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7208 (tppt) REVERT: B 780 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6150 (mp0) REVERT: B 825 LYS cc_start: 0.7733 (mmmm) cc_final: 0.7178 (mttp) REVERT: B 859 THR cc_start: 0.7834 (m) cc_final: 0.7567 (p) REVERT: B 918 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: B 933 LYS cc_start: 0.8129 (mttt) cc_final: 0.7536 (mtmm) REVERT: B 954 GLN cc_start: 0.7094 (mm110) cc_final: 0.6775 (mt0) REVERT: B 960 ASN cc_start: 0.7617 (m-40) cc_final: 0.7254 (m-40) REVERT: B 973 ILE cc_start: 0.8247 (tp) cc_final: 0.8025 (tp) REVERT: B 974 SER cc_start: 0.8346 (t) cc_final: 0.7975 (p) REVERT: C 38 TYR cc_start: 0.7565 (m-10) cc_final: 0.6155 (m-10) REVERT: C 44 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.7246 (ptt-90) REVERT: C 129 LYS cc_start: 0.6001 (mttt) cc_final: 0.5666 (mttt) REVERT: C 357 ARG cc_start: 0.6249 (tpp-160) cc_final: 0.5494 (tpp-160) REVERT: C 377 PHE cc_start: 0.7411 (t80) cc_final: 0.7133 (t80) REVERT: C 386 LYS cc_start: 0.7953 (mmtt) cc_final: 0.7534 (tptt) REVERT: C 396 TYR cc_start: 0.6102 (m-80) cc_final: 0.5801 (m-80) REVERT: C 506 GLN cc_start: 0.6494 (mt0) cc_final: 0.6245 (mt0) REVERT: C 597 VAL cc_start: 0.8096 (OUTLIER) cc_final: 0.7889 (t) REVERT: C 644 GLN cc_start: 0.7380 (tp40) cc_final: 0.6971 (tp-100) REVERT: C 663 ASP cc_start: 0.7100 (m-30) cc_final: 0.6793 (m-30) REVERT: C 711 SER cc_start: 0.8023 (p) cc_final: 0.7812 (p) REVERT: C 740 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.7020 (ttp) REVERT: C 824 ASN cc_start: 0.7970 (m-40) cc_final: 0.7584 (m-40) REVERT: C 856 ASN cc_start: 0.7712 (m110) cc_final: 0.7401 (m-40) REVERT: C 936 ASP cc_start: 0.7535 (m-30) cc_final: 0.7058 (m-30) REVERT: C 945 LEU cc_start: 0.7288 (mm) cc_final: 0.7013 (mp) REVERT: C 990 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: C 1005 GLN cc_start: 0.7574 (mm-40) cc_final: 0.7321 (mt0) REVERT: C 1010 GLN cc_start: 0.7560 (mm-40) cc_final: 0.7311 (mm-40) REVERT: C 1038 LYS cc_start: 0.8450 (mttt) cc_final: 0.8114 (mmmm) REVERT: C 1072 GLU cc_start: 0.7338 (pm20) cc_final: 0.6971 (pm20) REVERT: C 1123 SER cc_start: 0.8090 (t) cc_final: 0.7676 (m) outliers start: 74 outliers final: 51 residues processed: 512 average time/residue: 0.3545 time to fit residues: 279.9311 Evaluate side-chains 523 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 461 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 292 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 chunk 173 optimal weight: 0.9980 chunk 221 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 169 optimal weight: 0.6980 chunk 302 optimal weight: 0.8980 chunk 189 optimal weight: 0.9980 chunk 184 optimal weight: 0.5980 chunk 139 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 613 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C1119 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 moved from start: 0.5780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25135 Z= 0.219 Angle : 0.554 12.282 34196 Z= 0.291 Chirality : 0.044 0.173 3878 Planarity : 0.004 0.058 4436 Dihedral : 4.438 21.544 3365 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.25 % Favored : 96.59 % Rotamer: Outliers : 2.66 % Allowed : 11.51 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.14), residues: 3106 helix: 1.59 (0.21), residues: 680 sheet: 0.45 (0.18), residues: 728 loop : -0.96 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.005 0.001 HIS C1048 PHE 0.020 0.002 PHE B 92 TYR 0.020 0.001 TYR A 904 ARG 0.008 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 479 time to evaluate : 2.705 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: A 127 VAL cc_start: 0.7802 (t) cc_final: 0.7535 (m) REVERT: A 206 LYS cc_start: 0.8134 (tptm) cc_final: 0.7741 (tppp) REVERT: A 226 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7877 (mt) REVERT: A 240 THR cc_start: 0.6083 (m) cc_final: 0.5341 (p) REVERT: A 300 LYS cc_start: 0.8029 (mttt) cc_final: 0.7641 (mtpp) REVERT: A 353 TRP cc_start: 0.4039 (p90) cc_final: 0.3743 (p90) REVERT: A 605 SER cc_start: 0.8170 (t) cc_final: 0.7674 (m) REVERT: A 858 LEU cc_start: 0.8565 (mm) cc_final: 0.8271 (mt) REVERT: A 900 MET cc_start: 0.7655 (mtp) cc_final: 0.7380 (mtm) REVERT: A 914 ASN cc_start: 0.7194 (OUTLIER) cc_final: 0.6840 (m-40) REVERT: A 933 LYS cc_start: 0.7994 (ttmt) cc_final: 0.7728 (ttmp) REVERT: A 976 VAL cc_start: 0.8106 (t) cc_final: 0.7881 (t) REVERT: A 1013 ILE cc_start: 0.7609 (mm) cc_final: 0.7311 (mt) REVERT: A 1050 MET cc_start: 0.7977 (ptt) cc_final: 0.7723 (ptm) REVERT: A 1051 SER cc_start: 0.8108 (t) cc_final: 0.7633 (p) REVERT: A 1130 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7729 (mt) REVERT: A 1137 VAL cc_start: 0.8590 (t) cc_final: 0.8282 (m) REVERT: B 153 MET cc_start: -0.1510 (ttp) cc_final: -0.2470 (ttp) REVERT: B 531 THR cc_start: 0.6953 (OUTLIER) cc_final: 0.6670 (m) REVERT: B 725 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7107 (tt0) REVERT: B 765 ARG cc_start: 0.7000 (ttm-80) cc_final: 0.6614 (ttp-170) REVERT: B 776 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7313 (ttpp) REVERT: B 780 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6863 (mp0) REVERT: B 817 PHE cc_start: 0.7563 (t80) cc_final: 0.7286 (t80) REVERT: B 825 LYS cc_start: 0.7678 (mmmm) cc_final: 0.7171 (mttp) REVERT: B 859 THR cc_start: 0.7818 (m) cc_final: 0.7566 (p) REVERT: B 933 LYS cc_start: 0.8078 (mttt) cc_final: 0.7753 (mttt) REVERT: B 954 GLN cc_start: 0.7037 (mm110) cc_final: 0.6785 (mt0) REVERT: B 973 ILE cc_start: 0.8206 (tp) cc_final: 0.7985 (tp) REVERT: B 974 SER cc_start: 0.8352 (t) cc_final: 0.7970 (p) REVERT: C 38 TYR cc_start: 0.7579 (m-10) cc_final: 0.6729 (m-10) REVERT: C 44 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.7207 (ptt-90) REVERT: C 357 ARG cc_start: 0.6155 (tpp-160) cc_final: 0.5855 (tpp-160) REVERT: C 532 ASN cc_start: 0.7725 (t0) cc_final: 0.7398 (t0) REVERT: C 537 LYS cc_start: 0.8272 (mtpp) cc_final: 0.7913 (mtpp) REVERT: C 580 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7230 (mm-40) REVERT: C 644 GLN cc_start: 0.7160 (tp40) cc_final: 0.6884 (tp-100) REVERT: C 740 MET cc_start: 0.7309 (ttp) cc_final: 0.6995 (tmm) REVERT: C 777 ASN cc_start: 0.7919 (m-40) cc_final: 0.7685 (m-40) REVERT: C 936 ASP cc_start: 0.7483 (m-30) cc_final: 0.6861 (m-30) REVERT: C 945 LEU cc_start: 0.7222 (mm) cc_final: 0.6978 (mp) REVERT: C 990 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6917 (mp0) REVERT: C 1005 GLN cc_start: 0.7576 (mm-40) cc_final: 0.7285 (mt0) REVERT: C 1010 GLN cc_start: 0.7546 (mm-40) cc_final: 0.7295 (mm-40) REVERT: C 1028 LYS cc_start: 0.8396 (mttt) cc_final: 0.8148 (mtpp) REVERT: C 1123 SER cc_start: 0.8035 (t) cc_final: 0.7657 (m) outliers start: 73 outliers final: 52 residues processed: 515 average time/residue: 0.3758 time to fit residues: 296.0019 Evaluate side-chains 535 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 474 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 187 optimal weight: 4.9990 chunk 120 optimal weight: 0.0980 chunk 180 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 149 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 237 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 196 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A1119 ASN B 762 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 901 GLN B 955 ASN B 978 ASN C 519 HIS ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C 856 ASN C1119 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.6032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25135 Z= 0.238 Angle : 0.560 11.222 34196 Z= 0.296 Chirality : 0.045 0.223 3878 Planarity : 0.004 0.055 4436 Dihedral : 4.465 21.134 3365 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.67 % Favored : 96.17 % Rotamer: Outliers : 2.81 % Allowed : 11.77 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 3106 helix: 1.61 (0.21), residues: 675 sheet: 0.38 (0.18), residues: 732 loop : -0.96 (0.14), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.005 0.001 HIS C1048 PHE 0.037 0.002 PHE C 541 TYR 0.024 0.001 TYR A 904 ARG 0.008 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 475 time to evaluate : 2.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.7872 (t) cc_final: 0.7573 (m) REVERT: A 190 ARG cc_start: 0.7467 (mmt180) cc_final: 0.7226 (mmt180) REVERT: A 226 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7864 (mt) REVERT: A 240 THR cc_start: 0.6095 (m) cc_final: 0.5385 (p) REVERT: A 300 LYS cc_start: 0.8042 (mttt) cc_final: 0.7785 (mtmm) REVERT: A 353 TRP cc_start: 0.4180 (p90) cc_final: 0.3957 (p90) REVERT: A 605 SER cc_start: 0.8170 (t) cc_final: 0.7719 (m) REVERT: A 858 LEU cc_start: 0.8590 (mm) cc_final: 0.8292 (mt) REVERT: A 914 ASN cc_start: 0.7196 (OUTLIER) cc_final: 0.6992 (m-40) REVERT: A 933 LYS cc_start: 0.8008 (ttmt) cc_final: 0.7722 (ttmp) REVERT: A 1013 ILE cc_start: 0.7612 (mm) cc_final: 0.7324 (mt) REVERT: A 1028 LYS cc_start: 0.8345 (mttm) cc_final: 0.7942 (mttp) REVERT: A 1051 SER cc_start: 0.8117 (t) cc_final: 0.7640 (p) REVERT: A 1130 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7644 (mt) REVERT: A 1137 VAL cc_start: 0.8602 (t) cc_final: 0.8308 (m) REVERT: B 129 LYS cc_start: 0.6778 (ttmt) cc_final: 0.6421 (tptt) REVERT: B 153 MET cc_start: -0.1279 (ttp) cc_final: -0.2222 (ttp) REVERT: B 206 LYS cc_start: 0.6779 (tptp) cc_final: 0.6258 (tptp) REVERT: B 300 LYS cc_start: 0.7705 (ptpt) cc_final: 0.6801 (ptpt) REVERT: B 531 THR cc_start: 0.7059 (OUTLIER) cc_final: 0.6780 (m) REVERT: B 691 SER cc_start: 0.7345 (p) cc_final: 0.7124 (t) REVERT: B 725 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7087 (tt0) REVERT: B 765 ARG cc_start: 0.6994 (ttm-80) cc_final: 0.6612 (ttp-170) REVERT: B 776 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7351 (ttpp) REVERT: B 780 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6845 (mp0) REVERT: B 817 PHE cc_start: 0.7592 (t80) cc_final: 0.7292 (t80) REVERT: B 825 LYS cc_start: 0.7642 (mmmm) cc_final: 0.7402 (mtpp) REVERT: B 859 THR cc_start: 0.7827 (m) cc_final: 0.7572 (p) REVERT: B 933 LYS cc_start: 0.8091 (mttt) cc_final: 0.7757 (mttt) REVERT: B 954 GLN cc_start: 0.6985 (mm110) cc_final: 0.6772 (mt0) REVERT: B 973 ILE cc_start: 0.8190 (tp) cc_final: 0.7958 (tp) REVERT: B 974 SER cc_start: 0.8347 (t) cc_final: 0.7958 (p) REVERT: C 38 TYR cc_start: 0.7583 (m-10) cc_final: 0.6771 (m-10) REVERT: C 44 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.7199 (ptt-90) REVERT: C 102 ARG cc_start: 0.5761 (mmp-170) cc_final: 0.5411 (mmp-170) REVERT: C 129 LYS cc_start: 0.5670 (mttt) cc_final: 0.5452 (mmtt) REVERT: C 206 LYS cc_start: 0.7664 (tmtt) cc_final: 0.7399 (tmtt) REVERT: C 532 ASN cc_start: 0.7752 (t0) cc_final: 0.7402 (t0) REVERT: C 535 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7424 (mttm) REVERT: C 537 LYS cc_start: 0.8280 (mtpp) cc_final: 0.7955 (mtpp) REVERT: C 740 MET cc_start: 0.7321 (ttp) cc_final: 0.6981 (tmm) REVERT: C 777 ASN cc_start: 0.7908 (m-40) cc_final: 0.7681 (m-40) REVERT: C 936 ASP cc_start: 0.7459 (m-30) cc_final: 0.6961 (m-30) REVERT: C 945 LEU cc_start: 0.7259 (mm) cc_final: 0.7037 (mp) REVERT: C 990 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: C 1005 GLN cc_start: 0.7582 (mm-40) cc_final: 0.7290 (mt0) REVERT: C 1010 GLN cc_start: 0.7558 (mm-40) cc_final: 0.7320 (mm-40) REVERT: C 1028 LYS cc_start: 0.8403 (mttt) cc_final: 0.8131 (mtpp) REVERT: C 1123 SER cc_start: 0.8069 (t) cc_final: 0.7659 (m) outliers start: 77 outliers final: 55 residues processed: 513 average time/residue: 0.3955 time to fit residues: 309.0108 Evaluate side-chains 525 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 461 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 275 optimal weight: 1.9990 chunk 289 optimal weight: 0.6980 chunk 264 optimal weight: 0.8980 chunk 282 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 221 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 254 optimal weight: 2.9990 chunk 266 optimal weight: 0.5980 chunk 281 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A 804 GLN A 954 GLN A1119 ASN B 394 ASN B 751 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B 978 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 764 ASN C1119 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.6261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25135 Z= 0.264 Angle : 0.581 10.583 34196 Z= 0.308 Chirality : 0.045 0.281 3878 Planarity : 0.004 0.051 4436 Dihedral : 4.557 22.716 3365 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.93 % Favored : 95.91 % Rotamer: Outliers : 2.73 % Allowed : 12.24 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 3106 helix: 1.64 (0.21), residues: 669 sheet: 0.37 (0.18), residues: 714 loop : -1.01 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 886 HIS 0.005 0.001 HIS C1048 PHE 0.022 0.002 PHE B 927 TYR 0.026 0.002 TYR A1110 ARG 0.015 0.001 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 478 time to evaluate : 2.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.7952 (t) cc_final: 0.7657 (m) REVERT: A 191 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6750 (mm-30) REVERT: A 226 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7806 (mt) REVERT: A 240 THR cc_start: 0.6116 (m) cc_final: 0.5397 (p) REVERT: A 300 LYS cc_start: 0.8061 (mttt) cc_final: 0.7665 (mtpp) REVERT: A 353 TRP cc_start: 0.4158 (p90) cc_final: 0.3856 (p90) REVERT: A 605 SER cc_start: 0.8211 (t) cc_final: 0.7757 (m) REVERT: A 790 LYS cc_start: 0.6844 (mttt) cc_final: 0.6540 (mttt) REVERT: A 858 LEU cc_start: 0.8636 (mm) cc_final: 0.8331 (mt) REVERT: A 933 LYS cc_start: 0.7953 (ttmt) cc_final: 0.7689 (ttmp) REVERT: A 1013 ILE cc_start: 0.7621 (mm) cc_final: 0.7339 (mt) REVERT: A 1028 LYS cc_start: 0.8342 (mttm) cc_final: 0.7914 (mttp) REVERT: A 1051 SER cc_start: 0.8184 (t) cc_final: 0.7741 (p) REVERT: A 1130 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7670 (mt) REVERT: A 1137 VAL cc_start: 0.8605 (t) cc_final: 0.8323 (m) REVERT: B 113 LYS cc_start: 0.6340 (mttp) cc_final: 0.6122 (mttp) REVERT: B 129 LYS cc_start: 0.6778 (ttmt) cc_final: 0.6415 (tptt) REVERT: B 206 LYS cc_start: 0.6787 (tptp) cc_final: 0.6308 (tptp) REVERT: B 239 GLN cc_start: 0.6411 (tt0) cc_final: 0.5866 (tm-30) REVERT: B 300 LYS cc_start: 0.7690 (ptpt) cc_final: 0.6942 (ptpt) REVERT: B 531 THR cc_start: 0.7116 (OUTLIER) cc_final: 0.6813 (m) REVERT: B 535 LYS cc_start: 0.8558 (mttp) cc_final: 0.8357 (mptt) REVERT: B 691 SER cc_start: 0.7361 (p) cc_final: 0.7135 (t) REVERT: B 725 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7065 (tt0) REVERT: B 765 ARG cc_start: 0.7102 (ttm-80) cc_final: 0.6705 (ttp-170) REVERT: B 776 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7317 (ttpp) REVERT: B 780 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: B 817 PHE cc_start: 0.7664 (t80) cc_final: 0.7335 (t80) REVERT: B 825 LYS cc_start: 0.7622 (mmmm) cc_final: 0.7406 (mtpp) REVERT: B 859 THR cc_start: 0.7815 (m) cc_final: 0.7583 (p) REVERT: B 933 LYS cc_start: 0.8068 (mttt) cc_final: 0.7731 (mttt) REVERT: B 954 GLN cc_start: 0.7004 (mm110) cc_final: 0.6800 (mt0) REVERT: B 973 ILE cc_start: 0.8190 (tp) cc_final: 0.7959 (tp) REVERT: B 974 SER cc_start: 0.8353 (t) cc_final: 0.7958 (p) REVERT: B 1028 LYS cc_start: 0.7600 (mttt) cc_final: 0.7221 (mttm) REVERT: B 1101 HIS cc_start: 0.7980 (m90) cc_final: 0.7455 (m-70) REVERT: C 38 TYR cc_start: 0.7598 (m-10) cc_final: 0.6832 (m-10) REVERT: C 44 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7302 (ptt-90) REVERT: C 129 LYS cc_start: 0.5739 (mttt) cc_final: 0.5499 (mmtt) REVERT: C 206 LYS cc_start: 0.7580 (tmtt) cc_final: 0.7320 (tmtt) REVERT: C 386 LYS cc_start: 0.7981 (mmtt) cc_final: 0.7612 (tptt) REVERT: C 532 ASN cc_start: 0.7799 (t0) cc_final: 0.7461 (t0) REVERT: C 535 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7418 (mttm) REVERT: C 644 GLN cc_start: 0.7176 (tp40) cc_final: 0.6937 (tp-100) REVERT: C 740 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.6984 (tmm) REVERT: C 886 TRP cc_start: 0.8582 (p90) cc_final: 0.8348 (p90) REVERT: C 936 ASP cc_start: 0.7493 (m-30) cc_final: 0.6967 (m-30) REVERT: C 945 LEU cc_start: 0.7350 (mm) cc_final: 0.7067 (mp) REVERT: C 990 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6884 (mp0) REVERT: C 1005 GLN cc_start: 0.7601 (mm-40) cc_final: 0.7289 (mt0) REVERT: C 1010 GLN cc_start: 0.7559 (mm-40) cc_final: 0.7354 (mm-40) REVERT: C 1038 LYS cc_start: 0.8429 (mttt) cc_final: 0.8041 (mmmm) REVERT: C 1123 SER cc_start: 0.8061 (t) cc_final: 0.7693 (m) outliers start: 75 outliers final: 59 residues processed: 511 average time/residue: 0.4077 time to fit residues: 317.0351 Evaluate side-chains 536 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 468 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 185 optimal weight: 1.9990 chunk 298 optimal weight: 0.9980 chunk 182 optimal weight: 1.9990 chunk 141 optimal weight: 0.0980 chunk 207 optimal weight: 0.9990 chunk 312 optimal weight: 3.9990 chunk 287 optimal weight: 1.9990 chunk 249 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 192 optimal weight: 0.6980 chunk 152 optimal weight: 7.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 196 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A1119 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C1101 HIS C1119 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.6363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25135 Z= 0.194 Angle : 0.546 10.012 34196 Z= 0.289 Chirality : 0.044 0.197 3878 Planarity : 0.004 0.052 4436 Dihedral : 4.394 23.020 3365 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.38 % Favored : 96.46 % Rotamer: Outliers : 2.55 % Allowed : 12.71 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.15), residues: 3106 helix: 1.80 (0.21), residues: 668 sheet: 0.41 (0.18), residues: 738 loop : -1.04 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 436 HIS 0.005 0.001 HIS C1048 PHE 0.022 0.001 PHE B 927 TYR 0.021 0.001 TYR A 904 ARG 0.006 0.000 ARG C 355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 484 time to evaluate : 2.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.8002 (t) cc_final: 0.7723 (m) REVERT: A 190 ARG cc_start: 0.7375 (mmt180) cc_final: 0.7087 (mmt180) REVERT: A 191 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6772 (mm-30) REVERT: A 226 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7776 (mt) REVERT: A 353 TRP cc_start: 0.4317 (p90) cc_final: 0.4056 (p90) REVERT: A 583 GLU cc_start: 0.5508 (tp30) cc_final: 0.5256 (mm-30) REVERT: A 605 SER cc_start: 0.8048 (t) cc_final: 0.7623 (m) REVERT: A 858 LEU cc_start: 0.8596 (mm) cc_final: 0.8349 (mt) REVERT: A 933 LYS cc_start: 0.7938 (ttmt) cc_final: 0.7663 (ttmp) REVERT: A 1010 GLN cc_start: 0.7124 (mt0) cc_final: 0.6591 (mm110) REVERT: A 1013 ILE cc_start: 0.7638 (mm) cc_final: 0.7290 (mt) REVERT: A 1028 LYS cc_start: 0.8327 (mttm) cc_final: 0.7941 (mttp) REVERT: A 1051 SER cc_start: 0.8079 (t) cc_final: 0.7628 (p) REVERT: A 1130 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7746 (mt) REVERT: A 1137 VAL cc_start: 0.8614 (t) cc_final: 0.8306 (m) REVERT: B 129 LYS cc_start: 0.6715 (ttmt) cc_final: 0.6382 (tptt) REVERT: B 206 LYS cc_start: 0.6664 (tptp) cc_final: 0.6194 (tptp) REVERT: B 239 GLN cc_start: 0.6399 (tt0) cc_final: 0.5845 (tm-30) REVERT: B 300 LYS cc_start: 0.7649 (ptpt) cc_final: 0.6789 (ptmt) REVERT: B 531 THR cc_start: 0.7171 (OUTLIER) cc_final: 0.6852 (m) REVERT: B 535 LYS cc_start: 0.8553 (mttp) cc_final: 0.8336 (mptt) REVERT: B 691 SER cc_start: 0.7374 (p) cc_final: 0.7137 (t) REVERT: B 696 THR cc_start: 0.8352 (m) cc_final: 0.8075 (t) REVERT: B 725 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7062 (tt0) REVERT: B 747 THR cc_start: 0.7183 (p) cc_final: 0.6950 (t) REVERT: B 765 ARG cc_start: 0.7021 (ttm-80) cc_final: 0.6749 (ttp-170) REVERT: B 776 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7319 (ttpp) REVERT: B 780 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: B 814 LYS cc_start: 0.7273 (ptmm) cc_final: 0.7007 (ptmm) REVERT: B 817 PHE cc_start: 0.7583 (t80) cc_final: 0.7288 (t80) REVERT: B 825 LYS cc_start: 0.7580 (mmmm) cc_final: 0.7254 (mtpp) REVERT: B 859 THR cc_start: 0.7808 (m) cc_final: 0.7596 (p) REVERT: B 933 LYS cc_start: 0.7932 (mttt) cc_final: 0.7586 (mttt) REVERT: B 973 ILE cc_start: 0.8146 (tp) cc_final: 0.7921 (tp) REVERT: B 974 SER cc_start: 0.8360 (t) cc_final: 0.7961 (p) REVERT: B 1028 LYS cc_start: 0.7581 (mttt) cc_final: 0.7135 (mttm) REVERT: B 1101 HIS cc_start: 0.7949 (m90) cc_final: 0.7420 (m-70) REVERT: C 38 TYR cc_start: 0.7577 (m-10) cc_final: 0.6781 (m-10) REVERT: C 44 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.7159 (ptt-90) REVERT: C 129 LYS cc_start: 0.5862 (mttt) cc_final: 0.5568 (mmtt) REVERT: C 532 ASN cc_start: 0.7783 (t0) cc_final: 0.7427 (t0) REVERT: C 535 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7387 (mttm) REVERT: C 740 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.6949 (tmm) REVERT: C 777 ASN cc_start: 0.7813 (m-40) cc_final: 0.7591 (m-40) REVERT: C 886 TRP cc_start: 0.8592 (p90) cc_final: 0.8261 (p90) REVERT: C 936 ASP cc_start: 0.7374 (m-30) cc_final: 0.6743 (m-30) REVERT: C 945 LEU cc_start: 0.7250 (mm) cc_final: 0.6955 (mp) REVERT: C 990 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6847 (mp0) REVERT: C 1005 GLN cc_start: 0.7544 (mm-40) cc_final: 0.7280 (mt0) REVERT: C 1010 GLN cc_start: 0.7552 (mm-40) cc_final: 0.7342 (mm-40) REVERT: C 1038 LYS cc_start: 0.8436 (mttt) cc_final: 0.8029 (mmmm) REVERT: C 1122 VAL cc_start: 0.8515 (t) cc_final: 0.7897 (p) REVERT: C 1123 SER cc_start: 0.8032 (t) cc_final: 0.7700 (m) outliers start: 70 outliers final: 51 residues processed: 514 average time/residue: 0.3944 time to fit residues: 306.2986 Evaluate side-chains 530 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 470 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 1.9990 chunk 265 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 229 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 249 optimal weight: 0.4980 chunk 104 optimal weight: 0.0370 chunk 256 optimal weight: 4.9990 chunk 31 optimal weight: 0.0970 chunk 45 optimal weight: 5.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN A1119 ASN B 762 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN B1113 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C1119 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.200487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.167921 restraints weight = 38384.886| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 2.41 r_work: 0.3975 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3829 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.6434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25135 Z= 0.181 Angle : 0.547 9.175 34196 Z= 0.288 Chirality : 0.044 0.227 3878 Planarity : 0.004 0.050 4436 Dihedral : 4.305 23.068 3365 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.64 % Favored : 96.20 % Rotamer: Outliers : 2.22 % Allowed : 12.90 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.15), residues: 3106 helix: 1.90 (0.21), residues: 663 sheet: 0.45 (0.18), residues: 734 loop : -1.01 (0.14), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 436 HIS 0.004 0.001 HIS C1048 PHE 0.020 0.001 PHE B 927 TYR 0.022 0.001 TYR A 904 ARG 0.010 0.000 ARG C 190 =============================================================================== Job complete usr+sys time: 6839.60 seconds wall clock time: 123 minutes 34.51 seconds (7414.51 seconds total)