Starting phenix.real_space_refine on Tue Mar 19 15:17:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxi_32180/03_2024/7vxi_32180.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxi_32180/03_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_32180/03_2024/7vxi_32180.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxi_32180/03_2024/7vxi_32180.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxi_32180/03_2024/7vxi_32180.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxi_32180/03_2024/7vxi_32180.pdb" } 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 Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 12.24, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 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: 9.85 Conformation dependent library (CDL) restraints added in 4.7 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: 2.91 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: 10.89 Time building geometry restraints manager: 10.72 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: 100.15 - 106.94: 731 106.94 - 113.72: 13656 113.72 - 120.51: 9516 120.51 - 127.30: 10061 127.30 - 134.09: 232 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 2.440 nonbonded pdb=" OG1 THR B 912 " pdb=" OD1 ASN B 914 " model vdw 2.125 2.440 nonbonded pdb=" OD1 ASN B 422 " pdb=" N TYR B 423 " model vdw 2.126 2.520 nonbonded pdb=" OG1 THR C 33 " pdb=" O GLY C 219 " model vdw 2.150 2.440 nonbonded pdb=" O GLN C 563 " pdb=" NH1 ARG C 577 " model vdw 2.186 2.520 ... (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 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: 1.490 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: 8.040 Check model and map are aligned: 0.350 Set scattering table: 0.220 Process input model: 66.760 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.410 ------------------------------------------------------------------------------- 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 : 2.633 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: 0.4169 time to fit residues: 419.8019 Evaluate side-chains 506 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 506 time to evaluate : 3.482 ------------------------------------------------------------------------------- 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: 0.9990 chunk 132 optimal weight: 0.9990 chunk 81 optimal weight: 0.0470 chunk 160 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 246 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 149 optimal weight: 20.0000 chunk 183 optimal weight: 0.9980 chunk 285 optimal weight: 0.9980 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 239 GLN A 317 ASN A 498 GLN A 762 GLN A 895 GLN A 913 GLN A 955 ASN A1119 ASN B 675 GLN B 690 GLN B 751 ASN B 762 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 872 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1005 GLN B1101 HIS C 125 ASN C 134 GLN C 239 GLN C 544 ASN C 644 GLN C 751 ASN C 764 ASN C 856 ASN C 901 GLN C 955 ASN C1071 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6186 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 25135 Z= 0.245 Angle : 0.609 8.795 34196 Z= 0.328 Chirality : 0.047 0.175 3878 Planarity : 0.004 0.053 4436 Dihedral : 4.349 18.768 3365 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.77 % Favored : 98.16 % Rotamer: Outliers : 1.93 % Allowed : 5.76 % Favored : 92.31 % 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: -0.44 (0.14), residues: 3106 helix: 0.82 (0.20), residues: 667 sheet: 0.04 (0.17), residues: 712 loop : -0.87 (0.13), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 64 HIS 0.007 0.002 HIS C1064 PHE 0.024 0.002 PHE A 238 TYR 0.023 0.002 TYR B 265 ARG 0.010 0.001 ARG A 190 *********************** 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 593 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 540 time to evaluate : 2.666 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 190 ARG cc_start: 0.7267 (mmt180) cc_final: 0.7009 (mmt180) REVERT: A 300 LYS cc_start: 0.8006 (mttt) cc_final: 0.7473 (mmtp) REVERT: A 310 LYS cc_start: 0.8008 (ptmt) cc_final: 0.7761 (ptmm) REVERT: A 318 PHE cc_start: 0.7347 (t80) cc_final: 0.7134 (t80) REVERT: A 541 PHE cc_start: 0.6400 (p90) cc_final: 0.6118 (p90) REVERT: A 605 SER cc_start: 0.7947 (t) cc_final: 0.7591 (m) REVERT: A 716 THR cc_start: 0.8264 (p) cc_final: 0.7999 (t) REVERT: A 725 GLU cc_start: 0.6634 (mt-10) cc_final: 0.6422 (mt-10) REVERT: A 748 GLU cc_start: 0.6623 (mm-30) cc_final: 0.6300 (mm-30) REVERT: A 772 VAL cc_start: 0.7797 (t) cc_final: 0.7498 (p) REVERT: A 864 LEU cc_start: 0.8178 (tp) cc_final: 0.7853 (tt) REVERT: A 886 TRP cc_start: 0.7904 (p90) cc_final: 0.7612 (p90) REVERT: A 900 MET cc_start: 0.6480 (mmm) cc_final: 0.6044 (mtt) REVERT: A 902 MET cc_start: 0.7664 (mmt) cc_final: 0.7432 (tpt) REVERT: A 934 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7365 (tp) REVERT: A 952 VAL cc_start: 0.7984 (t) cc_final: 0.7760 (m) REVERT: A 976 VAL cc_start: 0.7364 (t) cc_final: 0.7156 (t) REVERT: A 1002 GLN cc_start: 0.7105 (OUTLIER) cc_final: 0.6684 (mp10) REVERT: A 1013 ILE cc_start: 0.7487 (mm) cc_final: 0.7244 (mt) REVERT: A 1019 ARG cc_start: 0.7399 (ttp-110) cc_final: 0.6980 (ttp-170) REVERT: A 1028 LYS cc_start: 0.7835 (mttt) cc_final: 0.7320 (mttp) REVERT: A 1057 PRO cc_start: 0.8300 (Cg_exo) cc_final: 0.8021 (Cg_endo) REVERT: B 33 THR cc_start: 0.6464 (p) cc_final: 0.5421 (m) REVERT: B 52 GLN cc_start: 0.7344 (tm-30) cc_final: 0.7137 (tm-30) REVERT: B 53 ASP cc_start: 0.6261 (t0) cc_final: 0.6051 (t0) REVERT: B 129 LYS cc_start: 0.6724 (ttmt) cc_final: 0.6424 (tptt) REVERT: B 193 VAL cc_start: 0.6897 (t) cc_final: 0.6697 (m) REVERT: B 300 LYS cc_start: 0.7541 (ptpt) cc_final: 0.6671 (ptpt) REVERT: B 313 TYR cc_start: 0.8111 (m-80) cc_final: 0.7774 (m-80) REVERT: B 577 ARG cc_start: 0.6331 (mtp180) cc_final: 0.6063 (mtp180) REVERT: B 651 ILE cc_start: 0.8065 (pt) cc_final: 0.7686 (mp) REVERT: B 917 TYR cc_start: 0.6136 (m-10) cc_final: 0.5445 (m-80) REVERT: B 957 GLN cc_start: 0.7532 (mm-40) cc_final: 0.7027 (mm-40) REVERT: B 983 ARG cc_start: 0.7288 (ttm-80) cc_final: 0.6914 (ttm-80) REVERT: B 994 ASP cc_start: 0.7312 (m-30) cc_final: 0.7086 (t70) REVERT: B 1028 LYS cc_start: 0.7818 (mttt) cc_final: 0.7443 (mttm) REVERT: B 1122 VAL cc_start: 0.8487 (t) cc_final: 0.8280 (p) REVERT: C 56 LEU cc_start: 0.8244 (tp) cc_final: 0.8040 (tt) REVERT: C 92 PHE cc_start: 0.6240 (t80) cc_final: 0.5890 (t80) REVERT: C 177 MET cc_start: 0.3761 (tpp) cc_final: 0.3416 (tpp) REVERT: C 357 ARG cc_start: 0.5861 (mtt90) cc_final: 0.5507 (mtt-85) REVERT: C 377 PHE cc_start: 0.7188 (t80) cc_final: 0.6985 (t80) REVERT: C 382 VAL cc_start: 0.8601 (p) cc_final: 0.8397 (t) REVERT: C 396 TYR cc_start: 0.5451 (m-80) cc_final: 0.5130 (m-80) REVERT: C 399 SER cc_start: 0.6918 (m) cc_final: 0.6556 (m) REVERT: C 400 PHE cc_start: 0.5470 (p90) cc_final: 0.5112 (p90) REVERT: C 655 HIS cc_start: 0.7537 (OUTLIER) cc_final: 0.6959 (t-90) REVERT: C 663 ASP cc_start: 0.6932 (m-30) cc_final: 0.6642 (m-30) REVERT: C 823 PHE cc_start: 0.6294 (m-10) cc_final: 0.5686 (m-80) REVERT: C 856 ASN cc_start: 0.7421 (OUTLIER) cc_final: 0.7075 (m-40) REVERT: C 884 SER cc_start: 0.8607 (m) cc_final: 0.8165 (p) REVERT: C 886 TRP cc_start: 0.8584 (p90) cc_final: 0.8337 (p90) REVERT: C 936 ASP cc_start: 0.7559 (m-30) cc_final: 0.7134 (m-30) REVERT: C 952 VAL cc_start: 0.7714 (t) cc_final: 0.7368 (m) REVERT: C 1005 GLN cc_start: 0.7714 (mm-40) cc_final: 0.7484 (mm-40) REVERT: C 1010 GLN cc_start: 0.7594 (mm-40) cc_final: 0.7264 (mm-40) REVERT: C 1017 GLU cc_start: 0.6940 (tt0) cc_final: 0.6727 (tt0) outliers start: 53 outliers final: 32 residues processed: 563 average time/residue: 0.3901 time to fit residues: 329.4122 Evaluate side-chains 496 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 460 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 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 734 THR 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 896 ILE 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 A residue 1136 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 754 LEU Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 982 SER 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 581 THR 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 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 158 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 237 optimal weight: 0.9990 chunk 194 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 285 optimal weight: 0.0050 chunk 308 optimal weight: 2.9990 chunk 254 optimal weight: 0.9980 chunk 283 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 229 optimal weight: 3.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- 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 563 GLN A 644 GLN A 774 GLN A 955 ASN B 755 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1005 GLN C 616 ASN C 655 HIS C 755 GLN C 764 ASN C1002 GLN C1119 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25135 Z= 0.213 Angle : 0.536 10.229 34196 Z= 0.285 Chirality : 0.044 0.165 3878 Planarity : 0.004 0.046 4436 Dihedral : 4.201 18.980 3365 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.54 % Favored : 97.39 % Rotamer: Outliers : 2.30 % Allowed : 8.12 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3106 helix: 1.26 (0.21), residues: 683 sheet: 0.43 (0.18), residues: 709 loop : -0.76 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 64 HIS 0.006 0.001 HIS C1048 PHE 0.021 0.002 PHE C 782 TYR 0.022 0.001 TYR A 265 ARG 0.006 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 570 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 507 time to evaluate : 2.778 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 190 ARG cc_start: 0.7289 (mmt180) cc_final: 0.7069 (mmt180) REVERT: A 202 LYS cc_start: 0.7532 (mttp) cc_final: 0.7281 (mptt) REVERT: A 300 LYS cc_start: 0.8090 (mttt) cc_final: 0.7537 (mtmm) REVERT: A 303 LEU cc_start: 0.7747 (mp) cc_final: 0.7507 (tt) REVERT: A 310 LYS cc_start: 0.8008 (ptmt) cc_final: 0.7754 (ptmm) REVERT: A 315 THR cc_start: 0.8144 (m) cc_final: 0.7897 (p) REVERT: A 318 PHE cc_start: 0.7448 (t80) cc_final: 0.7190 (t80) REVERT: A 541 PHE cc_start: 0.6517 (p90) cc_final: 0.6270 (p90) REVERT: A 543 PHE cc_start: 0.7219 (m-10) cc_final: 0.6994 (m-10) REVERT: A 605 SER cc_start: 0.8038 (t) cc_final: 0.7679 (m) REVERT: A 716 THR cc_start: 0.8412 (p) cc_final: 0.8070 (t) REVERT: A 772 VAL cc_start: 0.7882 (t) cc_final: 0.7657 (p) REVERT: A 773 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6394 (tm-30) REVERT: A 864 LEU cc_start: 0.8056 (tp) cc_final: 0.7835 (tt) REVERT: A 872 GLN cc_start: 0.7041 (tt0) cc_final: 0.6770 (tt0) REVERT: A 886 TRP cc_start: 0.8066 (p90) cc_final: 0.7660 (p90) REVERT: A 974 SER cc_start: 0.7599 (t) cc_final: 0.7207 (p) REVERT: A 976 VAL cc_start: 0.7753 (t) cc_final: 0.7454 (t) REVERT: A 983 ARG cc_start: 0.8031 (mtm180) cc_final: 0.7681 (mtm110) REVERT: A 1002 GLN cc_start: 0.7057 (OUTLIER) cc_final: 0.6554 (mp10) REVERT: A 1013 ILE cc_start: 0.7599 (mm) cc_final: 0.7342 (mt) REVERT: A 1028 LYS cc_start: 0.8142 (mttt) cc_final: 0.7586 (mttp) REVERT: B 129 LYS cc_start: 0.6766 (ttmt) cc_final: 0.6455 (tptt) REVERT: B 193 VAL cc_start: 0.6959 (t) cc_final: 0.6757 (m) REVERT: B 313 TYR cc_start: 0.8216 (m-80) cc_final: 0.7995 (m-80) REVERT: B 651 ILE cc_start: 0.8113 (pt) cc_final: 0.7904 (mp) REVERT: B 726 ILE cc_start: 0.8647 (mp) cc_final: 0.8431 (mm) REVERT: B 765 ARG cc_start: 0.6953 (ttm-80) cc_final: 0.6584 (ttp-170) REVERT: B 859 THR cc_start: 0.7858 (m) cc_final: 0.7567 (p) REVERT: B 918 GLU cc_start: 0.7537 (mp0) cc_final: 0.7156 (mp0) REVERT: B 933 LYS cc_start: 0.8036 (mttt) cc_final: 0.7588 (mtmt) REVERT: B 934 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8139 (tp) REVERT: B 957 GLN cc_start: 0.7407 (mm-40) cc_final: 0.6962 (mm-40) REVERT: B 973 ILE cc_start: 0.8151 (tp) cc_final: 0.7949 (pt) REVERT: B 974 SER cc_start: 0.8386 (t) cc_final: 0.8002 (p) REVERT: B 1073 LYS cc_start: 0.7897 (mttt) cc_final: 0.7688 (mptt) REVERT: B 1111 GLU cc_start: 0.6889 (tt0) cc_final: 0.6550 (tt0) REVERT: B 1122 VAL cc_start: 0.8614 (t) cc_final: 0.8305 (p) REVERT: C 56 LEU cc_start: 0.8267 (tp) cc_final: 0.8044 (tt) REVERT: C 92 PHE cc_start: 0.6348 (t80) cc_final: 0.5959 (t80) REVERT: C 129 LYS cc_start: 0.5594 (mttt) cc_final: 0.5387 (mttt) REVERT: C 357 ARG cc_start: 0.6137 (mtt90) cc_final: 0.5566 (mtt90) REVERT: C 364 ASP cc_start: 0.6759 (OUTLIER) cc_final: 0.6266 (t0) REVERT: C 399 SER cc_start: 0.7259 (m) cc_final: 0.6976 (m) REVERT: C 400 PHE cc_start: 0.5730 (p90) cc_final: 0.5264 (p90) REVERT: C 546 LEU cc_start: 0.7255 (tp) cc_final: 0.7042 (tp) REVERT: C 655 HIS cc_start: 0.7434 (OUTLIER) cc_final: 0.7120 (t70) REVERT: C 740 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.7130 (ttp) REVERT: C 776 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7856 (ttpt) REVERT: C 777 ASN cc_start: 0.7914 (m-40) cc_final: 0.7669 (m-40) REVERT: C 824 ASN cc_start: 0.7931 (m-40) cc_final: 0.7587 (m-40) REVERT: C 825 LYS cc_start: 0.7451 (ttmm) cc_final: 0.7199 (mtpp) REVERT: C 856 ASN cc_start: 0.7471 (m-40) cc_final: 0.7261 (m110) REVERT: C 867 ASP cc_start: 0.6997 (OUTLIER) cc_final: 0.6543 (t0) REVERT: C 884 SER cc_start: 0.8549 (m) cc_final: 0.8203 (p) REVERT: C 936 ASP cc_start: 0.7580 (m-30) cc_final: 0.7136 (m-30) REVERT: C 1005 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7389 (mm-40) REVERT: C 1010 GLN cc_start: 0.7593 (mm-40) cc_final: 0.7351 (mm-40) REVERT: C 1113 GLN cc_start: 0.7464 (mt0) cc_final: 0.7246 (mt0) outliers start: 63 outliers final: 36 residues processed: 536 average time/residue: 0.3948 time to fit residues: 319.8503 Evaluate side-chains 515 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 471 time to evaluate : 2.645 ------------------------------------------------------------------------------- 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 551 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1076 THR 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 934 ILE Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1072 GLU 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 610 VAL Chi-restraints excluded: chain C residue 655 HIS 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 776 LYS Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 955 ASN 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 1074 ASN Chi-restraints excluded: chain C residue 1084 ASP 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: 0.0050 chunk 214 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 191 optimal weight: 0.6980 chunk 286 optimal weight: 0.8980 chunk 303 optimal weight: 0.2980 chunk 149 optimal weight: 20.0000 chunk 271 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- 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 317 ASN B 779 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 ASN B 955 ASN B1106 GLN B1113 GLN C 99 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 764 ASN C 935 GLN C 954 GLN C1119 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25135 Z= 0.222 Angle : 0.535 11.860 34196 Z= 0.283 Chirality : 0.044 0.290 3878 Planarity : 0.004 0.079 4436 Dihedral : 4.237 18.906 3365 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.51 % Favored : 97.39 % Rotamer: Outliers : 2.51 % Allowed : 9.03 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.14), residues: 3106 helix: 1.46 (0.21), residues: 676 sheet: 0.51 (0.18), residues: 702 loop : -0.81 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 64 HIS 0.026 0.001 HIS C 655 PHE 0.025 0.002 PHE A 802 TYR 0.016 0.001 TYR A 904 ARG 0.005 0.000 ARG B1107 *********************** 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 580 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 511 time to evaluate : 2.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LYS cc_start: 0.7556 (mttp) cc_final: 0.7297 (mptt) REVERT: A 226 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7872 (mt) REVERT: A 300 LYS cc_start: 0.8084 (mttt) cc_final: 0.7746 (mtmm) REVERT: A 310 LYS cc_start: 0.8028 (ptmt) cc_final: 0.7809 (ptmm) REVERT: A 599 THR cc_start: 0.7586 (t) cc_final: 0.7364 (t) REVERT: A 605 SER cc_start: 0.8155 (t) cc_final: 0.7706 (m) REVERT: A 716 THR cc_start: 0.8480 (p) cc_final: 0.8184 (t) REVERT: A 914 ASN cc_start: 0.7225 (OUTLIER) cc_final: 0.6901 (m-40) REVERT: A 974 SER cc_start: 0.7649 (t) cc_final: 0.7360 (p) REVERT: A 976 VAL cc_start: 0.7876 (t) cc_final: 0.7563 (t) REVERT: A 1002 GLN cc_start: 0.7126 (OUTLIER) cc_final: 0.6659 (mp10) REVERT: A 1013 ILE cc_start: 0.7590 (mm) cc_final: 0.7322 (mt) REVERT: A 1019 ARG cc_start: 0.7405 (ttp-110) cc_final: 0.6944 (ttp80) REVERT: A 1028 LYS cc_start: 0.8188 (mttt) cc_final: 0.7795 (mttp) REVERT: B 129 LYS cc_start: 0.6786 (ttmt) cc_final: 0.6434 (tptt) REVERT: B 204 TYR cc_start: 0.5371 (m-80) cc_final: 0.5068 (m-80) REVERT: B 239 GLN cc_start: 0.5977 (tt0) cc_final: 0.5564 (tm-30) REVERT: B 313 TYR cc_start: 0.8271 (m-80) cc_final: 0.8037 (m-80) REVERT: B 314 GLN cc_start: 0.7276 (tm-30) cc_final: 0.6627 (tm-30) REVERT: B 663 ASP cc_start: 0.7051 (t70) cc_final: 0.6309 (t0) REVERT: B 726 ILE cc_start: 0.8751 (mp) cc_final: 0.8545 (mt) REVERT: B 747 THR cc_start: 0.7079 (p) cc_final: 0.6668 (t) REVERT: B 765 ARG cc_start: 0.6947 (ttm-80) cc_final: 0.6601 (ttp-170) REVERT: B 817 PHE cc_start: 0.8049 (t80) cc_final: 0.7744 (t80) REVERT: B 859 THR cc_start: 0.7821 (m) cc_final: 0.7583 (p) REVERT: B 918 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: B 933 LYS cc_start: 0.7936 (mttt) cc_final: 0.7626 (mmmm) REVERT: B 934 ILE cc_start: 0.8235 (tp) cc_final: 0.7937 (tp) REVERT: B 957 GLN cc_start: 0.7350 (mm-40) cc_final: 0.6973 (mm-40) REVERT: B 973 ILE cc_start: 0.8191 (tp) cc_final: 0.7965 (tp) REVERT: B 974 SER cc_start: 0.8384 (t) cc_final: 0.7987 (p) REVERT: B 1007 TYR cc_start: 0.8047 (t80) cc_final: 0.7663 (t80) REVERT: B 1073 LYS cc_start: 0.7965 (mttt) cc_final: 0.7745 (mptt) REVERT: B 1106 GLN cc_start: 0.6836 (mt0) cc_final: 0.6608 (mt0) REVERT: B 1122 VAL cc_start: 0.8632 (t) cc_final: 0.8339 (p) REVERT: C 45 SER cc_start: 0.7618 (OUTLIER) cc_final: 0.7346 (m) REVERT: C 129 LYS cc_start: 0.5938 (mttt) cc_final: 0.5628 (mttt) REVERT: C 310 LYS cc_start: 0.7791 (ptmm) cc_final: 0.7419 (ttpp) REVERT: C 323 THR cc_start: 0.7239 (m) cc_final: 0.6901 (p) REVERT: C 351 TYR cc_start: 0.5395 (t80) cc_final: 0.4917 (t80) REVERT: C 364 ASP cc_start: 0.6776 (OUTLIER) cc_final: 0.6235 (t0) REVERT: C 365 TYR cc_start: 0.6756 (m-80) cc_final: 0.6532 (m-80) REVERT: C 377 PHE cc_start: 0.7351 (t80) cc_final: 0.7040 (t80) REVERT: C 379 CYS cc_start: 0.4571 (m) cc_final: 0.4153 (m) REVERT: C 597 VAL cc_start: 0.8182 (p) cc_final: 0.7937 (t) REVERT: C 644 GLN cc_start: 0.7135 (tp40) cc_final: 0.6902 (tp-100) REVERT: C 663 ASP cc_start: 0.7078 (m-30) cc_final: 0.6842 (m-30) REVERT: C 777 ASN cc_start: 0.7892 (m-40) cc_final: 0.7657 (m-40) REVERT: C 824 ASN cc_start: 0.7886 (m-40) cc_final: 0.7574 (m-40) REVERT: C 825 LYS cc_start: 0.7447 (ttmm) cc_final: 0.7179 (mmmm) REVERT: C 856 ASN cc_start: 0.7562 (m-40) cc_final: 0.7290 (m-40) REVERT: C 867 ASP cc_start: 0.6898 (OUTLIER) cc_final: 0.6667 (t0) REVERT: C 884 SER cc_start: 0.8464 (m) cc_final: 0.8216 (p) REVERT: C 936 ASP cc_start: 0.7519 (m-30) cc_final: 0.7033 (m-30) REVERT: C 1005 GLN cc_start: 0.7596 (mm-40) cc_final: 0.7262 (mt0) REVERT: C 1010 GLN cc_start: 0.7592 (mm-40) cc_final: 0.7358 (mm-40) outliers start: 69 outliers final: 43 residues processed: 543 average time/residue: 0.3944 time to fit residues: 325.0317 Evaluate side-chains 520 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 470 time to evaluate : 2.596 ------------------------------------------------------------------------------- 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 302 THR 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 617 CYS Chi-restraints excluded: chain A residue 642 VAL 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 896 ILE 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 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 918 GLU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 875 SER 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 980 ILE Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 252 optimal weight: 6.9990 chunk 172 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 259 optimal weight: 0.9990 chunk 209 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 272 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS B 115 GLN B 751 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 ASN B 978 ASN B1005 GLN C 134 GLN C 196 ASN C 394 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 655 HIS ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C1106 GLN C1119 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 0.5945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 25135 Z= 0.521 Angle : 0.762 14.126 34196 Z= 0.405 Chirality : 0.052 0.236 3878 Planarity : 0.006 0.081 4436 Dihedral : 5.381 22.149 3365 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.64 % Favored : 95.24 % Rotamer: Outliers : 3.39 % Allowed : 9.87 % Favored : 86.74 % 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: -0.64 (0.14), residues: 3106 helix: 0.83 (0.20), residues: 673 sheet: 0.15 (0.18), residues: 729 loop : -1.22 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 353 HIS 0.010 0.002 HIS C 49 PHE 0.054 0.004 PHE B 541 TYR 0.029 0.003 TYR A 265 ARG 0.022 0.001 ARG A 466 *********************** 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 610 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 517 time to evaluate : 2.758 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 188 ASN cc_start: 0.7166 (m-40) cc_final: 0.6843 (p0) REVERT: A 226 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7926 (mt) REVERT: A 287 ASP cc_start: 0.7656 (t0) cc_final: 0.7363 (t70) REVERT: A 300 LYS cc_start: 0.8136 (mttt) cc_final: 0.7905 (mtmm) REVERT: A 310 LYS cc_start: 0.8081 (ptmt) cc_final: 0.7766 (ptmm) REVERT: A 319 ARG cc_start: 0.7034 (ttt180) cc_final: 0.6742 (ttt180) REVERT: A 605 SER cc_start: 0.8240 (t) cc_final: 0.7750 (m) REVERT: A 804 GLN cc_start: 0.7254 (mm-40) cc_final: 0.7026 (mm-40) REVERT: A 823 PHE cc_start: 0.6262 (m-10) cc_final: 0.5928 (m-80) REVERT: A 858 LEU cc_start: 0.8711 (mm) cc_final: 0.8408 (mt) REVERT: A 933 LYS cc_start: 0.8088 (ttmt) cc_final: 0.7834 (ttmp) REVERT: A 964 LYS cc_start: 0.8080 (mttp) cc_final: 0.7735 (mttp) REVERT: A 975 SER cc_start: 0.8327 (p) cc_final: 0.7985 (t) REVERT: A 1013 ILE cc_start: 0.7684 (mm) cc_final: 0.7393 (mt) REVERT: A 1019 ARG cc_start: 0.7188 (ttp-110) cc_final: 0.6931 (ttm110) REVERT: A 1028 LYS cc_start: 0.8284 (mttt) cc_final: 0.8058 (mttp) REVERT: B 33 THR cc_start: 0.6561 (p) cc_final: 0.5791 (m) REVERT: B 129 LYS cc_start: 0.6941 (ttmt) cc_final: 0.6484 (tptt) REVERT: B 313 TYR cc_start: 0.8411 (m-80) cc_final: 0.8083 (m-80) REVERT: B 725 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6974 (mt-10) REVERT: B 726 ILE cc_start: 0.8743 (mp) cc_final: 0.8450 (mt) REVERT: B 737 ASP cc_start: 0.7183 (t0) cc_final: 0.6952 (t70) REVERT: B 765 ARG cc_start: 0.7286 (ttm-80) cc_final: 0.6939 (ttp-170) REVERT: B 776 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7421 (ttmm) REVERT: B 817 PHE cc_start: 0.8048 (t80) cc_final: 0.7815 (t80) REVERT: B 859 THR cc_start: 0.7851 (m) cc_final: 0.7538 (p) REVERT: B 933 LYS cc_start: 0.8118 (mttt) cc_final: 0.7688 (mtmt) REVERT: B 934 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8309 (tp) REVERT: B 957 GLN cc_start: 0.7413 (mm-40) cc_final: 0.7180 (mm-40) REVERT: B 964 LYS cc_start: 0.7570 (ttmm) cc_final: 0.7312 (mtmm) REVERT: B 973 ILE cc_start: 0.8312 (tp) cc_final: 0.8077 (tp) REVERT: B 974 SER cc_start: 0.8347 (t) cc_final: 0.7990 (p) REVERT: B 1086 LYS cc_start: 0.7838 (mttm) cc_final: 0.7569 (mttp) REVERT: B 1101 HIS cc_start: 0.8007 (m90) cc_final: 0.7521 (m-70) REVERT: B 1125 ASN cc_start: 0.8276 (p0) cc_final: 0.8029 (p0) REVERT: C 45 SER cc_start: 0.7887 (OUTLIER) cc_final: 0.7623 (t) REVERT: C 129 LYS cc_start: 0.6001 (mttt) cc_final: 0.5692 (mttt) REVERT: C 224 GLU cc_start: 0.6210 (mp0) cc_final: 0.5979 (mp0) REVERT: C 310 LYS cc_start: 0.7974 (ptmm) cc_final: 0.7682 (ttpp) REVERT: C 321 GLN cc_start: 0.7272 (mm110) cc_final: 0.7044 (tp40) REVERT: C 532 ASN cc_start: 0.8058 (t0) cc_final: 0.7809 (t0) REVERT: C 537 LYS cc_start: 0.8355 (mtpp) cc_final: 0.7978 (mtpp) REVERT: C 574 ASP cc_start: 0.7572 (t0) cc_final: 0.7352 (t0) REVERT: C 644 GLN cc_start: 0.7289 (tp40) cc_final: 0.7058 (tp-100) REVERT: C 740 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7275 (tmt) REVERT: C 820 ASP cc_start: 0.7638 (m-30) cc_final: 0.7242 (m-30) REVERT: C 824 ASN cc_start: 0.8064 (m-40) cc_final: 0.7767 (m-40) REVERT: C 936 ASP cc_start: 0.7551 (m-30) cc_final: 0.7123 (m-30) REVERT: C 1005 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7383 (mt0) REVERT: C 1072 GLU cc_start: 0.7505 (pm20) cc_final: 0.7137 (pm20) REVERT: C 1123 SER cc_start: 0.8147 (t) cc_final: 0.7794 (m) outliers start: 93 outliers final: 62 residues processed: 568 average time/residue: 0.3803 time to fit residues: 328.4396 Evaluate side-chains 543 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 476 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 610 VAL 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 726 ILE 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 1136 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 193 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 660 TYR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 934 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 985 ASP Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1130 ILE 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 353 TRP 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 533 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 858 LEU 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 1031 GLU Chi-restraints excluded: chain C residue 1074 ASN 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: 0.7980 chunk 273 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 178 optimal weight: 0.6980 chunk 74 optimal weight: 0.2980 chunk 303 optimal weight: 0.8980 chunk 252 optimal weight: 0.4980 chunk 140 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 159 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 146 HIS ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN A1119 ASN B 115 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS C 764 ASN C1119 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.6005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25135 Z= 0.190 Angle : 0.564 14.127 34196 Z= 0.297 Chirality : 0.044 0.192 3878 Planarity : 0.004 0.060 4436 Dihedral : 4.680 20.918 3365 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.99 % Favored : 96.84 % Rotamer: Outliers : 2.37 % Allowed : 12.17 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.14), residues: 3106 helix: 1.48 (0.21), residues: 679 sheet: 0.33 (0.18), residues: 742 loop : -1.06 (0.14), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 64 HIS 0.004 0.001 HIS C1048 PHE 0.024 0.002 PHE C 392 TYR 0.015 0.001 TYR A 904 ARG 0.022 0.001 ARG B 102 *********************** 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 555 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 490 time to evaluate : 2.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7889 (mt) REVERT: A 287 ASP cc_start: 0.7573 (t0) cc_final: 0.7274 (t70) REVERT: A 298 GLU cc_start: 0.7433 (tt0) cc_final: 0.7058 (tt0) REVERT: A 300 LYS cc_start: 0.8081 (mttt) cc_final: 0.7832 (mttm) REVERT: A 310 LYS cc_start: 0.8111 (ptmt) cc_final: 0.7775 (ptmm) REVERT: A 605 SER cc_start: 0.8179 (t) cc_final: 0.7729 (m) REVERT: A 739 THR cc_start: 0.8207 (t) cc_final: 0.7760 (p) REVERT: A 764 ASN cc_start: 0.7831 (m-40) cc_final: 0.7511 (m110) REVERT: A 773 GLU cc_start: 0.7030 (tt0) cc_final: 0.6738 (tt0) REVERT: A 775 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.7022 (t0) REVERT: A 858 LEU cc_start: 0.8652 (mm) cc_final: 0.8348 (mt) REVERT: A 933 LYS cc_start: 0.8016 (ttmt) cc_final: 0.7739 (ttmp) REVERT: A 976 VAL cc_start: 0.8089 (OUTLIER) cc_final: 0.7775 (t) REVERT: A 1010 GLN cc_start: 0.7130 (mt0) cc_final: 0.6660 (mm110) REVERT: A 1013 ILE cc_start: 0.7597 (mm) cc_final: 0.7232 (mt) REVERT: A 1019 ARG cc_start: 0.7082 (ttp-110) cc_final: 0.6556 (ttp-170) REVERT: A 1051 SER cc_start: 0.8165 (t) cc_final: 0.7685 (p) REVERT: A 1137 VAL cc_start: 0.8592 (t) cc_final: 0.8225 (m) REVERT: B 129 LYS cc_start: 0.6823 (ttmt) cc_final: 0.6440 (tptt) REVERT: B 153 MET cc_start: -0.1613 (ttp) cc_final: -0.2603 (ttp) REVERT: B 206 LYS cc_start: 0.6747 (tptp) cc_final: 0.6509 (tptp) REVERT: B 313 TYR cc_start: 0.8377 (m-80) cc_final: 0.8111 (m-80) REVERT: B 725 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6882 (mt-10) REVERT: B 765 ARG cc_start: 0.7198 (ttm-80) cc_final: 0.6958 (ttp-170) REVERT: B 817 PHE cc_start: 0.7896 (t80) cc_final: 0.7645 (t80) REVERT: B 859 THR cc_start: 0.7828 (m) cc_final: 0.7550 (p) REVERT: B 918 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7255 (mp0) REVERT: B 933 LYS cc_start: 0.8038 (mttt) cc_final: 0.7557 (mtmt) REVERT: B 934 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8148 (tp) REVERT: B 954 GLN cc_start: 0.7049 (mm110) cc_final: 0.6730 (mt0) REVERT: B 957 GLN cc_start: 0.7408 (mm-40) cc_final: 0.6982 (mm-40) REVERT: B 973 ILE cc_start: 0.8234 (tp) cc_final: 0.8004 (tp) REVERT: B 974 SER cc_start: 0.8409 (t) cc_final: 0.8051 (p) REVERT: B 1086 LYS cc_start: 0.7763 (mttm) cc_final: 0.7515 (mttp) REVERT: B 1125 ASN cc_start: 0.8141 (p0) cc_final: 0.7931 (p0) REVERT: C 38 TYR cc_start: 0.7719 (m-10) cc_final: 0.6939 (m-10) REVERT: C 129 LYS cc_start: 0.5963 (mttt) cc_final: 0.5638 (mttt) REVERT: C 230 PRO cc_start: 0.8578 (Cg_exo) cc_final: 0.8348 (Cg_endo) REVERT: C 310 LYS cc_start: 0.7800 (ptmm) cc_final: 0.7393 (ttpp) REVERT: C 357 ARG cc_start: 0.6498 (mtt-85) cc_final: 0.6054 (tpp-160) REVERT: C 537 LYS cc_start: 0.8286 (mtpp) cc_final: 0.7942 (mtpp) REVERT: C 574 ASP cc_start: 0.7595 (t0) cc_final: 0.7342 (t0) REVERT: C 610 VAL cc_start: 0.8479 (OUTLIER) cc_final: 0.8023 (p) REVERT: C 655 HIS cc_start: 0.7343 (OUTLIER) cc_final: 0.7127 (t70) REVERT: C 740 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.7243 (tmt) REVERT: C 820 ASP cc_start: 0.7470 (m-30) cc_final: 0.7148 (m-30) REVERT: C 824 ASN cc_start: 0.7851 (m-40) cc_final: 0.7558 (m-40) REVERT: C 867 ASP cc_start: 0.6746 (t0) cc_final: 0.6527 (t0) REVERT: C 936 ASP cc_start: 0.7497 (m-30) cc_final: 0.6982 (m-30) REVERT: C 1005 GLN cc_start: 0.7573 (mm-40) cc_final: 0.7299 (mt0) REVERT: C 1010 GLN cc_start: 0.7562 (mm-40) cc_final: 0.7214 (mm-40) REVERT: C 1017 GLU cc_start: 0.6507 (tt0) cc_final: 0.6033 (tt0) REVERT: C 1072 GLU cc_start: 0.7444 (pm20) cc_final: 0.7092 (pm20) REVERT: C 1123 SER cc_start: 0.8101 (t) cc_final: 0.7798 (m) outliers start: 65 outliers final: 49 residues processed: 516 average time/residue: 0.3885 time to fit residues: 305.4186 Evaluate side-chains 530 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 474 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 708 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 914 ASN Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 317 ASN 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 780 GLU Chi-restraints excluded: chain B residue 934 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 1005 GLN 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 274 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 292 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 chunk 221 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 255 optimal weight: 9.9990 chunk 169 optimal weight: 2.9990 chunk 302 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A1119 ASN B 115 GLN B 207 HIS ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 955 ASN B1005 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C 969 ASN C1119 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.6571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 25135 Z= 0.513 Angle : 0.743 12.420 34196 Z= 0.396 Chirality : 0.052 0.268 3878 Planarity : 0.006 0.146 4436 Dihedral : 5.431 24.787 3365 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.31 % Favored : 94.53 % Rotamer: Outliers : 3.35 % Allowed : 11.66 % Favored : 84.99 % 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: -0.78 (0.14), residues: 3106 helix: 0.93 (0.20), residues: 673 sheet: 0.00 (0.18), residues: 738 loop : -1.40 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 64 HIS 0.018 0.002 HIS C 655 PHE 0.050 0.003 PHE B 541 TYR 0.031 0.003 TYR A 38 ARG 0.026 0.001 ARG B 102 *********************** 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 584 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 492 time to evaluate : 2.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6802 (tt0) REVERT: A 188 ASN cc_start: 0.7349 (OUTLIER) cc_final: 0.6809 (p0) REVERT: A 226 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7850 (mt) REVERT: A 310 LYS cc_start: 0.8160 (ptmt) cc_final: 0.7815 (ptmm) REVERT: A 605 SER cc_start: 0.8372 (t) cc_final: 0.7808 (m) REVERT: A 612 TYR cc_start: 0.8175 (m-80) cc_final: 0.7858 (m-80) REVERT: A 739 THR cc_start: 0.8273 (t) cc_final: 0.7892 (p) REVERT: A 773 GLU cc_start: 0.7087 (tt0) cc_final: 0.6778 (tt0) REVERT: A 858 LEU cc_start: 0.8847 (mm) cc_final: 0.8601 (mt) REVERT: A 933 LYS cc_start: 0.8083 (ttmt) cc_final: 0.7844 (ttmp) REVERT: A 1013 ILE cc_start: 0.7758 (mm) cc_final: 0.7424 (mt) REVERT: A 1019 ARG cc_start: 0.7158 (ttp-110) cc_final: 0.6527 (ttp-170) REVERT: A 1051 SER cc_start: 0.8165 (t) cc_final: 0.7803 (p) REVERT: B 129 LYS cc_start: 0.6912 (ttmt) cc_final: 0.6427 (tptt) REVERT: B 153 MET cc_start: -0.1237 (ttp) cc_final: -0.2442 (ttp) REVERT: B 206 LYS cc_start: 0.6952 (tptp) cc_final: 0.6678 (tptp) REVERT: B 239 GLN cc_start: 0.6494 (tt0) cc_final: 0.6009 (tm-30) REVERT: B 313 TYR cc_start: 0.8363 (m-80) cc_final: 0.7965 (m-80) REVERT: B 696 THR cc_start: 0.8477 (m) cc_final: 0.8147 (t) REVERT: B 725 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6892 (mt-10) REVERT: B 726 ILE cc_start: 0.8729 (mp) cc_final: 0.8369 (mt) REVERT: B 804 GLN cc_start: 0.7451 (tp40) cc_final: 0.7065 (mm-40) REVERT: B 817 PHE cc_start: 0.7977 (t80) cc_final: 0.7528 (t80) REVERT: B 859 THR cc_start: 0.7848 (m) cc_final: 0.7543 (p) REVERT: B 918 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7291 (mp0) REVERT: B 933 LYS cc_start: 0.8128 (mttt) cc_final: 0.7692 (mtmt) REVERT: B 934 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8338 (tp) REVERT: B 954 GLN cc_start: 0.7072 (mm110) cc_final: 0.6790 (mt0) REVERT: B 957 GLN cc_start: 0.7398 (mm-40) cc_final: 0.7173 (mm-40) REVERT: B 959 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7743 (mt) REVERT: B 973 ILE cc_start: 0.8346 (tp) cc_final: 0.8082 (tp) REVERT: B 974 SER cc_start: 0.8443 (t) cc_final: 0.8042 (p) REVERT: B 1086 LYS cc_start: 0.7853 (mttm) cc_final: 0.7587 (mttp) REVERT: B 1101 HIS cc_start: 0.7975 (m90) cc_final: 0.7449 (m-70) REVERT: C 129 LYS cc_start: 0.5949 (mttt) cc_final: 0.5674 (mttt) REVERT: C 190 ARG cc_start: 0.6899 (mmt180) cc_final: 0.6506 (mmm160) REVERT: C 224 GLU cc_start: 0.6315 (mp0) cc_final: 0.6050 (mp0) REVERT: C 310 LYS cc_start: 0.7965 (ptmm) cc_final: 0.7694 (ttpp) REVERT: C 355 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.7104 (ttm170) REVERT: C 357 ARG cc_start: 0.6973 (mtt-85) cc_final: 0.6657 (tpp-160) REVERT: C 396 TYR cc_start: 0.5976 (m-80) cc_final: 0.5527 (m-80) REVERT: C 532 ASN cc_start: 0.8085 (t0) cc_final: 0.7846 (t0) REVERT: C 537 LYS cc_start: 0.8432 (mtpp) cc_final: 0.8060 (mtpp) REVERT: C 574 ASP cc_start: 0.7663 (t0) cc_final: 0.7349 (t0) REVERT: C 578 ASP cc_start: 0.6798 (t0) cc_final: 0.6502 (t0) REVERT: C 740 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.7096 (tmt) REVERT: C 820 ASP cc_start: 0.7585 (m-30) cc_final: 0.7377 (m-30) REVERT: C 936 ASP cc_start: 0.7558 (m-30) cc_final: 0.7119 (m-30) REVERT: C 1005 GLN cc_start: 0.7674 (mm-40) cc_final: 0.7359 (mt0) REVERT: C 1017 GLU cc_start: 0.6576 (tt0) cc_final: 0.6034 (tt0) REVERT: C 1031 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7471 (mt-10) REVERT: C 1072 GLU cc_start: 0.7547 (pm20) cc_final: 0.7155 (pm20) REVERT: C 1123 SER cc_start: 0.8114 (t) cc_final: 0.7780 (m) outliers start: 92 outliers final: 62 residues processed: 528 average time/residue: 0.4048 time to fit residues: 323.7190 Evaluate side-chains 550 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 480 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 90 VAL 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 320 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 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 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 976 VAL Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1136 THR 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 660 TYR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1045 LYS 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 227 VAL 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 355 ARG Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 699 LEU 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 823 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 187 optimal weight: 0.7980 chunk 120 optimal weight: 0.0060 chunk 180 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 59 optimal weight: 0.1980 chunk 58 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 206 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 237 optimal weight: 0.7980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN A 613 GLN A 913 GLN A 935 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 137 ASN B 804 GLN B1005 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN C 764 ASN C1119 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.6532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25135 Z= 0.180 Angle : 0.563 13.060 34196 Z= 0.294 Chirality : 0.044 0.179 3878 Planarity : 0.004 0.049 4436 Dihedral : 4.714 21.975 3365 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.38 % Favored : 96.46 % Rotamer: Outliers : 2.40 % Allowed : 13.04 % Favored : 84.55 % 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: -0.31 (0.15), residues: 3106 helix: 1.52 (0.21), residues: 681 sheet: 0.27 (0.18), residues: 723 loop : -1.18 (0.14), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 64 HIS 0.003 0.001 HIS C1048 PHE 0.023 0.001 PHE A 823 TYR 0.020 0.001 TYR B 91 ARG 0.008 0.001 ARG C 190 *********************** 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 559 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 493 time to evaluate : 2.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASN cc_start: 0.7268 (OUTLIER) cc_final: 0.6821 (p0) REVERT: A 226 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7872 (mt) REVERT: A 298 GLU cc_start: 0.7451 (tt0) cc_final: 0.7120 (tt0) REVERT: A 300 LYS cc_start: 0.8113 (mttm) cc_final: 0.7836 (mtmm) REVERT: A 310 LYS cc_start: 0.8143 (ptmt) cc_final: 0.7827 (ptmm) REVERT: A 605 SER cc_start: 0.8214 (t) cc_final: 0.7701 (m) REVERT: A 739 THR cc_start: 0.8200 (t) cc_final: 0.7855 (p) REVERT: A 773 GLU cc_start: 0.6895 (tt0) cc_final: 0.6552 (tt0) REVERT: A 858 LEU cc_start: 0.8733 (mm) cc_final: 0.8471 (mt) REVERT: A 933 LYS cc_start: 0.7974 (ttmt) cc_final: 0.7690 (ttmp) REVERT: A 976 VAL cc_start: 0.8048 (OUTLIER) cc_final: 0.7744 (t) REVERT: A 1010 GLN cc_start: 0.7091 (mt0) cc_final: 0.6617 (mm110) REVERT: A 1013 ILE cc_start: 0.7650 (mm) cc_final: 0.7254 (mt) REVERT: A 1019 ARG cc_start: 0.7131 (ttp-110) cc_final: 0.6310 (ttp-170) REVERT: A 1028 LYS cc_start: 0.8394 (mmtp) cc_final: 0.8179 (mmtp) REVERT: A 1051 SER cc_start: 0.8060 (t) cc_final: 0.7623 (p) REVERT: A 1091 ARG cc_start: 0.7528 (ttm-80) cc_final: 0.7140 (ttm-80) REVERT: A 1137 VAL cc_start: 0.8612 (t) cc_final: 0.8281 (m) REVERT: B 129 LYS cc_start: 0.6734 (ttmt) cc_final: 0.6386 (tptt) REVERT: B 239 GLN cc_start: 0.6478 (tt0) cc_final: 0.5903 (tm-30) REVERT: B 696 THR cc_start: 0.8420 (m) cc_final: 0.8132 (t) REVERT: B 725 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6796 (mt-10) REVERT: B 726 ILE cc_start: 0.8701 (mp) cc_final: 0.8375 (mt) REVERT: B 765 ARG cc_start: 0.6969 (ttm-80) cc_final: 0.6711 (ttp-170) REVERT: B 804 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.7051 (mm-40) REVERT: B 817 PHE cc_start: 0.7786 (t80) cc_final: 0.7440 (t80) REVERT: B 859 THR cc_start: 0.7809 (m) cc_final: 0.7547 (p) REVERT: B 918 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7199 (mp0) REVERT: B 933 LYS cc_start: 0.8012 (mttt) cc_final: 0.7530 (mtmt) REVERT: B 954 GLN cc_start: 0.6985 (mm110) cc_final: 0.6725 (mt0) REVERT: B 973 ILE cc_start: 0.8181 (tp) cc_final: 0.7921 (tp) REVERT: B 974 SER cc_start: 0.8423 (t) cc_final: 0.8057 (p) REVERT: B 990 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6466 (mt-10) REVERT: B 1086 LYS cc_start: 0.7809 (mttm) cc_final: 0.7544 (mttp) REVERT: B 1101 HIS cc_start: 0.7979 (m90) cc_final: 0.7478 (m-70) REVERT: C 38 TYR cc_start: 0.7711 (m-10) cc_final: 0.6967 (m-10) REVERT: C 129 LYS cc_start: 0.5954 (mttt) cc_final: 0.5670 (mttt) REVERT: C 190 ARG cc_start: 0.6848 (mmt180) cc_final: 0.6566 (mmm160) REVERT: C 310 LYS cc_start: 0.7772 (ptmm) cc_final: 0.7528 (ttpp) REVERT: C 357 ARG cc_start: 0.6903 (mtt-85) cc_final: 0.6594 (tpp-160) REVERT: C 537 LYS cc_start: 0.8331 (mtpp) cc_final: 0.8005 (mtpp) REVERT: C 574 ASP cc_start: 0.7631 (t0) cc_final: 0.7339 (t0) REVERT: C 578 ASP cc_start: 0.6691 (t0) cc_final: 0.6382 (t0) REVERT: C 610 VAL cc_start: 0.8475 (t) cc_final: 0.7994 (p) REVERT: C 777 ASN cc_start: 0.7829 (m-40) cc_final: 0.7615 (m-40) REVERT: C 820 ASP cc_start: 0.7420 (m-30) cc_final: 0.7195 (m-30) REVERT: C 936 ASP cc_start: 0.7440 (m-30) cc_final: 0.6818 (m-30) REVERT: C 990 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6843 (mp0) REVERT: C 1005 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7279 (mt0) REVERT: C 1010 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7260 (mm-40) REVERT: C 1017 GLU cc_start: 0.6537 (tt0) cc_final: 0.5934 (tt0) REVERT: C 1031 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7376 (mt-10) REVERT: C 1072 GLU cc_start: 0.7421 (pm20) cc_final: 0.7095 (pm20) REVERT: C 1123 SER cc_start: 0.8118 (t) cc_final: 0.7776 (m) outliers start: 66 outliers final: 45 residues processed: 522 average time/residue: 0.3938 time to fit residues: 312.4376 Evaluate side-chains 527 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 475 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 206 LYS 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 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 CYS 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 976 VAL Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1005 GLN 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 227 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 439 ASN Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU 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 1031 GLU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 275 optimal weight: 3.9990 chunk 289 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 chunk 282 optimal weight: 0.9980 chunk 169 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 chunk 221 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 254 optimal weight: 3.9990 chunk 266 optimal weight: 0.6980 chunk 281 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 764 ASN A 913 GLN A 935 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1005 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 764 ASN C 969 ASN C1119 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 moved from start: 0.6673 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= 0.282 Angle : 0.599 11.712 34196 Z= 0.316 Chirality : 0.046 0.247 3878 Planarity : 0.005 0.056 4436 Dihedral : 4.753 23.087 3365 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.60 % Favored : 95.24 % Rotamer: Outliers : 2.55 % Allowed : 13.30 % Favored : 84.15 % 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: -0.38 (0.15), residues: 3106 helix: 1.50 (0.20), residues: 682 sheet: 0.21 (0.18), residues: 724 loop : -1.23 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 64 HIS 0.005 0.001 HIS C1048 PHE 0.031 0.002 PHE A 823 TYR 0.019 0.002 TYR C 204 ARG 0.008 0.001 ARG A 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 548 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 478 time to evaluate : 2.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.7958 (t) cc_final: 0.7542 (m) REVERT: A 171 VAL cc_start: 0.7717 (OUTLIER) cc_final: 0.7491 (t) REVERT: A 188 ASN cc_start: 0.7252 (OUTLIER) cc_final: 0.6923 (p0) REVERT: A 226 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7856 (mt) REVERT: A 237 ARG cc_start: 0.7028 (mtp-110) cc_final: 0.6807 (mtp85) REVERT: A 298 GLU cc_start: 0.7461 (tt0) cc_final: 0.7153 (tt0) REVERT: A 310 LYS cc_start: 0.8137 (ptmt) cc_final: 0.7837 (ptmm) REVERT: A 605 SER cc_start: 0.8274 (t) cc_final: 0.7728 (m) REVERT: A 739 THR cc_start: 0.8276 (t) cc_final: 0.7919 (p) REVERT: A 773 GLU cc_start: 0.6932 (tt0) cc_final: 0.6537 (tt0) REVERT: A 775 ASP cc_start: 0.7375 (t0) cc_final: 0.7134 (t0) REVERT: A 858 LEU cc_start: 0.8796 (mm) cc_final: 0.8552 (mt) REVERT: A 933 LYS cc_start: 0.7971 (ttmt) cc_final: 0.7703 (ttmp) REVERT: A 1010 GLN cc_start: 0.7129 (mt0) cc_final: 0.6646 (mm110) REVERT: A 1013 ILE cc_start: 0.7725 (mm) cc_final: 0.7340 (mt) REVERT: A 1019 ARG cc_start: 0.7147 (ttp-110) cc_final: 0.6278 (ttp-170) REVERT: A 1051 SER cc_start: 0.8117 (t) cc_final: 0.7726 (p) REVERT: A 1137 VAL cc_start: 0.8652 (t) cc_final: 0.8342 (m) REVERT: B 153 MET cc_start: -0.1202 (ttp) cc_final: -0.2664 (ttp) REVERT: B 239 GLN cc_start: 0.6478 (tt0) cc_final: 0.5989 (tm-30) REVERT: B 696 THR cc_start: 0.8435 (m) cc_final: 0.8132 (t) REVERT: B 725 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6855 (mt-10) REVERT: B 726 ILE cc_start: 0.8716 (mp) cc_final: 0.8352 (mt) REVERT: B 765 ARG cc_start: 0.7091 (ttm-80) cc_final: 0.6818 (ttp-170) REVERT: B 817 PHE cc_start: 0.7811 (t80) cc_final: 0.7600 (t80) REVERT: B 859 THR cc_start: 0.7829 (m) cc_final: 0.7561 (p) REVERT: B 918 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7235 (mp0) REVERT: B 933 LYS cc_start: 0.8068 (mttt) cc_final: 0.7806 (mmtm) REVERT: B 954 GLN cc_start: 0.6971 (mm110) cc_final: 0.6750 (mt0) REVERT: B 973 ILE cc_start: 0.8206 (tp) cc_final: 0.7943 (tp) REVERT: B 974 SER cc_start: 0.8427 (t) cc_final: 0.8058 (p) REVERT: B 990 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.6491 (mt-10) REVERT: B 1101 HIS cc_start: 0.7986 (m90) cc_final: 0.7450 (m-70) REVERT: C 38 TYR cc_start: 0.7739 (m-10) cc_final: 0.7020 (m-10) REVERT: C 129 LYS cc_start: 0.6007 (mttt) cc_final: 0.5723 (mttt) REVERT: C 190 ARG cc_start: 0.6879 (mmt180) cc_final: 0.6670 (mmm160) REVERT: C 357 ARG cc_start: 0.6936 (mtt-85) cc_final: 0.6571 (tpp-160) REVERT: C 396 TYR cc_start: 0.5656 (m-80) cc_final: 0.5045 (m-80) REVERT: C 537 LYS cc_start: 0.8374 (mtpp) cc_final: 0.8056 (mtpp) REVERT: C 574 ASP cc_start: 0.7622 (t0) cc_final: 0.7307 (t0) REVERT: C 740 MET cc_start: 0.7354 (tmt) cc_final: 0.7008 (tmt) REVERT: C 777 ASN cc_start: 0.7848 (m-40) cc_final: 0.7605 (m-40) REVERT: C 825 LYS cc_start: 0.7988 (mmmm) cc_final: 0.7583 (mttm) REVERT: C 936 ASP cc_start: 0.7484 (m-30) cc_final: 0.6982 (m-30) REVERT: C 1005 GLN cc_start: 0.7605 (mm-40) cc_final: 0.7317 (mt0) REVERT: C 1017 GLU cc_start: 0.6533 (tt0) cc_final: 0.5900 (tt0) REVERT: C 1031 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: C 1072 GLU cc_start: 0.7462 (pm20) cc_final: 0.7130 (pm20) REVERT: C 1123 SER cc_start: 0.8122 (t) cc_final: 0.7778 (m) outliers start: 70 outliers final: 57 residues processed: 510 average time/residue: 0.4065 time to fit residues: 317.2687 Evaluate side-chains 532 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 470 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 SER 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 206 LYS 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 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 642 VAL Chi-restraints excluded: chain A residue 649 CYS 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 976 VAL Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1005 GLN 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 227 VAL 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 312 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU 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 1031 GLU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 185 optimal weight: 0.3980 chunk 298 optimal weight: 0.3980 chunk 182 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 207 optimal weight: 0.0030 chunk 312 optimal weight: 0.6980 chunk 287 optimal weight: 0.9990 chunk 249 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 192 optimal weight: 0.6980 chunk 152 optimal weight: 5.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 913 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1005 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.6701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25135 Z= 0.177 Angle : 0.559 11.422 34196 Z= 0.294 Chirality : 0.044 0.191 3878 Planarity : 0.004 0.047 4436 Dihedral : 4.533 21.613 3365 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.77 % Favored : 96.07 % Rotamer: Outliers : 2.19 % Allowed : 13.92 % Favored : 83.90 % 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: -0.21 (0.15), residues: 3106 helix: 1.70 (0.21), residues: 683 sheet: 0.36 (0.19), residues: 707 loop : -1.16 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 64 HIS 0.003 0.001 HIS C1048 PHE 0.023 0.001 PHE A 823 TYR 0.024 0.001 TYR A1110 ARG 0.011 0.000 ARG C 983 ********************** 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 536 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 476 time to evaluate : 2.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.7918 (OUTLIER) cc_final: 0.7581 (m) REVERT: A 188 ASN cc_start: 0.7240 (OUTLIER) cc_final: 0.6831 (p0) REVERT: A 226 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7874 (mt) REVERT: A 240 THR cc_start: 0.5953 (m) cc_final: 0.5416 (p) REVERT: A 298 GLU cc_start: 0.7508 (tt0) cc_final: 0.7138 (tt0) REVERT: A 300 LYS cc_start: 0.8368 (mtmm) cc_final: 0.8038 (mtmm) REVERT: A 306 PHE cc_start: 0.7219 (m-10) cc_final: 0.7004 (m-80) REVERT: A 310 LYS cc_start: 0.8105 (ptmt) cc_final: 0.7819 (ptmm) REVERT: A 739 THR cc_start: 0.8197 (t) cc_final: 0.7898 (p) REVERT: A 858 LEU cc_start: 0.8722 (mm) cc_final: 0.8476 (mt) REVERT: A 916 LEU cc_start: 0.7987 (tt) cc_final: 0.7733 (tp) REVERT: A 933 LYS cc_start: 0.7942 (ttmt) cc_final: 0.7682 (ttmp) REVERT: A 1010 GLN cc_start: 0.7087 (mt0) cc_final: 0.6631 (mm110) REVERT: A 1013 ILE cc_start: 0.7718 (mm) cc_final: 0.7308 (mt) REVERT: A 1031 GLU cc_start: 0.7313 (mp0) cc_final: 0.7066 (mp0) REVERT: A 1051 SER cc_start: 0.7996 (t) cc_final: 0.7595 (p) REVERT: A 1137 VAL cc_start: 0.8632 (t) cc_final: 0.8307 (m) REVERT: B 153 MET cc_start: -0.1015 (ttp) cc_final: -0.2509 (ttp) REVERT: B 239 GLN cc_start: 0.6456 (tt0) cc_final: 0.5983 (tm-30) REVERT: B 696 THR cc_start: 0.8376 (m) cc_final: 0.8097 (t) REVERT: B 725 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6802 (mt-10) REVERT: B 726 ILE cc_start: 0.8699 (mp) cc_final: 0.8343 (mt) REVERT: B 765 ARG cc_start: 0.6930 (ttm-80) cc_final: 0.6681 (ttp-170) REVERT: B 808 ASP cc_start: 0.6661 (p0) cc_final: 0.4827 (p0) REVERT: B 814 LYS cc_start: 0.7208 (ptmm) cc_final: 0.7002 (ptmm) REVERT: B 817 PHE cc_start: 0.7767 (t80) cc_final: 0.7554 (t80) REVERT: B 859 THR cc_start: 0.7841 (m) cc_final: 0.7619 (p) REVERT: B 973 ILE cc_start: 0.8146 (tp) cc_final: 0.7899 (tp) REVERT: B 974 SER cc_start: 0.8438 (t) cc_final: 0.8083 (p) REVERT: B 990 GLU cc_start: 0.6677 (OUTLIER) cc_final: 0.6458 (mt-10) REVERT: B 1101 HIS cc_start: 0.7980 (m90) cc_final: 0.7477 (m-70) REVERT: C 38 TYR cc_start: 0.7680 (m-10) cc_final: 0.6938 (m-10) REVERT: C 44 ARG cc_start: 0.7299 (mtt90) cc_final: 0.7085 (mtt-85) REVERT: C 129 LYS cc_start: 0.5979 (mttt) cc_final: 0.5640 (mttt) REVERT: C 310 LYS cc_start: 0.7768 (ptmm) cc_final: 0.7529 (ttpp) REVERT: C 355 ARG cc_start: 0.7207 (ptm160) cc_final: 0.6924 (ptm160) REVERT: C 357 ARG cc_start: 0.7061 (mtt-85) cc_final: 0.6691 (tpp-160) REVERT: C 396 TYR cc_start: 0.5630 (m-80) cc_final: 0.4736 (m-80) REVERT: C 537 LYS cc_start: 0.8332 (mtpp) cc_final: 0.8031 (mtpp) REVERT: C 574 ASP cc_start: 0.7600 (t0) cc_final: 0.7295 (t0) REVERT: C 610 VAL cc_start: 0.8428 (t) cc_final: 0.7988 (p) REVERT: C 740 MET cc_start: 0.7321 (tmt) cc_final: 0.6999 (tmt) REVERT: C 777 ASN cc_start: 0.7701 (m-40) cc_final: 0.7490 (m-40) REVERT: C 820 ASP cc_start: 0.7312 (m-30) cc_final: 0.7030 (m-30) REVERT: C 824 ASN cc_start: 0.7688 (m-40) cc_final: 0.7432 (m-40) REVERT: C 936 ASP cc_start: 0.7426 (m-30) cc_final: 0.6813 (m-30) REVERT: C 990 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6801 (mp0) REVERT: C 1005 GLN cc_start: 0.7561 (mm-40) cc_final: 0.7273 (mt0) REVERT: C 1010 GLN cc_start: 0.7584 (mm-40) cc_final: 0.7248 (mm-40) REVERT: C 1031 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7358 (mt-10) REVERT: C 1072 GLU cc_start: 0.7440 (pm20) cc_final: 0.7132 (pm20) REVERT: C 1122 VAL cc_start: 0.8593 (t) cc_final: 0.7992 (p) REVERT: C 1123 SER cc_start: 0.8131 (t) cc_final: 0.7813 (m) outliers start: 60 outliers final: 49 residues processed: 503 average time/residue: 0.3880 time to fit residues: 294.5779 Evaluate side-chains 520 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 465 time to evaluate : 2.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 206 LYS 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 587 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 CYS 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 1136 THR 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 716 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1005 GLN 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 227 VAL 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 312 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 761 THR 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 1031 GLU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 0.0010 chunk 265 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 229 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 249 optimal weight: 0.4980 chunk 104 optimal weight: 0.0980 chunk 256 optimal weight: 3.9990 chunk 31 optimal weight: 0.0000 chunk 45 optimal weight: 9.9990 overall best weight: 0.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 804 GLN B 919 ASN B1005 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 969 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.200934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.169477 restraints weight = 38424.577| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 2.32 r_work: 0.3988 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3843 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.6709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25135 Z= 0.154 Angle : 0.549 11.717 34196 Z= 0.286 Chirality : 0.044 0.170 3878 Planarity : 0.004 0.054 4436 Dihedral : 4.348 20.888 3365 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.15 % Favored : 95.69 % Rotamer: Outliers : 2.00 % Allowed : 14.35 % Favored : 83.64 % 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: -0.05 (0.15), residues: 3106 helix: 1.92 (0.21), residues: 676 sheet: 0.43 (0.19), residues: 715 loop : -1.08 (0.14), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 64 HIS 0.004 0.001 HIS A1048 PHE 0.033 0.001 PHE C 541 TYR 0.027 0.001 TYR A 904 ARG 0.007 0.000 ARG A 237 =============================================================================== Job complete usr+sys time: 6797.27 seconds wall clock time: 121 minutes 48.60 seconds (7308.60 seconds total)