Starting phenix.real_space_refine on Tue Dec 12 22:32:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb3_31513/12_2023/7fb3_31513.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb3_31513/12_2023/7fb3_31513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb3_31513/12_2023/7fb3_31513.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb3_31513/12_2023/7fb3_31513.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb3_31513/12_2023/7fb3_31513.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb3_31513/12_2023/7fb3_31513.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 14636 2.51 5 N 3812 2.21 5 O 4367 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 53": "OD1" <-> "OD2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 745": "OD1" <-> "OD2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 178": "OD1" <-> "OD2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 775": "OD1" <-> "OD2" Residue "B ASP 796": "OD1" <-> "OD2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B ASP 1041": "OD1" <-> "OD2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1139": "OD1" <-> "OD2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "B ASP 1146": "OD1" <-> "OD2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 568": "OD1" <-> "OD2" Residue "C ASP 571": "OD1" <-> "OD2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C ASP 663": "OD1" <-> "OD2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1144": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 22920 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1045, 8175 Classifications: {'peptide': 1045} Link IDs: {'PTRANS': 52, 'TRANS': 992} Chain breaks: 6 Chain: "B" Number of atoms: 6606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 849, 6606 Classifications: {'peptide': 849} Link IDs: {'PTRANS': 42, 'TRANS': 806} Chain breaks: 7 Chain: "C" Number of atoms: 8139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8139 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 53, 'TRANS': 988} Chain breaks: 6 Time building chain proxies: 12.29, per 1000 atoms: 0.54 Number of scatterers: 22920 At special positions: 0 Unit cell: (141.44, 131.92, 176.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 4367 8.00 N 3812 7.00 C 14636 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 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=2.04 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=2.04 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 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 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: 9.64 Conformation dependent library (CDL) restraints added in 4.7 seconds 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5506 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 50 sheets defined 24.4% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.524A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.669A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.675A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.368A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 removed outlier: 3.601A pdb=" N TYR A 505 " --> pdb=" O GLY A 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 502 through 505' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.608A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 783 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 912 through 916 Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.704A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.942A 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 1033 removed outlier: 5.524A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.877A 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 737 through 744 Processing helix chain 'B' and resid 748 through 753 Processing helix chain 'B' and resid 754 through 756 No H-bonds generated for 'chain 'B' and resid 754 through 756' Processing helix chain 'B' and resid 757 through 782 removed outlier: 3.676A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.517A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.550A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 941 through 944 removed outlier: 4.030A pdb=" N ALA B 944 " --> pdb=" O THR B 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 941 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.118A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (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 1032 removed outlier: 6.009A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.364A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.681A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.218A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.879A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 852 through 856 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.699A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.616A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.309A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.958A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.460A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.249A 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 Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 51 removed outlier: 3.821A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.606A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.572A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 90 through 94 Processing sheet with id=AA6, first strand: chain 'A' and resid 128 through 131 Processing sheet with id=AA7, first strand: chain 'A' and resid 195 through 197 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 317 removed outlier: 4.616A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.620A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) 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 538 through 543 removed outlier: 3.747A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.416A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.226A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.566A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.313A 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 1125 removed outlier: 4.495A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 removed outlier: 3.538A pdb=" N VAL A1104 " --> pdb=" O GLN A1113 " (cutoff:3.500A) 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 36 through 37 removed outlier: 6.854A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.854A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY B 268 " --> pdb=" O TYR B 91 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 48 through 49 removed outlier: 3.627A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.742A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.318A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 538 through 543 Processing sheet with id=AD1, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.560A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.731A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.990A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.473A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1080 through 1082 removed outlier: 3.679A pdb=" N VAL B1133 " --> pdb=" O ALA B1080 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AD8, first strand: chain 'C' and resid 29 through 30 removed outlier: 4.026A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 52 through 55 removed outlier: 7.653A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.460A 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: 5.938A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.753A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 191 through 197 removed outlier: 3.744A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.315A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 376 through 380 Processing sheet with id=AE6, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.544A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 566 through 567 removed outlier: 4.167A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 664 through 665 Processing sheet with id=AE9, first strand: chain 'C' and resid 712 through 722 removed outlier: 6.594A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 712 through 722 removed outlier: 6.594A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF4, first strand: chain 'C' and resid 1086 through 1090 removed outlier: 5.736A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1094 through 1097 800 hydrogen bonds defined for protein. 2163 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: 9.41 Time building geometry restraints manager: 10.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7433 1.35 - 1.47: 5861 1.47 - 1.60: 10004 1.60 - 1.72: 0 1.72 - 1.85: 134 Bond restraints: 23432 Sorted by residual: bond pdb=" C GLN A 173 " pdb=" N PRO A 174 " ideal model delta sigma weight residual 1.330 1.360 -0.030 1.19e-02 7.06e+03 6.38e+00 bond pdb=" C VAL B 620 " pdb=" N PRO B 621 " ideal model delta sigma weight residual 1.331 1.343 -0.012 7.90e-03 1.60e+04 2.18e+00 bond pdb=" CA ILE C1115 " pdb=" CB ILE C1115 " ideal model delta sigma weight residual 1.540 1.524 0.016 1.36e-02 5.41e+03 1.47e+00 bond pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " ideal model delta sigma weight residual 1.808 1.846 -0.038 3.30e-02 9.18e+02 1.34e+00 bond pdb=" CA ILE C 909 " pdb=" C ILE C 909 " ideal model delta sigma weight residual 1.530 1.517 0.013 1.12e-02 7.97e+03 1.34e+00 ... (remaining 23427 not shown) Histogram of bond angle deviations from ideal: 99.76 - 106.76: 691 106.76 - 113.76: 12921 113.76 - 120.76: 9746 120.76 - 127.75: 8381 127.75 - 134.75: 140 Bond angle restraints: 31879 Sorted by residual: angle pdb=" C ARG B 328 " pdb=" N PHE B 329 " pdb=" CA PHE B 329 " ideal model delta sigma weight residual 121.80 134.75 -12.95 2.44e+00 1.68e-01 2.82e+01 angle pdb=" N ASN A 603 " pdb=" CA ASN A 603 " pdb=" C ASN A 603 " ideal model delta sigma weight residual 114.56 108.08 6.48 1.27e+00 6.20e-01 2.60e+01 angle pdb=" C HIS A 207 " pdb=" N THR A 208 " pdb=" CA THR A 208 " ideal model delta sigma weight residual 120.49 127.64 -7.15 1.42e+00 4.96e-01 2.54e+01 angle pdb=" N VAL B 213 " pdb=" CA VAL B 213 " pdb=" C VAL B 213 " ideal model delta sigma weight residual 113.20 109.13 4.07 9.60e-01 1.09e+00 1.79e+01 angle pdb=" N THR A 618 " pdb=" CA THR A 618 " pdb=" C THR A 618 " ideal model delta sigma weight residual 112.93 108.35 4.58 1.12e+00 7.97e-01 1.67e+01 ... (remaining 31874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 12605 17.97 - 35.94: 1137 35.94 - 53.92: 193 53.92 - 71.89: 38 71.89 - 89.86: 28 Dihedral angle restraints: 14001 sinusoidal: 5462 harmonic: 8539 Sorted by residual: dihedral pdb=" CA ARG A 78 " pdb=" C ARG A 78 " pdb=" N PHE A 79 " pdb=" CA PHE A 79 " ideal model delta harmonic sigma weight residual 180.00 136.54 43.46 0 5.00e+00 4.00e-02 7.55e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual 93.00 170.03 -77.03 1 1.00e+01 1.00e-02 7.44e+01 dihedral pdb=" CA CYS A 617 " pdb=" C CYS A 617 " pdb=" N THR A 618 " pdb=" CA THR A 618 " ideal model delta harmonic sigma weight residual 180.00 142.98 37.02 0 5.00e+00 4.00e-02 5.48e+01 ... (remaining 13998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2487 0.040 - 0.080: 819 0.080 - 0.119: 292 0.119 - 0.159: 41 0.159 - 0.199: 4 Chirality restraints: 3643 Sorted by residual: chirality pdb=" CA PHE B 329 " pdb=" N PHE B 329 " pdb=" C PHE B 329 " pdb=" CB PHE B 329 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.90e-01 chirality pdb=" CA ILE B 119 " pdb=" N ILE B 119 " pdb=" C ILE B 119 " pdb=" CB ILE B 119 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.45e-01 chirality pdb=" CA CYS A 617 " pdb=" N CYS A 617 " pdb=" C CYS A 617 " pdb=" CB CYS A 617 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 3640 not shown) Planarity restraints: 4139 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 861 " -0.041 5.00e-02 4.00e+02 6.25e-02 6.25e+00 pdb=" N PRO C 862 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO C 862 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 862 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B1078 " 0.033 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO B1079 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B1079 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B1079 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A1078 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO A1079 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A1079 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1079 " 0.028 5.00e-02 4.00e+02 ... (remaining 4136 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 458 2.67 - 3.23: 22273 3.23 - 3.79: 33823 3.79 - 4.34: 46793 4.34 - 4.90: 77738 Nonbonded interactions: 181085 Sorted by model distance: nonbonded pdb=" OG1 THR B 108 " pdb=" O ASN B 234 " model vdw 2.114 2.440 nonbonded pdb=" N LEU C 24 " pdb=" O THR C 76 " model vdw 2.159 2.520 nonbonded pdb=" OG1 THR A 108 " pdb=" O ASN A 234 " model vdw 2.174 2.440 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.193 2.440 nonbonded pdb=" OE1 GLN C 965 " pdb=" OG SER C1003 " model vdw 2.221 2.440 ... (remaining 181080 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 24 through 144 or resid 153 through 245 or resid 261 throu \ gh 827 or resid 851 through 1146)) selection = (chain 'C' and (resid 24 through 620 or resid 641 through 1146)) } 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=0.00 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: 0.790 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: 4.950 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 64.670 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 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 : 0.003 0.038 23432 Z= 0.218 Angle : 0.653 12.952 31879 Z= 0.380 Chirality : 0.044 0.199 3643 Planarity : 0.004 0.063 4139 Dihedral : 14.252 89.860 8393 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.23 % Allowed : 4.17 % Favored : 95.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.07 % 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: -4.11 (0.13), residues: 2892 helix: -0.71 (0.20), residues: 639 sheet: -2.85 (0.18), residues: 559 loop : -3.70 (0.12), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 886 HIS 0.004 0.001 HIS C1064 PHE 0.022 0.001 PHE C 906 TYR 0.018 0.001 TYR B 756 ARG 0.005 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 250 time to evaluate : 2.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 255 average time/residue: 0.3922 time to fit residues: 151.2455 Evaluate side-chains 160 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 156 time to evaluate : 2.885 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1995 time to fit residues: 5.3935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 246 optimal weight: 8.9990 chunk 221 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 75 optimal weight: 0.0770 chunk 149 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 228 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 chunk 265 optimal weight: 2.9990 overall best weight: 1.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 282 ASN A 321 GLN ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN A 439 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 690 GLN A 751 ASN A 787 GLN A 872 GLN A 919 ASN A 954 GLN A 957 GLN A 969 ASN A1023 ASN A1054 GLN A1064 HIS B 99 ASN ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 331 ASN B 607 GLN B 658 ASN B 751 ASN B 919 ASN B 925 ASN B 954 GLN B 955 ASN B 965 GLN B1011 GLN B1023 ASN B1064 HIS B1071 GLN B1074 ASN B1106 GLN B1119 ASN C 99 ASN C 122 ASN C 448 ASN C 450 ASN C 460 ASN C 481 ASN C 487 ASN C 493 GLN C 519 HIS C 607 GLN C 755 GLN C 872 GLN C 907 ASN C 920 GLN C 925 ASN C 954 GLN C 955 ASN C1002 GLN C1005 GLN C1023 ASN C1054 GLN C1058 HIS C1064 HIS C1083 HIS C1134 ASN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23432 Z= 0.211 Angle : 0.562 12.434 31879 Z= 0.292 Chirality : 0.044 0.186 3643 Planarity : 0.004 0.045 4139 Dihedral : 4.819 40.262 3127 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.86 % Allowed : 9.82 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.15), residues: 2892 helix: 0.91 (0.22), residues: 626 sheet: -2.38 (0.19), residues: 591 loop : -3.23 (0.13), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 436 HIS 0.003 0.001 HIS A1048 PHE 0.028 0.001 PHE B 329 TYR 0.022 0.001 TYR C 351 ARG 0.005 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 175 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 9 residues processed: 194 average time/residue: 0.3771 time to fit residues: 114.1235 Evaluate side-chains 159 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 150 time to evaluate : 2.803 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2151 time to fit residues: 7.5177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 147 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 220 optimal weight: 10.0000 chunk 180 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 265 optimal weight: 2.9990 chunk 286 optimal weight: 0.7980 chunk 236 optimal weight: 0.8980 chunk 263 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 213 optimal weight: 4.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN C 448 ASN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23432 Z= 0.214 Angle : 0.544 11.970 31879 Z= 0.281 Chirality : 0.043 0.187 3643 Planarity : 0.005 0.141 4139 Dihedral : 4.683 41.234 3127 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 1.48 % Allowed : 12.15 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.15), residues: 2892 helix: 1.59 (0.22), residues: 626 sheet: -2.01 (0.19), residues: 592 loop : -2.94 (0.13), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 104 HIS 0.002 0.001 HIS A 207 PHE 0.021 0.001 PHE A 192 TYR 0.023 0.001 TYR C 351 ARG 0.006 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 167 time to evaluate : 2.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 21 residues processed: 200 average time/residue: 0.3469 time to fit residues: 112.4164 Evaluate side-chains 172 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 151 time to evaluate : 2.723 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2154 time to fit residues: 12.5177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 262 optimal weight: 5.9990 chunk 199 optimal weight: 20.0000 chunk 137 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 178 optimal weight: 0.8980 chunk 266 optimal weight: 3.9990 chunk 282 optimal weight: 3.9990 chunk 139 optimal weight: 0.0060 chunk 252 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 360 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 ASN C 493 GLN C 965 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23432 Z= 0.158 Angle : 0.518 13.596 31879 Z= 0.267 Chirality : 0.043 0.195 3643 Planarity : 0.004 0.049 4139 Dihedral : 4.431 39.553 3127 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.17 % Allowed : 13.75 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.15), residues: 2892 helix: 2.12 (0.22), residues: 617 sheet: -1.64 (0.20), residues: 591 loop : -2.73 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 104 HIS 0.001 0.000 HIS A 655 PHE 0.021 0.001 PHE A 192 TYR 0.024 0.001 TYR C 351 ARG 0.006 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 171 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 9 residues processed: 197 average time/residue: 0.3449 time to fit residues: 109.3170 Evaluate side-chains 160 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 151 time to evaluate : 2.838 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2064 time to fit residues: 7.1698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 235 optimal weight: 0.0070 chunk 160 optimal weight: 0.0570 chunk 4 optimal weight: 9.9990 chunk 210 optimal weight: 8.9990 chunk 116 optimal weight: 30.0000 chunk 240 optimal weight: 4.9990 chunk 195 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 253 optimal weight: 0.5980 chunk 71 optimal weight: 5.9990 overall best weight: 2.1320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN C1074 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 23432 Z= 0.328 Angle : 0.583 14.238 31879 Z= 0.300 Chirality : 0.045 0.198 3643 Planarity : 0.004 0.046 4139 Dihedral : 4.603 39.667 3127 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 1.71 % Allowed : 14.80 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.15), residues: 2892 helix: 1.93 (0.22), residues: 626 sheet: -1.58 (0.20), residues: 591 loop : -2.72 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 104 HIS 0.004 0.001 HIS A1088 PHE 0.029 0.002 PHE A 192 TYR 0.021 0.001 TYR C 351 ARG 0.004 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 152 time to evaluate : 2.740 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 16 residues processed: 189 average time/residue: 0.3347 time to fit residues: 103.0986 Evaluate side-chains 162 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 146 time to evaluate : 2.621 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2180 time to fit residues: 10.4937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 94 optimal weight: 1.9990 chunk 254 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 165 optimal weight: 0.1980 chunk 69 optimal weight: 0.8980 chunk 282 optimal weight: 0.8980 chunk 234 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 148 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 487 ASN C 607 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 23432 Z= 0.165 Angle : 0.526 14.714 31879 Z= 0.270 Chirality : 0.043 0.194 3643 Planarity : 0.004 0.047 4139 Dihedral : 4.413 38.661 3127 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.82 % Allowed : 16.32 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.16), residues: 2892 helix: 2.27 (0.22), residues: 620 sheet: -1.42 (0.20), residues: 598 loop : -2.57 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 104 HIS 0.001 0.000 HIS C1088 PHE 0.028 0.001 PHE A 192 TYR 0.033 0.001 TYR C 505 ARG 0.005 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 166 time to evaluate : 2.699 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 7 residues processed: 184 average time/residue: 0.3617 time to fit residues: 107.4089 Evaluate side-chains 153 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 146 time to evaluate : 2.487 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3700 time to fit residues: 7.5361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 272 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 160 optimal weight: 0.8980 chunk 206 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 237 optimal weight: 4.9990 chunk 157 optimal weight: 0.4980 chunk 281 optimal weight: 0.8980 chunk 176 optimal weight: 0.7980 chunk 171 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 965 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23432 Z= 0.163 Angle : 0.525 15.126 31879 Z= 0.270 Chirality : 0.043 0.192 3643 Planarity : 0.004 0.047 4139 Dihedral : 4.313 37.464 3127 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.70 % Allowed : 17.02 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.16), residues: 2892 helix: 2.37 (0.22), residues: 620 sheet: -1.24 (0.21), residues: 602 loop : -2.47 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 104 HIS 0.005 0.000 HIS A 207 PHE 0.031 0.001 PHE A 192 TYR 0.041 0.001 TYR C 505 ARG 0.004 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 160 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 6 residues processed: 176 average time/residue: 0.3370 time to fit residues: 97.6172 Evaluate side-chains 157 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 151 time to evaluate : 2.656 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2207 time to fit residues: 6.0244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 174 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 191 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 221 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN B 544 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23432 Z= 0.279 Angle : 0.572 16.679 31879 Z= 0.294 Chirality : 0.044 0.189 3643 Planarity : 0.004 0.050 4139 Dihedral : 4.473 36.422 3127 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.47 % Allowed : 17.84 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.62 (0.16), residues: 2892 helix: 2.19 (0.22), residues: 622 sheet: -1.19 (0.21), residues: 596 loop : -2.47 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP A 104 HIS 0.004 0.001 HIS A1088 PHE 0.033 0.001 PHE A 192 TYR 0.021 0.001 TYR A 904 ARG 0.004 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 156 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 163 average time/residue: 0.3540 time to fit residues: 96.2120 Evaluate side-chains 155 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 149 time to evaluate : 2.829 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2376 time to fit residues: 6.3146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 256 optimal weight: 0.9990 chunk 269 optimal weight: 2.9990 chunk 245 optimal weight: 7.9990 chunk 262 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 205 optimal weight: 30.0000 chunk 80 optimal weight: 0.9990 chunk 236 optimal weight: 1.9990 chunk 248 optimal weight: 0.0570 chunk 261 optimal weight: 0.9980 overall best weight: 1.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN C 965 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23432 Z= 0.185 Angle : 0.544 16.782 31879 Z= 0.278 Chirality : 0.043 0.177 3643 Planarity : 0.004 0.048 4139 Dihedral : 4.337 35.510 3127 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.27 % Allowed : 18.35 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.47 (0.16), residues: 2892 helix: 2.38 (0.22), residues: 621 sheet: -1.11 (0.21), residues: 601 loop : -2.39 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 104 HIS 0.004 0.000 HIS A 207 PHE 0.034 0.001 PHE A 192 TYR 0.054 0.001 TYR C 505 ARG 0.007 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 157 time to evaluate : 2.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 163 average time/residue: 0.3490 time to fit residues: 92.3886 Evaluate side-chains 150 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 146 time to evaluate : 2.436 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2317 time to fit residues: 5.4865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 172 optimal weight: 1.9990 chunk 277 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 131 optimal weight: 0.0570 chunk 192 optimal weight: 9.9990 chunk 290 optimal weight: 3.9990 chunk 267 optimal weight: 0.9980 chunk 231 optimal weight: 30.0000 chunk 24 optimal weight: 0.8980 chunk 178 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23432 Z= 0.187 Angle : 0.556 17.439 31879 Z= 0.283 Chirality : 0.043 0.165 3643 Planarity : 0.004 0.047 4139 Dihedral : 4.305 34.724 3127 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 0.16 % Allowed : 18.66 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.41 (0.16), residues: 2892 helix: 2.41 (0.22), residues: 621 sheet: -1.08 (0.21), residues: 606 loop : -2.34 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A 104 HIS 0.005 0.000 HIS A 207 PHE 0.037 0.001 PHE A 192 TYR 0.022 0.001 TYR C 351 ARG 0.007 0.000 ARG B 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 158 time to evaluate : 2.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 160 average time/residue: 0.3517 time to fit residues: 91.7720 Evaluate side-chains 152 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 150 time to evaluate : 2.622 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2647 time to fit residues: 4.2733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 184 optimal weight: 3.9990 chunk 246 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 213 optimal weight: 0.9990 chunk 34 optimal weight: 0.1980 chunk 64 optimal weight: 2.9990 chunk 232 optimal weight: 0.0870 chunk 97 optimal weight: 0.8980 chunk 238 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN C 99 ASN C 122 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.154763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.093729 restraints weight = 36610.066| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.21 r_work: 0.3208 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23432 Z= 0.148 Angle : 0.528 16.178 31879 Z= 0.271 Chirality : 0.043 0.167 3643 Planarity : 0.004 0.093 4139 Dihedral : 4.222 33.685 3127 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.08 % Allowed : 18.89 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.29 (0.16), residues: 2892 helix: 2.64 (0.22), residues: 611 sheet: -1.05 (0.21), residues: 606 loop : -2.28 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 104 HIS 0.005 0.000 HIS A 207 PHE 0.036 0.001 PHE A 192 TYR 0.050 0.001 TYR C 505 ARG 0.019 0.000 ARG B 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4461.47 seconds wall clock time: 82 minutes 20.75 seconds (4940.75 seconds total)