Starting phenix.real_space_refine on Wed Jul 24 05:50:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0t_42869/07_2024/8v0t_42869.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0t_42869/07_2024/8v0t_42869.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/8v0t_42869/07_2024/8v0t_42869.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0t_42869/07_2024/8v0t_42869.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0t_42869/07_2024/8v0t_42869.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0t_42869/07_2024/8v0t_42869.cif" } 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= 0.041 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 114 5.16 5 C 15822 2.51 5 N 4089 2.21 5 O 4752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 24777 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8133 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 Chain: "B" Number of atoms: 8133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8133 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 Chain: "C" Number of atoms: 8133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8133 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 14.81, per 1000 atoms: 0.60 Number of scatterers: 24777 At special positions: 0 Unit cell: (140.4, 130.68, 174.96, 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 114 16.00 O 4752 8.00 N 4089 7.00 C 15822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, 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=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " 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 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1134 " " NAG A1308 " - " ASN A 282 " " NAG A1309 " - " ASN A 801 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 282 " " NAG B1309 " - " ASN B 801 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C1134 " " NAG C1308 " - " ASN C 282 " " NAG C1309 " - " ASN C 801 " Time building additional restraints: 8.84 Conformation dependent library (CDL) restraints added in 4.7 seconds 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5862 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 51 sheets defined 25.5% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.173A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.777A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 368' Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.910A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 4.035A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.750A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.846A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 836 through 842 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.508A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.717A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.536A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.702A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (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 removed outlier: 3.530A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.570A pdb=" N ALA A 989 " --> pdb=" O ASP A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.629A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.767A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.846A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.676A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 842 removed outlier: 3.591A pdb=" N GLY B 842 " --> pdb=" O GLY B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 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 909 removed outlier: 3.663A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.549A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.651A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (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 removed outlier: 3.522A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.943A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 366 through 372 removed outlier: 3.707A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.720A pdb=" N GLU C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 407' Processing helix chain 'C' and resid 417 through 422 removed outlier: 4.013A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 443 removed outlier: 3.858A pdb=" N SER C 443 " --> pdb=" O LYS C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.778A pdb=" N HIS C 505 " --> pdb=" O GLY C 502 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 502 through 506' Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.505A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 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 removed outlier: 3.677A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.641A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 842 removed outlier: 4.009A pdb=" N GLY C 842 " --> pdb=" O GLY C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.540A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.659A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.579A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (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 984 removed outlier: 3.574A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.587A pdb=" N ALA C 989 " --> pdb=" O ASP C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.022A 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: 7.617A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.844A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.735A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 316 removed outlier: 7.184A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.695A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.711A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.639A 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 565 through 566 removed outlier: 7.188A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.002A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.959A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.747A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 722 Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 722 removed outlier: 5.864A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.594A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC3, first strand: chain 'B' and resid 25 through 30 removed outlier: 7.629A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.576A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.739A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 140 through 142 Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.092A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.604A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 356 through 358 Processing sheet with id=AD1, first strand: chain 'B' and resid 400 through 403 Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD3, first strand: chain 'B' and resid 584 through 586 removed outlier: 6.392A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.033A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.632A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 712 through 713 removed outlier: 3.788A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.394A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.575A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.798A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.070A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL C 193 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR C 208 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LYS C 206 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER C 205 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N HIS C 207 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.584A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.265A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 324 through 326 removed outlier: 4.236A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.053A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.869A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.985A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 722 Processing sheet with id=AF3, first strand: chain 'C' and resid 718 through 722 removed outlier: 6.107A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.587A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF6, first strand: chain 'C' and resid 1094 through 1097 894 hydrogen bonds defined for protein. 2445 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.62 Time building geometry restraints manager: 9.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7723 1.34 - 1.46: 6328 1.46 - 1.59: 11144 1.59 - 1.72: 2 1.72 - 1.84: 141 Bond restraints: 25338 Sorted by residual: bond pdb=" CA ASN A 196 " pdb=" CB ASN A 196 " ideal model delta sigma weight residual 1.527 1.641 -0.114 2.48e-02 1.63e+03 2.10e+01 bond pdb=" CB PRO A 209 " pdb=" CG PRO A 209 " ideal model delta sigma weight residual 1.492 1.646 -0.154 5.00e-02 4.00e+02 9.52e+00 bond pdb=" C1 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.92e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.12e+00 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.10e+00 ... (remaining 25333 not shown) Histogram of bond angle deviations from ideal: 96.38 - 103.90: 358 103.90 - 111.42: 10545 111.42 - 118.94: 9575 118.94 - 126.46: 13698 126.46 - 133.98: 294 Bond angle restraints: 34470 Sorted by residual: angle pdb=" CA PRO A 209 " pdb=" N PRO A 209 " pdb=" CD PRO A 209 " ideal model delta sigma weight residual 112.00 98.90 13.10 1.40e+00 5.10e-01 8.75e+01 angle pdb=" C GLU A 619 " pdb=" N VAL A 620 " pdb=" CA VAL A 620 " ideal model delta sigma weight residual 120.33 124.67 -4.34 8.00e-01 1.56e+00 2.94e+01 angle pdb=" CA PRO C 82 " pdb=" N PRO C 82 " pdb=" CD PRO C 82 " ideal model delta sigma weight residual 112.00 104.48 7.52 1.40e+00 5.10e-01 2.88e+01 angle pdb=" N GLY A 103 " pdb=" CA GLY A 103 " pdb=" C GLY A 103 " ideal model delta sigma weight residual 111.09 117.45 -6.36 1.33e+00 5.65e-01 2.28e+01 angle pdb=" CG1 ILE C 128 " pdb=" CB ILE C 128 " pdb=" CG2 ILE C 128 " ideal model delta sigma weight residual 110.70 96.38 14.32 3.00e+00 1.11e-01 2.28e+01 ... (remaining 34465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 13906 18.06 - 36.12: 1283 36.12 - 54.17: 209 54.17 - 72.23: 54 72.23 - 90.29: 31 Dihedral angle restraints: 15483 sinusoidal: 6378 harmonic: 9105 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -176.29 90.29 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS B 840 " pdb=" SG CYS B 840 " pdb=" SG CYS B 851 " pdb=" CB CYS B 851 " ideal model delta sinusoidal sigma weight residual 93.00 174.87 -81.87 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 146.97 -53.97 1 1.00e+01 1.00e-02 3.95e+01 ... (remaining 15480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 3610 0.096 - 0.192: 357 0.192 - 0.288: 24 0.288 - 0.384: 4 0.384 - 0.480: 1 Chirality restraints: 3996 Sorted by residual: chirality pdb=" CB ILE A 101 " pdb=" CA ILE A 101 " pdb=" CG1 ILE A 101 " pdb=" CG2 ILE A 101 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.76e+00 chirality pdb=" CB VAL B 511 " pdb=" CA VAL B 511 " pdb=" CG1 VAL B 511 " pdb=" CG2 VAL B 511 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CB ILE C 128 " pdb=" CA ILE C 128 " pdb=" CG1 ILE C 128 " pdb=" CG2 ILE C 128 " both_signs ideal model delta sigma weight residual False 2.64 2.98 -0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 3993 not shown) Planarity restraints: 4452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 208 " 0.080 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO A 209 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO A 209 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 209 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 81 " 0.065 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO C 82 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO C 82 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 82 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 64 " 0.032 2.00e-02 2.50e+03 2.15e-02 1.15e+01 pdb=" CG TRP A 64 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP A 64 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 64 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 64 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 64 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 64 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 64 " 0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 64 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 64 " -0.000 2.00e-02 2.50e+03 ... (remaining 4449 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 7476 2.83 - 3.35: 20010 3.35 - 3.86: 39712 3.86 - 4.38: 43523 4.38 - 4.90: 79167 Nonbonded interactions: 189888 Sorted by model distance: nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.310 2.440 nonbonded pdb=" O ALA C 879 " pdb=" OG1 THR C 883 " model vdw 2.312 2.440 nonbonded pdb=" OH TYR C 37 " pdb=" OD2 ASP C 53 " model vdw 2.313 2.440 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.332 2.440 nonbonded pdb=" OH TYR A 37 " pdb=" OD2 ASP A 53 " model vdw 2.334 2.440 ... (remaining 189883 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' selection = chain 'B' selection = chain 'C' } 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: 1.510 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: 0.030 Extract box with map and model: 1.080 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 70.280 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.120 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.154 25338 Z= 0.381 Angle : 0.823 14.319 34470 Z= 0.438 Chirality : 0.057 0.480 3996 Planarity : 0.007 0.112 4425 Dihedral : 14.432 87.196 9498 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.84 % Favored : 94.13 % Rotamer: Outliers : 0.04 % Allowed : 0.33 % Favored : 99.63 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.14), residues: 3081 helix: -0.64 (0.17), residues: 698 sheet: -0.52 (0.20), residues: 613 loop : -1.76 (0.13), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP A 64 HIS 0.009 0.001 HIS C 207 PHE 0.046 0.003 PHE C 906 TYR 0.042 0.002 TYR B 170 ARG 0.009 0.001 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 208 time to evaluate : 2.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 PRO cc_start: 0.8246 (Cg_endo) cc_final: 0.7733 (Cg_exo) REVERT: A 902 MET cc_start: 0.8293 (mmt) cc_final: 0.8011 (mmt) REVERT: B 388 ASN cc_start: 0.8339 (m110) cc_final: 0.8115 (t0) REVERT: B 740 MET cc_start: 0.8071 (mmm) cc_final: 0.7758 (tpp) REVERT: B 904 TYR cc_start: 0.7889 (m-10) cc_final: 0.7000 (m-10) REVERT: B 1084 ASP cc_start: 0.7808 (t70) cc_final: 0.7448 (t0) REVERT: C 135 PHE cc_start: 0.4848 (m-10) cc_final: 0.4592 (m-10) REVERT: C 754 LEU cc_start: 0.8535 (mp) cc_final: 0.8267 (mt) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.3275 time to fit residues: 113.8884 Evaluate side-chains 166 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 5.9990 chunk 236 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 chunk 80 optimal weight: 0.5980 chunk 159 optimal weight: 0.3980 chunk 126 optimal weight: 0.7980 chunk 244 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 148 optimal weight: 9.9990 chunk 182 optimal weight: 0.9980 chunk 283 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 613 GLN B 556 ASN B 955 ASN B1010 GLN C 66 HIS C 134 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 25338 Z= 0.162 Angle : 0.508 9.597 34470 Z= 0.268 Chirality : 0.044 0.237 3996 Planarity : 0.004 0.056 4425 Dihedral : 6.262 56.251 3909 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.02 % Favored : 95.94 % Rotamer: Outliers : 0.44 % Allowed : 5.56 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.15), residues: 3081 helix: 1.07 (0.19), residues: 710 sheet: -0.28 (0.20), residues: 643 loop : -1.57 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 64 HIS 0.004 0.001 HIS B 49 PHE 0.016 0.001 PHE C 906 TYR 0.018 0.001 TYR B 170 ARG 0.005 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 192 time to evaluate : 2.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 PRO cc_start: 0.8177 (Cg_endo) cc_final: 0.7969 (Cg_exo) REVERT: A 979 ASP cc_start: 0.7837 (m-30) cc_final: 0.7461 (m-30) REVERT: B 904 TYR cc_start: 0.7697 (m-10) cc_final: 0.6642 (m-10) REVERT: B 1084 ASP cc_start: 0.7723 (t70) cc_final: 0.7210 (t0) outliers start: 12 outliers final: 8 residues processed: 198 average time/residue: 0.3108 time to fit residues: 103.9124 Evaluate side-chains 182 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 174 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 235 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 283 optimal weight: 3.9990 chunk 306 optimal weight: 4.9990 chunk 252 optimal weight: 10.0000 chunk 281 optimal weight: 0.0980 chunk 96 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 613 GLN A 675 GLN B 239 GLN B 437 ASN B 487 ASN B 955 ASN B1010 GLN C 134 GLN C 409 GLN C 564 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25338 Z= 0.268 Angle : 0.538 9.041 34470 Z= 0.281 Chirality : 0.045 0.248 3996 Planarity : 0.004 0.048 4425 Dihedral : 6.027 53.766 3909 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.16 % Favored : 94.81 % Rotamer: Outliers : 0.92 % Allowed : 8.91 % Favored : 90.17 % 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: -0.82 (0.15), residues: 3081 helix: 1.51 (0.20), residues: 699 sheet: -0.29 (0.20), residues: 634 loop : -1.57 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 64 HIS 0.005 0.001 HIS A1064 PHE 0.026 0.002 PHE A 906 TYR 0.012 0.001 TYR C 204 ARG 0.003 0.000 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 181 time to evaluate : 2.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 979 ASP cc_start: 0.7857 (m-30) cc_final: 0.7495 (m-30) REVERT: B 388 ASN cc_start: 0.8831 (t0) cc_final: 0.8214 (m110) REVERT: B 437 ASN cc_start: 0.5384 (OUTLIER) cc_final: 0.5095 (t0) REVERT: B 904 TYR cc_start: 0.7811 (m-10) cc_final: 0.6822 (m-10) REVERT: B 1138 TYR cc_start: 0.8348 (t80) cc_final: 0.8044 (t80) REVERT: C 140 PHE cc_start: 0.6318 (p90) cc_final: 0.5943 (p90) outliers start: 25 outliers final: 18 residues processed: 195 average time/residue: 0.3271 time to fit residues: 108.7409 Evaluate side-chains 190 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 171 time to evaluate : 2.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 6.9990 chunk 213 optimal weight: 0.8980 chunk 147 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 284 optimal weight: 1.9990 chunk 301 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 269 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 314 GLN A 613 GLN A 675 GLN B 239 GLN B 955 ASN B1010 GLN C 66 HIS C 321 GLN C 409 GLN C 853 GLN C 913 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25338 Z= 0.225 Angle : 0.511 8.675 34470 Z= 0.268 Chirality : 0.044 0.242 3996 Planarity : 0.004 0.050 4425 Dihedral : 5.805 53.921 3909 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.77 % Favored : 95.20 % Rotamer: Outliers : 1.33 % Allowed : 10.87 % Favored : 87.81 % 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: -0.70 (0.15), residues: 3081 helix: 1.76 (0.20), residues: 698 sheet: -0.33 (0.20), residues: 640 loop : -1.52 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 64 HIS 0.004 0.001 HIS A1064 PHE 0.025 0.001 PHE B 400 TYR 0.020 0.001 TYR B 170 ARG 0.004 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 185 time to evaluate : 2.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6543 (m-70) cc_final: 0.6181 (m170) REVERT: A 364 ASP cc_start: 0.5873 (t70) cc_final: 0.4523 (p0) REVERT: A 979 ASP cc_start: 0.7841 (m-30) cc_final: 0.7489 (m-30) REVERT: B 170 TYR cc_start: 0.7105 (t80) cc_final: 0.6587 (t80) REVERT: B 388 ASN cc_start: 0.8822 (t0) cc_final: 0.8199 (m110) REVERT: B 904 TYR cc_start: 0.7806 (m-10) cc_final: 0.6787 (m-10) REVERT: C 140 PHE cc_start: 0.6303 (p90) cc_final: 0.5939 (p90) REVERT: C 226 LEU cc_start: 0.8626 (tt) cc_final: 0.8345 (tt) REVERT: C 339 HIS cc_start: 0.4295 (OUTLIER) cc_final: 0.3724 (p90) outliers start: 36 outliers final: 25 residues processed: 205 average time/residue: 0.3187 time to fit residues: 109.8594 Evaluate side-chains 205 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 179 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 10.0000 chunk 171 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 224 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 257 optimal weight: 6.9990 chunk 208 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 270 optimal weight: 0.8980 chunk 76 optimal weight: 0.4980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 613 GLN A 675 GLN B 644 GLN B 955 ASN C 409 GLN C 853 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 25338 Z= 0.325 Angle : 0.567 9.195 34470 Z= 0.296 Chirality : 0.046 0.254 3996 Planarity : 0.004 0.046 4425 Dihedral : 5.936 57.609 3909 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.07 % Favored : 93.90 % Rotamer: Outliers : 1.62 % Allowed : 11.75 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.15), residues: 3081 helix: 1.59 (0.20), residues: 710 sheet: -0.35 (0.20), residues: 646 loop : -1.60 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 64 HIS 0.006 0.001 HIS A1064 PHE 0.024 0.002 PHE A 906 TYR 0.019 0.001 TYR B 170 ARG 0.003 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 184 time to evaluate : 2.609 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6422 (m-70) cc_final: 0.6050 (m170) REVERT: A 364 ASP cc_start: 0.6232 (t70) cc_final: 0.5679 (m-30) REVERT: A 424 LYS cc_start: 0.7272 (tptt) cc_final: 0.7007 (tptp) REVERT: A 902 MET cc_start: 0.8310 (mmt) cc_final: 0.8091 (mmt) REVERT: A 979 ASP cc_start: 0.7864 (m-30) cc_final: 0.7503 (m-30) REVERT: B 170 TYR cc_start: 0.7056 (t80) cc_final: 0.6574 (t80) REVERT: B 388 ASN cc_start: 0.8880 (t0) cc_final: 0.8264 (m110) REVERT: B 437 ASN cc_start: 0.5689 (p0) cc_final: 0.5443 (p0) REVERT: B 663 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.8144 (t0) REVERT: B 904 TYR cc_start: 0.7812 (m-10) cc_final: 0.6851 (m-10) REVERT: C 140 PHE cc_start: 0.6373 (p90) cc_final: 0.6000 (p90) REVERT: C 339 HIS cc_start: 0.4325 (OUTLIER) cc_final: 0.3554 (p-80) REVERT: C 585 LEU cc_start: 0.5230 (OUTLIER) cc_final: 0.4986 (pp) outliers start: 44 outliers final: 32 residues processed: 214 average time/residue: 0.3205 time to fit residues: 114.6786 Evaluate side-chains 207 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 172 time to evaluate : 2.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 4.9990 chunk 271 optimal weight: 0.9990 chunk 59 optimal weight: 0.0060 chunk 177 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 301 optimal weight: 1.9990 chunk 250 optimal weight: 0.0980 chunk 139 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 314 GLN A 613 GLN A 675 GLN B 762 GLN B 955 ASN C 49 HIS C 853 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25338 Z= 0.147 Angle : 0.483 8.508 34470 Z= 0.252 Chirality : 0.044 0.238 3996 Planarity : 0.003 0.047 4425 Dihedral : 5.525 54.254 3909 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.45 % Favored : 95.52 % Rotamer: Outliers : 1.62 % Allowed : 12.82 % Favored : 85.56 % 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: -0.52 (0.15), residues: 3081 helix: 2.14 (0.20), residues: 690 sheet: -0.23 (0.20), residues: 636 loop : -1.49 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 64 HIS 0.004 0.001 HIS A 207 PHE 0.016 0.001 PHE B 400 TYR 0.017 0.001 TYR B 170 ARG 0.003 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 186 time to evaluate : 2.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6289 (mp) REVERT: A 277 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8169 (mt) REVERT: A 364 ASP cc_start: 0.6285 (t70) cc_final: 0.5679 (m-30) REVERT: A 424 LYS cc_start: 0.7243 (tptt) cc_final: 0.7020 (tptp) REVERT: A 979 ASP cc_start: 0.7802 (m-30) cc_final: 0.7440 (m-30) REVERT: B 170 TYR cc_start: 0.6889 (t80) cc_final: 0.6422 (t80) REVERT: B 388 ASN cc_start: 0.8846 (t0) cc_final: 0.8223 (m110) REVERT: B 437 ASN cc_start: 0.5684 (p0) cc_final: 0.5142 (t0) REVERT: B 904 TYR cc_start: 0.7773 (m-10) cc_final: 0.6733 (m-10) REVERT: C 84 LEU cc_start: 0.7563 (mp) cc_final: 0.7218 (mp) REVERT: C 140 PHE cc_start: 0.6379 (p90) cc_final: 0.5981 (p90) REVERT: C 339 HIS cc_start: 0.4336 (OUTLIER) cc_final: 0.3669 (p90) REVERT: C 357 ARG cc_start: 0.7890 (mtp180) cc_final: 0.7413 (mtp180) REVERT: C 585 LEU cc_start: 0.5484 (OUTLIER) cc_final: 0.5279 (pp) REVERT: C 646 ARG cc_start: 0.7944 (tmt-80) cc_final: 0.7622 (tmt-80) outliers start: 44 outliers final: 28 residues processed: 218 average time/residue: 0.3255 time to fit residues: 117.6409 Evaluate side-chains 211 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 179 time to evaluate : 2.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 882 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 171 optimal weight: 1.9990 chunk 220 optimal weight: 0.1980 chunk 170 optimal weight: 0.9990 chunk 254 optimal weight: 6.9990 chunk 168 optimal weight: 0.2980 chunk 300 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 138 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN B 239 GLN B 955 ASN C 853 GLN C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25338 Z= 0.142 Angle : 0.477 8.866 34470 Z= 0.248 Chirality : 0.043 0.238 3996 Planarity : 0.003 0.047 4425 Dihedral : 5.223 53.764 3909 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.93 % Favored : 95.03 % Rotamer: Outliers : 1.33 % Allowed : 13.44 % Favored : 85.23 % 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: -0.40 (0.15), residues: 3081 helix: 2.21 (0.20), residues: 703 sheet: -0.16 (0.20), residues: 631 loop : -1.42 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 64 HIS 0.004 0.001 HIS B 207 PHE 0.016 0.001 PHE B 201 TYR 0.015 0.001 TYR B 170 ARG 0.003 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 188 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.6278 (mp) REVERT: A 277 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8122 (mt) REVERT: A 424 LYS cc_start: 0.7248 (tptt) cc_final: 0.7027 (tptp) REVERT: A 979 ASP cc_start: 0.7822 (m-30) cc_final: 0.7475 (m-30) REVERT: B 170 TYR cc_start: 0.6753 (t80) cc_final: 0.6294 (t80) REVERT: B 388 ASN cc_start: 0.8817 (t0) cc_final: 0.8179 (m110) REVERT: B 437 ASN cc_start: 0.5569 (p0) cc_final: 0.5081 (t0) REVERT: B 904 TYR cc_start: 0.7787 (m-10) cc_final: 0.6712 (m-10) REVERT: C 84 LEU cc_start: 0.7553 (mp) cc_final: 0.7142 (mp) REVERT: C 128 ILE cc_start: 0.7453 (mt) cc_final: 0.7196 (mt) REVERT: C 140 PHE cc_start: 0.6385 (p90) cc_final: 0.5974 (p90) REVERT: C 339 HIS cc_start: 0.4350 (OUTLIER) cc_final: 0.3701 (p90) REVERT: C 357 ARG cc_start: 0.7873 (mtp180) cc_final: 0.7464 (mtp180) REVERT: C 394 ASN cc_start: 0.7438 (m-40) cc_final: 0.7084 (m110) REVERT: C 646 ARG cc_start: 0.7880 (tmt-80) cc_final: 0.7533 (tmt-80) outliers start: 36 outliers final: 27 residues processed: 214 average time/residue: 0.3160 time to fit residues: 112.7815 Evaluate side-chains 208 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 178 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 59 optimal weight: 0.0870 chunk 58 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 236 optimal weight: 0.5980 overall best weight: 1.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN B 239 GLN B 955 ASN C 853 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25338 Z= 0.256 Angle : 0.536 9.249 34470 Z= 0.278 Chirality : 0.045 0.243 3996 Planarity : 0.004 0.048 4425 Dihedral : 5.463 56.211 3909 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.39 % Favored : 94.58 % Rotamer: Outliers : 1.40 % Allowed : 13.78 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.15), residues: 3081 helix: 2.06 (0.20), residues: 698 sheet: -0.20 (0.20), residues: 640 loop : -1.51 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 64 HIS 0.006 0.001 HIS A1064 PHE 0.018 0.001 PHE B 400 TYR 0.015 0.001 TYR B 170 ARG 0.004 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 174 time to evaluate : 2.985 Fit side-chains revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.6433 (mp) REVERT: A 190 ARG cc_start: 0.7400 (mmt-90) cc_final: 0.7031 (mmt180) REVERT: A 277 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8186 (mt) REVERT: A 424 LYS cc_start: 0.7253 (tptt) cc_final: 0.6957 (tptp) REVERT: A 514 SER cc_start: 0.7700 (OUTLIER) cc_final: 0.7413 (p) REVERT: A 979 ASP cc_start: 0.7847 (m-30) cc_final: 0.7492 (m-30) REVERT: B 170 TYR cc_start: 0.6745 (t80) cc_final: 0.6319 (t80) REVERT: B 388 ASN cc_start: 0.8869 (t0) cc_final: 0.8256 (m110) REVERT: B 904 TYR cc_start: 0.7806 (m-10) cc_final: 0.6745 (m-10) REVERT: C 84 LEU cc_start: 0.7659 (mp) cc_final: 0.7301 (mp) REVERT: C 128 ILE cc_start: 0.7577 (mt) cc_final: 0.7339 (mt) REVERT: C 140 PHE cc_start: 0.6374 (p90) cc_final: 0.5967 (p90) REVERT: C 339 HIS cc_start: 0.4279 (OUTLIER) cc_final: 0.3627 (p90) REVERT: C 569 ILE cc_start: 0.6133 (OUTLIER) cc_final: 0.5435 (mp) REVERT: C 646 ARG cc_start: 0.8015 (tmt-80) cc_final: 0.7647 (tmt-80) outliers start: 38 outliers final: 28 residues processed: 202 average time/residue: 0.3213 time to fit residues: 107.9797 Evaluate side-chains 205 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 172 time to evaluate : 2.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 1.9990 chunk 288 optimal weight: 1.9990 chunk 262 optimal weight: 0.2980 chunk 280 optimal weight: 0.9990 chunk 168 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 220 optimal weight: 0.2980 chunk 85 optimal weight: 2.9990 chunk 253 optimal weight: 7.9990 chunk 265 optimal weight: 2.9990 chunk 279 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN B 955 ASN C 394 ASN C 853 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25338 Z= 0.176 Angle : 0.494 8.850 34470 Z= 0.257 Chirality : 0.044 0.238 3996 Planarity : 0.003 0.049 4425 Dihedral : 5.297 54.103 3909 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.71 % Favored : 95.26 % Rotamer: Outliers : 1.40 % Allowed : 13.78 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 3081 helix: 2.19 (0.20), residues: 696 sheet: -0.14 (0.20), residues: 631 loop : -1.46 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 64 HIS 0.004 0.001 HIS A1064 PHE 0.015 0.001 PHE B 201 TYR 0.015 0.001 TYR B 170 ARG 0.003 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 177 time to evaluate : 2.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6264 (mp) REVERT: A 190 ARG cc_start: 0.7384 (mmt-90) cc_final: 0.7170 (mpt180) REVERT: A 277 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8180 (mt) REVERT: A 424 LYS cc_start: 0.7267 (tptt) cc_final: 0.6978 (tptp) REVERT: A 514 SER cc_start: 0.7706 (OUTLIER) cc_final: 0.7469 (p) REVERT: A 564 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7168 (mm110) REVERT: A 979 ASP cc_start: 0.7787 (m-30) cc_final: 0.7431 (m-30) REVERT: B 170 TYR cc_start: 0.6757 (t80) cc_final: 0.6338 (t80) REVERT: B 388 ASN cc_start: 0.8836 (t0) cc_final: 0.8052 (m-40) REVERT: B 586 ASP cc_start: 0.7329 (m-30) cc_final: 0.7084 (m-30) REVERT: B 904 TYR cc_start: 0.7802 (m-10) cc_final: 0.6733 (m-10) REVERT: C 84 LEU cc_start: 0.7551 (mp) cc_final: 0.7155 (mp) REVERT: C 128 ILE cc_start: 0.7530 (mt) cc_final: 0.7317 (mt) REVERT: C 140 PHE cc_start: 0.6389 (p90) cc_final: 0.5958 (p90) REVERT: C 339 HIS cc_start: 0.4228 (OUTLIER) cc_final: 0.3526 (p90) REVERT: C 357 ARG cc_start: 0.8138 (mtp180) cc_final: 0.7638 (mtp180) REVERT: C 394 ASN cc_start: 0.7470 (m-40) cc_final: 0.7096 (m110) REVERT: C 569 ILE cc_start: 0.6020 (OUTLIER) cc_final: 0.5345 (mp) REVERT: C 646 ARG cc_start: 0.7961 (tmt-80) cc_final: 0.7617 (tmt-80) outliers start: 38 outliers final: 29 residues processed: 203 average time/residue: 0.3192 time to fit residues: 107.7995 Evaluate side-chains 208 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 173 time to evaluate : 2.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 0.9990 chunk 296 optimal weight: 3.9990 chunk 180 optimal weight: 0.5980 chunk 140 optimal weight: 0.0000 chunk 205 optimal weight: 4.9990 chunk 310 optimal weight: 2.9990 chunk 286 optimal weight: 3.9990 chunk 247 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 191 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN B 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25338 Z= 0.227 Angle : 0.517 9.616 34470 Z= 0.268 Chirality : 0.045 0.244 3996 Planarity : 0.004 0.052 4425 Dihedral : 5.357 55.728 3909 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.16 % Favored : 94.81 % Rotamer: Outliers : 1.36 % Allowed : 13.89 % Favored : 84.75 % 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: -0.50 (0.15), residues: 3081 helix: 2.11 (0.20), residues: 696 sheet: -0.14 (0.20), residues: 631 loop : -1.50 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 64 HIS 0.005 0.001 HIS A1064 PHE 0.036 0.001 PHE B 400 TYR 0.015 0.001 TYR C1067 ARG 0.003 0.000 ARG C 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 170 time to evaluate : 2.715 Fit side-chains REVERT: A 118 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6398 (mp) REVERT: A 277 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8201 (mt) REVERT: A 424 LYS cc_start: 0.7275 (tptt) cc_final: 0.6977 (tptp) REVERT: A 514 SER cc_start: 0.7810 (OUTLIER) cc_final: 0.7556 (p) REVERT: A 979 ASP cc_start: 0.7771 (m-30) cc_final: 0.7402 (m-30) REVERT: B 170 TYR cc_start: 0.6766 (t80) cc_final: 0.6357 (t80) REVERT: B 388 ASN cc_start: 0.8842 (t0) cc_final: 0.8061 (m-40) REVERT: B 586 ASP cc_start: 0.7368 (m-30) cc_final: 0.7084 (m-30) REVERT: B 904 TYR cc_start: 0.7797 (m-10) cc_final: 0.6727 (m-10) REVERT: B 1043 CYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7289 (p) REVERT: C 84 LEU cc_start: 0.7607 (mp) cc_final: 0.7233 (mp) REVERT: C 128 ILE cc_start: 0.7498 (mt) cc_final: 0.7260 (mt) REVERT: C 140 PHE cc_start: 0.6413 (p90) cc_final: 0.5980 (p90) REVERT: C 339 HIS cc_start: 0.4215 (OUTLIER) cc_final: 0.3518 (p90) REVERT: C 357 ARG cc_start: 0.8080 (mtp180) cc_final: 0.7558 (mtp180) REVERT: C 394 ASN cc_start: 0.7378 (m-40) cc_final: 0.6918 (m110) REVERT: C 569 ILE cc_start: 0.6030 (OUTLIER) cc_final: 0.5359 (mp) REVERT: C 646 ARG cc_start: 0.7937 (tmt-80) cc_final: 0.7605 (tmt-80) outliers start: 37 outliers final: 30 residues processed: 197 average time/residue: 0.3228 time to fit residues: 106.9225 Evaluate side-chains 206 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 170 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 2.9990 chunk 263 optimal weight: 4.9990 chunk 75 optimal weight: 0.0030 chunk 228 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 247 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 chunk 254 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 45 optimal weight: 0.1980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 207 HIS ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN B 955 ASN C 853 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.201284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.127075 restraints weight = 29945.135| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.93 r_work: 0.3285 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25338 Z= 0.133 Angle : 0.471 9.073 34470 Z= 0.245 Chirality : 0.043 0.230 3996 Planarity : 0.003 0.052 4425 Dihedral : 5.064 53.922 3909 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.48 % Favored : 95.49 % Rotamer: Outliers : 1.29 % Allowed : 14.00 % Favored : 84.71 % 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: -0.33 (0.15), residues: 3081 helix: 2.35 (0.20), residues: 698 sheet: -0.04 (0.21), residues: 610 loop : -1.43 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 64 HIS 0.003 0.001 HIS B 207 PHE 0.028 0.001 PHE B 400 TYR 0.014 0.001 TYR B 170 ARG 0.002 0.000 ARG B 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4529.07 seconds wall clock time: 82 minutes 14.80 seconds (4934.80 seconds total)