Starting phenix.real_space_refine on Fri Aug 9 05:20:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0v_42871/08_2024/8v0v_42871.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0v_42871/08_2024/8v0v_42871.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/8v0v_42871/08_2024/8v0v_42871.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0v_42871/08_2024/8v0v_42871.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0v_42871/08_2024/8v0v_42871.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0v_42871/08_2024/8v0v_42871.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= 0.054 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 15985 2.51 5 N 4115 2.21 5 O 4837 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 53": "OD1" <-> "OD2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 586": "OD1" <-> "OD2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 568": "OD1" <-> "OD2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25051 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 8159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8159 Classifications: {'peptide': 1044} Link IDs: {'PTRANS': 52, 'TRANS': 991} Chain breaks: 6 Chain: "B" Number of atoms: 8159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8159 Classifications: {'peptide': 1044} Link IDs: {'PTRANS': 52, 'TRANS': 991} Chain breaks: 6 Chain: "A" Number of atoms: 8159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8159 Classifications: {'peptide': 1044} Link IDs: {'PTRANS': 52, 'TRANS': 991} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 13.31, per 1000 atoms: 0.53 Number of scatterers: 25051 At special positions: 0 Unit cell: (137.16, 131.76, 180.36, 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 4837 8.00 N 4115 7.00 C 15985 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS 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=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 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=2.05 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=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS 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 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=2.02 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=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS 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=2.04 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " 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 234 " " NAG A1310 " - " 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 234 " " NAG B1310 " - " 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 " " NAG D 1 " - " ASN C 717 " " NAG E 1 " - " ASN C1098 " " NAG F 1 " - " ASN B 717 " " NAG G 1 " - " ASN B1098 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A1098 " Time building additional restraints: 9.24 Conformation dependent library (CDL) restraints added in 4.7 seconds 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5880 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 50 sheets defined 25.1% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.39 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.049A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.638A pdb=" N PHE C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 4.025A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.391A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 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 782 removed outlier: 3.612A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.554A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 842 removed outlier: 3.556A pdb=" N GLY C 842 " --> pdb=" O GLY C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.622A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.806A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.965A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 4.703A 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: 3.506A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1140 through 1150 removed outlier: 4.505A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.630A pdb=" N ASN B 343 " --> pdb=" O HIS B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.208A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.582A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) 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 760 through 783 removed outlier: 3.791A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 836 through 842 removed outlier: 3.751A pdb=" N GLY B 842 " --> pdb=" O GLY B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.683A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 918 removed outlier: 4.020A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.964A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 4.655A 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 Processing helix chain 'B' and resid 985 through 1032 Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.314A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.824A pdb=" N ASN A 343 " --> pdb=" O HIS A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.927A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.730A 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: 3.820A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 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: 3.640A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.585A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 842 Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.599A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.618A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.080A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 Processing sheet with id=AA1, first strand: chain 'C' and resid 25 through 30 removed outlier: 7.544A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.007A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 104 removed outlier: 4.063A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 120 through 121 removed outlier: 3.978A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.098A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AA9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.514A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'C' and resid 565 through 566 removed outlier: 6.982A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.988A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 701 through 703 Processing sheet with id=AB6, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.524A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.998A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.535A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 787 through 788 Processing sheet with id=AC1, first strand: chain 'C' and resid 1081 through 1083 Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.540A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.495A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.008A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC6, first strand: chain 'B' and resid 128 through 129 removed outlier: 3.819A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 140 through 141 Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.431A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.062A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.774A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 660 removed outlier: 3.503A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.538A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.972A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.598A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD9, first strand: chain 'B' and resid 1081 through 1083 Processing sheet with id=AE1, first strand: chain 'A' and resid 25 through 30 removed outlier: 8.215A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.922A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.855A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AE5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.367A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AE7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.695A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.071A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AF2, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.007A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.550A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AF5, first strand: chain 'A' and resid 1094 through 1097 929 hydrogen bonds defined for protein. 2562 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: 11.08 Time building geometry restraints manager: 10.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7972 1.35 - 1.47: 6614 1.47 - 1.60: 10885 1.60 - 1.73: 0 1.73 - 1.85: 141 Bond restraints: 25612 Sorted by residual: bond pdb=" C ALA A1056 " pdb=" N PRO A1057 " ideal model delta sigma weight residual 1.332 1.361 -0.029 1.12e-02 7.97e+03 6.90e+00 bond pdb=" C GLN B1142 " pdb=" N PRO B1143 " ideal model delta sigma weight residual 1.337 1.369 -0.032 1.24e-02 6.50e+03 6.77e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.95e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 4.97e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.88e+00 ... (remaining 25607 not shown) Histogram of bond angle deviations from ideal: 93.49 - 101.63: 30 101.63 - 109.78: 3616 109.78 - 117.92: 15627 117.92 - 126.06: 15259 126.06 - 134.21: 306 Bond angle restraints: 34838 Sorted by residual: angle pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " ideal model delta sigma weight residual 114.40 129.41 -15.01 2.30e+00 1.89e-01 4.26e+01 angle pdb=" CG1 ILE C 105 " pdb=" CB ILE C 105 " pdb=" CG2 ILE C 105 " ideal model delta sigma weight residual 110.70 93.49 17.21 3.00e+00 1.11e-01 3.29e+01 angle pdb=" CA CYS B 525 " pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " ideal model delta sigma weight residual 114.40 127.31 -12.91 2.30e+00 1.89e-01 3.15e+01 angle pdb=" CA CYS B 391 " pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " ideal model delta sigma weight residual 114.40 127.15 -12.75 2.30e+00 1.89e-01 3.07e+01 angle pdb=" N ASN C 122 " pdb=" CA ASN C 122 " pdb=" C ASN C 122 " ideal model delta sigma weight residual 112.59 106.41 6.18 1.22e+00 6.72e-01 2.56e+01 ... (remaining 34833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 14145 18.05 - 36.11: 1383 36.11 - 54.16: 213 54.16 - 72.22: 58 72.22 - 90.27: 32 Dihedral angle restraints: 15831 sinusoidal: 6699 harmonic: 9132 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual -86.00 -13.99 -72.01 1 1.00e+01 1.00e-02 6.63e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual 93.00 22.11 70.89 1 1.00e+01 1.00e-02 6.46e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual -86.00 -16.29 -69.71 1 1.00e+01 1.00e-02 6.27e+01 ... (remaining 15828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 4040 0.154 - 0.308: 32 0.308 - 0.462: 4 0.462 - 0.616: 1 0.616 - 0.770: 1 Chirality restraints: 4078 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" CB ILE B 101 " pdb=" CA ILE B 101 " pdb=" CG1 ILE B 101 " pdb=" CG2 ILE B 101 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.52 2.00e-01 2.50e+01 6.65e+00 chirality pdb=" CB ILE C 105 " pdb=" CA ILE C 105 " pdb=" CG1 ILE C 105 " pdb=" CG2 ILE C 105 " both_signs ideal model delta sigma weight residual False 2.64 3.06 -0.41 2.00e-01 2.50e+01 4.23e+00 ... (remaining 4075 not shown) Planarity restraints: 4486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 224 " -0.070 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO B 225 " 0.185 5.00e-02 4.00e+02 pdb=" CA PRO B 225 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 225 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 105 " 0.021 2.00e-02 2.50e+03 4.17e-02 1.73e+01 pdb=" C ILE C 105 " -0.072 2.00e-02 2.50e+03 pdb=" O ILE C 105 " 0.027 2.00e-02 2.50e+03 pdb=" N PHE C 106 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 126 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C VAL A 126 " 0.067 2.00e-02 2.50e+03 pdb=" O VAL A 126 " -0.026 2.00e-02 2.50e+03 pdb=" N VAL A 127 " -0.022 2.00e-02 2.50e+03 ... (remaining 4483 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6588 2.81 - 3.33: 19978 3.33 - 3.85: 39864 3.85 - 4.38: 44794 4.38 - 4.90: 81296 Nonbonded interactions: 192520 Sorted by model distance: nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.286 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.331 3.040 nonbonded pdb=" O THR B 393 " pdb=" OG1 THR B 523 " model vdw 2.336 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.344 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.347 3.040 ... (remaining 192515 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 24 through 1150 or resid 1301 through 1309)) selection = (chain 'B' and (resid 24 through 1150 or resid 1301 through 1309)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 1.730 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: 0.010 Extract box with map and model: 1.050 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 67.110 Find NCS groups from input model: 1.580 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 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 : 0.005 0.058 25612 Z= 0.324 Angle : 0.808 17.208 34838 Z= 0.424 Chirality : 0.056 0.770 4078 Planarity : 0.006 0.107 4451 Dihedral : 14.517 90.274 9828 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.08 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.13), residues: 3090 helix: -0.61 (0.17), residues: 688 sheet: 0.28 (0.19), residues: 654 loop : -1.79 (0.13), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 436 HIS 0.006 0.001 HIS C 207 PHE 0.040 0.002 PHE B 906 TYR 0.038 0.002 TYR C 170 ARG 0.011 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 2.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 568 ASP cc_start: 0.7254 (t70) cc_final: 0.6944 (t0) REVERT: B 586 ASP cc_start: 0.8404 (m-30) cc_final: 0.8056 (m-30) REVERT: A 237 ARG cc_start: 0.7119 (mtp-110) cc_final: 0.6896 (mtp-110) REVERT: A 394 ASN cc_start: 0.6402 (m-40) cc_final: 0.6030 (m-40) REVERT: A 396 TYR cc_start: 0.8494 (m-80) cc_final: 0.8190 (m-10) REVERT: A 440 LYS cc_start: 0.8734 (ttpp) cc_final: 0.8403 (ttmt) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.3608 time to fit residues: 138.2946 Evaluate side-chains 196 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 2.644 ------------------------------------------------------------------------------- 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: 3.9990 chunk 236 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 159 optimal weight: 0.3980 chunk 126 optimal weight: 0.9990 chunk 244 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 chunk 182 optimal weight: 0.9980 chunk 283 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS B 196 ASN ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 613 GLN B 675 GLN A 207 HIS ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 901 GLN A 955 ASN A1083 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25612 Z= 0.164 Angle : 0.522 7.674 34838 Z= 0.273 Chirality : 0.043 0.238 4078 Planarity : 0.004 0.069 4451 Dihedral : 5.755 53.855 4212 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.69 % Favored : 96.21 % Rotamer: Outliers : 0.66 % Allowed : 5.76 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3090 helix: 0.90 (0.20), residues: 704 sheet: 0.46 (0.20), residues: 642 loop : -1.58 (0.13), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.004 0.001 HIS C 207 PHE 0.025 0.001 PHE C 168 TYR 0.020 0.001 TYR C 170 ARG 0.006 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 214 time to evaluate : 2.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 529 LYS cc_start: 0.8702 (mmmt) cc_final: 0.8484 (mmtt) REVERT: A 237 ARG cc_start: 0.7051 (mtp-110) cc_final: 0.6823 (mtp-110) REVERT: A 394 ASN cc_start: 0.6795 (m-40) cc_final: 0.6420 (m-40) REVERT: A 440 LYS cc_start: 0.8731 (ttpp) cc_final: 0.8474 (ttmt) REVERT: A 923 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8275 (mp) REVERT: A 1050 MET cc_start: 0.8304 (ptm) cc_final: 0.7982 (ptm) outliers start: 18 outliers final: 14 residues processed: 225 average time/residue: 0.3498 time to fit residues: 127.5935 Evaluate side-chains 215 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 200 time to evaluate : 2.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 833 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 235 optimal weight: 8.9990 chunk 192 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 283 optimal weight: 0.9980 chunk 306 optimal weight: 0.3980 chunk 252 optimal weight: 0.7980 chunk 281 optimal weight: 20.0000 chunk 96 optimal weight: 0.9990 chunk 227 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 360 ASN ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN A 207 HIS ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 675 GLN A 907 ASN A 955 ASN A1083 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25612 Z= 0.170 Angle : 0.506 8.331 34838 Z= 0.263 Chirality : 0.043 0.244 4078 Planarity : 0.004 0.059 4451 Dihedral : 5.263 53.761 4212 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.05 % Favored : 95.86 % Rotamer: Outliers : 1.03 % Allowed : 7.67 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3090 helix: 1.57 (0.20), residues: 691 sheet: 0.58 (0.20), residues: 618 loop : -1.50 (0.13), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 64 HIS 0.004 0.001 HIS C 207 PHE 0.026 0.001 PHE C 168 TYR 0.019 0.001 TYR A1067 ARG 0.004 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 202 time to evaluate : 2.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 237 ARG cc_start: 0.6878 (mtp-110) cc_final: 0.6616 (mtp-110) REVERT: B 501 TYR cc_start: 0.7331 (m-10) cc_final: 0.7040 (m-10) REVERT: A 394 ASN cc_start: 0.6885 (m-40) cc_final: 0.6549 (m-40) REVERT: A 440 LYS cc_start: 0.8731 (ttpp) cc_final: 0.8463 (ttmt) REVERT: A 1050 MET cc_start: 0.8450 (ptm) cc_final: 0.8167 (ptm) outliers start: 28 outliers final: 20 residues processed: 221 average time/residue: 0.3560 time to fit residues: 127.3707 Evaluate side-chains 215 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 195 time to evaluate : 2.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 833 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 4.9990 chunk 213 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 284 optimal weight: 2.9990 chunk 301 optimal weight: 0.8980 chunk 148 optimal weight: 0.0370 chunk 269 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B1106 GLN A 207 HIS ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25612 Z= 0.190 Angle : 0.510 10.349 34838 Z= 0.264 Chirality : 0.043 0.249 4078 Planarity : 0.004 0.056 4451 Dihedral : 5.094 53.689 4212 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.01 % Favored : 95.89 % Rotamer: Outliers : 1.36 % Allowed : 9.14 % Favored : 89.50 % 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: -0.35 (0.15), residues: 3090 helix: 1.78 (0.20), residues: 691 sheet: 0.57 (0.20), residues: 642 loop : -1.46 (0.13), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.004 0.001 HIS A1088 PHE 0.025 0.001 PHE C 168 TYR 0.018 0.001 TYR A1067 ARG 0.007 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 211 time to evaluate : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 LYS cc_start: 0.7242 (ttmm) cc_final: 0.6561 (pttt) REVERT: C 529 LYS cc_start: 0.8707 (mmmt) cc_final: 0.8082 (mmtt) REVERT: B 237 ARG cc_start: 0.6921 (mtp-110) cc_final: 0.6697 (mtp-110) REVERT: B 501 TYR cc_start: 0.7506 (m-10) cc_final: 0.7161 (m-10) REVERT: B 960 ASN cc_start: 0.7416 (m-40) cc_final: 0.7121 (t0) REVERT: A 394 ASN cc_start: 0.6980 (m-40) cc_final: 0.6604 (m-40) REVERT: A 1050 MET cc_start: 0.8516 (ptm) cc_final: 0.8227 (ptm) outliers start: 37 outliers final: 25 residues processed: 239 average time/residue: 0.3543 time to fit residues: 137.0275 Evaluate side-chains 221 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 196 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 833 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 224 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 257 optimal weight: 0.9980 chunk 208 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 270 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 804 GLN C 965 GLN B 675 GLN ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25612 Z= 0.195 Angle : 0.506 8.736 34838 Z= 0.262 Chirality : 0.044 0.311 4078 Planarity : 0.003 0.055 4451 Dihedral : 5.017 53.874 4212 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.37 % Favored : 95.53 % Rotamer: Outliers : 1.47 % Allowed : 10.32 % Favored : 88.22 % 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: -0.29 (0.15), residues: 3090 helix: 1.79 (0.20), residues: 701 sheet: 0.53 (0.20), residues: 648 loop : -1.39 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.004 0.001 HIS A1083 PHE 0.026 0.001 PHE C 168 TYR 0.017 0.001 TYR A1067 ARG 0.003 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 206 time to evaluate : 2.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 LYS cc_start: 0.7202 (ttmm) cc_final: 0.6483 (pttt) REVERT: C 170 TYR cc_start: 0.7259 (t80) cc_final: 0.7032 (t80) REVERT: C 529 LYS cc_start: 0.8547 (mmmt) cc_final: 0.7900 (mmtt) REVERT: B 237 ARG cc_start: 0.6953 (mtp-110) cc_final: 0.6686 (mtp-110) REVERT: B 501 TYR cc_start: 0.7738 (m-10) cc_final: 0.7400 (m-10) REVERT: B 960 ASN cc_start: 0.7459 (m-40) cc_final: 0.7187 (t0) REVERT: A 394 ASN cc_start: 0.7014 (m-40) cc_final: 0.6616 (m-40) REVERT: A 460 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7379 (mtmm) REVERT: A 564 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7560 (mm-40) REVERT: A 646 ARG cc_start: 0.7406 (tpt-90) cc_final: 0.6697 (tpp80) REVERT: A 1050 MET cc_start: 0.8536 (ptm) cc_final: 0.8277 (ptm) outliers start: 40 outliers final: 29 residues processed: 236 average time/residue: 0.3470 time to fit residues: 132.1101 Evaluate side-chains 228 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 198 time to evaluate : 2.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 833 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 5.9990 chunk 271 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 301 optimal weight: 0.1980 chunk 250 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 99 optimal weight: 0.0980 chunk 158 optimal weight: 0.0030 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 804 GLN B 675 GLN A 207 HIS A 339 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25612 Z= 0.176 Angle : 0.511 12.221 34838 Z= 0.262 Chirality : 0.044 0.486 4078 Planarity : 0.003 0.055 4451 Dihedral : 5.137 54.020 4212 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.14 % Favored : 95.76 % Rotamer: Outliers : 1.65 % Allowed : 10.32 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.15), residues: 3090 helix: 1.89 (0.20), residues: 701 sheet: 0.56 (0.20), residues: 648 loop : -1.37 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS A1083 PHE 0.024 0.001 PHE C 168 TYR 0.018 0.001 TYR B1067 ARG 0.005 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 204 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 LYS cc_start: 0.7195 (ttmm) cc_final: 0.6476 (pttt) REVERT: C 170 TYR cc_start: 0.7349 (t80) cc_final: 0.7040 (t80) REVERT: C 529 LYS cc_start: 0.8533 (mmmt) cc_final: 0.7863 (mmtt) REVERT: B 237 ARG cc_start: 0.6975 (mtp-110) cc_final: 0.6690 (mtp-110) REVERT: B 501 TYR cc_start: 0.7773 (m-10) cc_final: 0.7438 (m-10) REVERT: B 960 ASN cc_start: 0.7476 (m-40) cc_final: 0.7175 (t0) REVERT: A 394 ASN cc_start: 0.6991 (m-40) cc_final: 0.6595 (m-40) REVERT: A 460 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7420 (mtmm) REVERT: A 564 GLN cc_start: 0.7900 (mm-40) cc_final: 0.7538 (mm-40) outliers start: 45 outliers final: 31 residues processed: 238 average time/residue: 0.3541 time to fit residues: 137.0440 Evaluate side-chains 230 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 198 time to evaluate : 2.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 833 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 chunk 254 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 chunk 300 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS B 544 ASN B 675 GLN A 239 GLN A 245 HIS A 409 GLN A 675 GLN A 901 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 25612 Z= 0.331 Angle : 0.592 11.041 34838 Z= 0.305 Chirality : 0.046 0.278 4078 Planarity : 0.004 0.053 4451 Dihedral : 5.562 61.483 4212 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.11 % Favored : 94.79 % Rotamer: Outliers : 1.76 % Allowed : 10.72 % Favored : 87.52 % 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: -0.45 (0.14), residues: 3090 helix: 1.68 (0.20), residues: 697 sheet: 0.36 (0.20), residues: 653 loop : -1.46 (0.13), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.005 0.001 HIS A1058 PHE 0.022 0.002 PHE C 377 TYR 0.020 0.002 TYR C 265 ARG 0.004 0.000 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 212 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 ASP cc_start: 0.7969 (m-30) cc_final: 0.7680 (m-30) REVERT: C 129 LYS cc_start: 0.7216 (ttmm) cc_final: 0.6522 (pttt) REVERT: C 417 ASN cc_start: 0.7738 (m-40) cc_final: 0.7435 (t0) REVERT: C 529 LYS cc_start: 0.8493 (mmmt) cc_final: 0.8285 (mmmt) REVERT: C 578 ASP cc_start: 0.8485 (t0) cc_final: 0.8153 (t0) REVERT: C 690 GLN cc_start: 0.7516 (mm110) cc_final: 0.7250 (mm110) REVERT: C 977 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7797 (mp) REVERT: B 64 TRP cc_start: 0.6936 (t-100) cc_final: 0.6407 (t60) REVERT: B 237 ARG cc_start: 0.7060 (mtp-110) cc_final: 0.6740 (mtp-110) REVERT: B 501 TYR cc_start: 0.7814 (m-10) cc_final: 0.7519 (m-10) REVERT: B 960 ASN cc_start: 0.7619 (m-40) cc_final: 0.7277 (t0) REVERT: B 977 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7857 (mp) REVERT: A 281 GLU cc_start: 0.7543 (pm20) cc_final: 0.7305 (pm20) REVERT: A 389 ASP cc_start: 0.8163 (m-30) cc_final: 0.7948 (m-30) REVERT: A 394 ASN cc_start: 0.7154 (m-40) cc_final: 0.6762 (m-40) REVERT: A 460 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7414 (mtmm) REVERT: A 564 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7532 (mm-40) REVERT: A 646 ARG cc_start: 0.7599 (tpt-90) cc_final: 0.6796 (tpp80) outliers start: 48 outliers final: 39 residues processed: 248 average time/residue: 0.3558 time to fit residues: 142.2858 Evaluate side-chains 245 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 203 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 833 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 chunk 179 optimal weight: 0.4980 chunk 90 optimal weight: 0.8980 chunk 59 optimal weight: 0.2980 chunk 58 optimal weight: 0.5980 chunk 191 optimal weight: 5.9990 chunk 204 optimal weight: 0.6980 chunk 148 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 ASN C 207 HIS B 675 GLN A 207 HIS A 239 GLN A 901 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25612 Z= 0.148 Angle : 0.504 11.414 34838 Z= 0.260 Chirality : 0.043 0.233 4078 Planarity : 0.003 0.055 4451 Dihedral : 5.172 55.104 4212 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.79 % Favored : 96.12 % Rotamer: Outliers : 1.40 % Allowed : 11.67 % Favored : 86.93 % 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: -0.19 (0.15), residues: 3090 helix: 2.12 (0.20), residues: 689 sheet: 0.48 (0.20), residues: 648 loop : -1.37 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.002 0.000 HIS B 66 PHE 0.029 0.001 PHE C 168 TYR 0.017 0.001 TYR A1067 ARG 0.006 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 202 time to evaluate : 2.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 ASP cc_start: 0.7943 (m-30) cc_final: 0.7641 (m-30) REVERT: C 129 LYS cc_start: 0.7131 (ttmm) cc_final: 0.6399 (pttt) REVERT: C 171 VAL cc_start: 0.8570 (t) cc_final: 0.8150 (m) REVERT: C 529 LYS cc_start: 0.8444 (mmmt) cc_final: 0.8134 (mmmt) REVERT: C 578 ASP cc_start: 0.8442 (t0) cc_final: 0.8171 (t0) REVERT: B 237 ARG cc_start: 0.6977 (mtp-110) cc_final: 0.6691 (mtp-110) REVERT: B 501 TYR cc_start: 0.7837 (m-10) cc_final: 0.7476 (m-10) REVERT: B 960 ASN cc_start: 0.7507 (m-40) cc_final: 0.7195 (t0) REVERT: A 281 GLU cc_start: 0.7536 (pm20) cc_final: 0.7299 (pm20) REVERT: A 389 ASP cc_start: 0.8122 (m-30) cc_final: 0.7869 (m-30) REVERT: A 394 ASN cc_start: 0.7058 (m-40) cc_final: 0.6632 (m-40) REVERT: A 564 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7522 (mm-40) outliers start: 38 outliers final: 29 residues processed: 232 average time/residue: 0.3397 time to fit residues: 128.2255 Evaluate side-chains 223 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 194 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 833 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 1092 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 0.8980 chunk 288 optimal weight: 2.9990 chunk 262 optimal weight: 0.4980 chunk 280 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 220 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 253 optimal weight: 5.9990 chunk 265 optimal weight: 2.9990 chunk 279 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 ASN C 207 HIS B 675 GLN A 207 HIS A 239 GLN A 675 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25612 Z= 0.199 Angle : 0.523 10.852 34838 Z= 0.268 Chirality : 0.044 0.234 4078 Planarity : 0.003 0.054 4451 Dihedral : 5.060 53.875 4212 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.50 % Favored : 95.40 % Rotamer: Outliers : 1.43 % Allowed : 12.04 % Favored : 86.53 % 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: -0.18 (0.15), residues: 3090 helix: 2.12 (0.20), residues: 689 sheet: 0.45 (0.20), residues: 653 loop : -1.35 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS A1058 PHE 0.025 0.001 PHE C 168 TYR 0.017 0.001 TYR A1067 ARG 0.004 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 194 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 ASP cc_start: 0.7950 (m-30) cc_final: 0.7641 (m-30) REVERT: C 129 LYS cc_start: 0.7121 (ttmm) cc_final: 0.6440 (pttt) REVERT: C 529 LYS cc_start: 0.8443 (mmmt) cc_final: 0.8192 (mmmt) REVERT: C 578 ASP cc_start: 0.8454 (t0) cc_final: 0.8174 (t0) REVERT: B 64 TRP cc_start: 0.6982 (t-100) cc_final: 0.6374 (t60) REVERT: B 237 ARG cc_start: 0.7045 (mtp-110) cc_final: 0.6724 (mtp-110) REVERT: B 501 TYR cc_start: 0.7830 (m-10) cc_final: 0.7467 (m-10) REVERT: B 960 ASN cc_start: 0.7510 (m-40) cc_final: 0.7206 (t0) REVERT: A 281 GLU cc_start: 0.7532 (pm20) cc_final: 0.7292 (pm20) REVERT: A 389 ASP cc_start: 0.8024 (m-30) cc_final: 0.7790 (m-30) REVERT: A 394 ASN cc_start: 0.7153 (m-40) cc_final: 0.6749 (m-40) REVERT: A 564 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7533 (mm-40) outliers start: 39 outliers final: 33 residues processed: 227 average time/residue: 0.3316 time to fit residues: 122.1313 Evaluate side-chains 226 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 193 time to evaluate : 2.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 833 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 1092 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 0.5980 chunk 296 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 chunk 310 optimal weight: 0.8980 chunk 286 optimal weight: 1.9990 chunk 247 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 191 optimal weight: 0.9980 chunk 151 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 ASN C 207 HIS B 675 GLN A 207 HIS A 239 GLN A 675 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25612 Z= 0.174 Angle : 0.508 10.001 34838 Z= 0.260 Chirality : 0.043 0.238 4078 Planarity : 0.003 0.055 4451 Dihedral : 4.875 54.222 4212 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.98 % Favored : 95.92 % Rotamer: Outliers : 1.32 % Allowed : 12.11 % Favored : 86.56 % 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: -0.13 (0.15), residues: 3090 helix: 2.17 (0.20), residues: 689 sheet: 0.46 (0.20), residues: 657 loop : -1.31 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS A1083 PHE 0.026 0.001 PHE C 168 TYR 0.016 0.001 TYR A1067 ARG 0.005 0.000 ARG A 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 192 time to evaluate : 2.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 ASP cc_start: 0.7941 (m-30) cc_final: 0.7631 (m-30) REVERT: C 129 LYS cc_start: 0.7124 (ttmm) cc_final: 0.6424 (pttt) REVERT: C 417 ASN cc_start: 0.7773 (m-40) cc_final: 0.7497 (t0) REVERT: C 529 LYS cc_start: 0.8473 (mmmt) cc_final: 0.8165 (mmmt) REVERT: C 578 ASP cc_start: 0.8444 (t0) cc_final: 0.8168 (t0) REVERT: B 64 TRP cc_start: 0.6961 (t-100) cc_final: 0.6346 (t60) REVERT: B 237 ARG cc_start: 0.7013 (mtp-110) cc_final: 0.6709 (mtp-110) REVERT: B 501 TYR cc_start: 0.7839 (m-10) cc_final: 0.7485 (m-10) REVERT: B 960 ASN cc_start: 0.7500 (m-40) cc_final: 0.7189 (t0) REVERT: A 394 ASN cc_start: 0.7097 (m-40) cc_final: 0.6692 (m-40) REVERT: A 452 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.7025 (pt) REVERT: A 564 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7534 (mm-40) outliers start: 36 outliers final: 33 residues processed: 221 average time/residue: 0.3536 time to fit residues: 128.4650 Evaluate side-chains 223 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 189 time to evaluate : 2.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 833 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 1092 GLU 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: 0.7980 chunk 75 optimal weight: 1.9990 chunk 228 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 68 optimal weight: 0.2980 chunk 247 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 254 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 ASN C 207 HIS C1088 HIS B 675 GLN A 207 HIS A 239 GLN A 675 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.163533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.114740 restraints weight = 28541.639| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.84 r_work: 0.2955 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25612 Z= 0.252 Angle : 0.546 9.969 34838 Z= 0.280 Chirality : 0.045 0.231 4078 Planarity : 0.004 0.054 4451 Dihedral : 5.036 53.243 4212 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.79 % Favored : 95.11 % Rotamer: Outliers : 1.43 % Allowed : 12.15 % Favored : 86.42 % 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: -0.26 (0.15), residues: 3090 helix: 1.98 (0.20), residues: 697 sheet: 0.33 (0.19), residues: 665 loop : -1.36 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.004 0.001 HIS A1058 PHE 0.026 0.001 PHE C 168 TYR 0.017 0.001 TYR A1067 ARG 0.004 0.000 ARG A 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4706.95 seconds wall clock time: 85 minutes 46.47 seconds (5146.47 seconds total)