Starting phenix.real_space_refine on Fri Aug 9 03:53:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0u_42870/08_2024/8v0u_42870.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0u_42870/08_2024/8v0u_42870.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0u_42870/08_2024/8v0u_42870.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0u_42870/08_2024/8v0u_42870.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0u_42870/08_2024/8v0u_42870.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0u_42870/08_2024/8v0u_42870.cif" } resolution = 3.3 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= 0.034 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 15831 2.51 5 N 4082 2.21 5 O 4784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 568": "OD1" <-> "OD2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 808": "OD1" <-> "OD2" Residue "A PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "B ASP 994": "OD1" <-> "OD2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 398": "OD1" <-> "OD2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 467": "OD1" <-> "OD2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 574": "OD1" <-> "OD2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C ASP 745": "OD1" <-> "OD2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1092": "OE1" <-> "OE2" 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: 24811 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 8095 Classifications: {'peptide': 1036} Link IDs: {'PTRANS': 51, 'TRANS': 984} Chain breaks: 6 Chain: "B" Number of atoms: 8075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8075 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 50, 'TRANS': 982} Chain breaks: 6 Chain: "C" Number of atoms: 8095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 8095 Classifications: {'peptide': 1036} Link IDs: {'PTRANS': 51, 'TRANS': 984} 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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 13.64, per 1000 atoms: 0.55 Number of scatterers: 24811 At special positions: 0 Unit cell: (136.08, 129.6, 177.12, 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 4784 8.00 N 4082 7.00 C 15831 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 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 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 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=2.02 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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 801 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 282 " " NAG B1309 " - " ASN B 801 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C1134 " " NAG C1308 " - " ASN C 282 " " NAG C1309 " - " ASN C 801 " " NAG D 1 " - " ASN A1098 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN B1098 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN C1098 " " NAG I 1 " - " ASN C 717 " Time building additional restraints: 9.42 Conformation dependent library (CDL) restraints added in 4.5 seconds 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5826 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 49 sheets defined 26.3% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.043A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.884A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.901A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 752 Processing helix chain 'A' and resid 753 through 757 removed outlier: 4.013A pdb=" N GLY A 757 " --> pdb=" O LEU A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.777A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.592A 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 removed outlier: 3.681A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) 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 909 removed outlier: 3.680A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.600A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.659A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.738A 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 helix chain 'A' and resid 1140 through 1148 removed outlier: 4.149A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.514A pdb=" N ASN B 343 " --> pdb=" O HIS B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 366 No H-bonds generated for 'chain 'B' and resid 364 through 366' Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.517A 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 758 through 783 removed outlier: 3.637A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.753A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 842 removed outlier: 3.511A pdb=" N GLY B 842 " --> pdb=" O GLY B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.645A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.746A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.669A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 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: 3.547A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 4.520A 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 1141 through 1148 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.946A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.794A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.794A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (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 removed outlier: 3.667A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.676A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 836 through 842 removed outlier: 3.522A pdb=" N CYS C 840 " --> pdb=" O GLN C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 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 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.321A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.737A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.602A 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 Processing helix chain 'C' and resid 985 through 1032 Processing helix chain 'C' and resid 1141 through 1148 removed outlier: 3.503A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 30 removed outlier: 7.700A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE A 201 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.741A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.849A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.513A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.995A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 540 removed outlier: 5.656A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.999A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.649A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 722 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 722 removed outlier: 6.944A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.624A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AC2, first strand: chain 'B' and resid 25 through 26 removed outlier: 7.474A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.942A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 116 through 120 removed outlier: 3.552A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 189 through 190 Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 317 removed outlier: 7.079A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.687A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 538 through 539 Processing sheet with id=AD2, first strand: chain 'B' and resid 565 through 566 removed outlier: 7.212A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.931A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.874A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 722 removed outlier: 7.007A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.636A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AE2, first strand: chain 'C' and resid 25 through 26 removed outlier: 7.960A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.559A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.507A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.986A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.500A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.844A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.604A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.010A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.648A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.505A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 943 hydrogen bonds defined for protein. 2589 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.54 Time building geometry restraints manager: 10.33 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: 7904 1.35 - 1.47: 6523 1.47 - 1.60: 10800 1.60 - 1.73: 0 1.73 - 1.85: 141 Bond restraints: 25368 Sorted by residual: bond pdb=" CA ASN C 61 " pdb=" CB ASN C 61 " ideal model delta sigma weight residual 1.525 1.565 -0.041 1.47e-02 4.63e+03 7.63e+00 bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.60e+00 bond pdb=" C1 NAG A1309 " pdb=" O5 NAG A1309 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.93e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.72e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.61e+00 ... (remaining 25363 not shown) Histogram of bond angle deviations from ideal: 97.97 - 105.19: 458 105.19 - 112.42: 12773 112.42 - 119.64: 8349 119.64 - 126.86: 12659 126.86 - 134.08: 261 Bond angle restraints: 34500 Sorted by residual: angle pdb=" C PHE A 32 " pdb=" N THR A 33 " pdb=" CA THR A 33 " ideal model delta sigma weight residual 121.54 129.74 -8.20 1.91e+00 2.74e-01 1.84e+01 angle pdb=" C PHE B 32 " pdb=" N THR B 33 " pdb=" CA THR B 33 " ideal model delta sigma weight residual 122.46 128.42 -5.96 1.41e+00 5.03e-01 1.79e+01 angle pdb=" C PHE C 32 " pdb=" N THR C 33 " pdb=" CA THR C 33 " ideal model delta sigma weight residual 121.54 129.42 -7.88 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C CYS C 131 " pdb=" N GLU C 132 " pdb=" CA GLU C 132 " ideal model delta sigma weight residual 121.54 128.95 -7.41 1.91e+00 2.74e-01 1.51e+01 angle pdb=" C ILE C 197 " pdb=" N ASP C 198 " pdb=" CA ASP C 198 " ideal model delta sigma weight residual 121.54 128.81 -7.27 1.91e+00 2.74e-01 1.45e+01 ... (remaining 34495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 13906 17.58 - 35.16: 1402 35.16 - 52.74: 240 52.74 - 70.32: 56 70.32 - 87.91: 39 Dihedral angle restraints: 15643 sinusoidal: 6595 harmonic: 9048 Sorted by residual: dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -5.67 -80.33 1 1.00e+01 1.00e-02 7.99e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -15.04 -70.96 1 1.00e+01 1.00e-02 6.47e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -21.34 -64.66 1 1.00e+01 1.00e-02 5.49e+01 ... (remaining 15640 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3468 0.079 - 0.158: 524 0.158 - 0.237: 33 0.237 - 0.316: 2 0.316 - 0.395: 2 Chirality restraints: 4029 Sorted by residual: chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" C2 NAG F 1 " pdb=" C1 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" N2 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.11 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CB ILE C 101 " pdb=" CA ILE C 101 " pdb=" CG1 ILE C 101 " pdb=" CG2 ILE C 101 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 4026 not shown) Planarity restraints: 4444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 133 " 0.024 2.00e-02 2.50e+03 2.72e-02 1.30e+01 pdb=" CG PHE A 133 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE A 133 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 133 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 133 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 133 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 133 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 383 " -0.049 5.00e-02 4.00e+02 7.39e-02 8.74e+00 pdb=" N PRO B 384 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 384 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 384 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " 0.042 5.00e-02 4.00e+02 6.27e-02 6.29e+00 pdb=" N PRO C 521 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " 0.035 5.00e-02 4.00e+02 ... (remaining 4441 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6424 2.80 - 3.33: 19927 3.33 - 3.85: 39540 3.85 - 4.38: 44007 4.38 - 4.90: 80317 Nonbonded interactions: 190215 Sorted by model distance: nonbonded pdb=" O ALA A 879 " pdb=" OG1 THR A 883 " model vdw 2.280 3.040 nonbonded pdb=" OD1 ASN C 360 " pdb=" OG1 THR C 523 " model vdw 2.289 3.040 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.295 3.040 nonbonded pdb=" OG1 THR B 108 " pdb=" O ASN B 234 " model vdw 2.304 3.040 nonbonded pdb=" OG SER A 735 " pdb=" OG1 THR A 859 " model vdw 2.305 3.040 ... (remaining 190210 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 69 or resid 84 through 1148 or resid 1301 throu \ gh 1309)) selection = chain 'B' selection = (chain 'C' and (resid 24 through 69 or resid 84 through 1148 or resid 1301 throu \ gh 1309)) } 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.990 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 67.340 Find NCS groups from input model: 1.280 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: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 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 0.048 25368 Z= 0.298 Angle : 0.758 10.167 34500 Z= 0.399 Chirality : 0.053 0.395 4029 Planarity : 0.006 0.074 4411 Dihedral : 14.478 87.905 9697 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.73 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.14), residues: 3063 helix: -0.83 (0.16), residues: 708 sheet: -0.05 (0.19), residues: 728 loop : -1.72 (0.14), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 886 HIS 0.004 0.001 HIS B 519 PHE 0.063 0.002 PHE A 133 TYR 0.029 0.001 TYR B 453 ARG 0.010 0.000 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 3.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 SER cc_start: 0.8896 (t) cc_final: 0.8665 (t) REVERT: A 571 ASP cc_start: 0.7484 (t0) cc_final: 0.7237 (t0) REVERT: B 1135 ASN cc_start: 0.7590 (t0) cc_final: 0.7258 (t0) REVERT: C 303 LEU cc_start: 0.8124 (mt) cc_final: 0.7878 (mt) REVERT: C 1101 HIS cc_start: 0.7151 (m90) cc_final: 0.6569 (m90) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.3127 time to fit residues: 120.9247 Evaluate side-chains 190 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 0.6980 chunk 234 optimal weight: 0.9990 chunk 129 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 242 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 147 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 280 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 HIS B 394 ASN B1002 GLN C 556 ASN C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25368 Z= 0.249 Angle : 0.535 9.796 34500 Z= 0.280 Chirality : 0.045 0.300 4029 Planarity : 0.004 0.052 4411 Dihedral : 6.214 57.297 4140 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.56 % Allowed : 6.15 % Favored : 93.29 % 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: -0.93 (0.14), residues: 3063 helix: 0.68 (0.19), residues: 727 sheet: -0.01 (0.19), residues: 721 loop : -1.55 (0.14), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.006 0.001 HIS B1048 PHE 0.021 0.001 PHE C 238 TYR 0.025 0.001 TYR B 453 ARG 0.004 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 204 time to evaluate : 2.672 Fit side-chains REVERT: A 305 SER cc_start: 0.8898 (t) cc_final: 0.8626 (t) REVERT: A 458 LYS cc_start: 0.7565 (mtmt) cc_final: 0.7315 (pttm) REVERT: B 592 PHE cc_start: 0.7450 (p90) cc_final: 0.7168 (p90) REVERT: B 1135 ASN cc_start: 0.7538 (t0) cc_final: 0.7229 (t0) REVERT: C 200 TYR cc_start: 0.7247 (m-80) cc_final: 0.7047 (m-80) REVERT: C 319 ARG cc_start: 0.8048 (ttm-80) cc_final: 0.7605 (ttm110) REVERT: C 556 ASN cc_start: 0.8024 (t0) cc_final: 0.7806 (m-40) REVERT: C 564 GLN cc_start: 0.7249 (OUTLIER) cc_final: 0.6529 (tm-30) REVERT: C 574 ASP cc_start: 0.8195 (t0) cc_final: 0.7970 (t0) REVERT: C 886 TRP cc_start: 0.8260 (p90) cc_final: 0.7716 (p90) REVERT: C 1101 HIS cc_start: 0.7182 (m90) cc_final: 0.6623 (m90) outliers start: 15 outliers final: 11 residues processed: 211 average time/residue: 0.3397 time to fit residues: 117.1305 Evaluate side-chains 200 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 188 time to evaluate : 2.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 233 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 281 optimal weight: 0.9990 chunk 303 optimal weight: 0.0970 chunk 250 optimal weight: 0.8980 chunk 278 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN A 505 HIS A 613 GLN A 762 GLN B 613 GLN B1002 GLN C 926 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25368 Z= 0.208 Angle : 0.501 9.615 34500 Z= 0.261 Chirality : 0.044 0.267 4029 Planarity : 0.004 0.045 4411 Dihedral : 5.640 55.997 4140 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.63 % Allowed : 8.93 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.15), residues: 3063 helix: 1.22 (0.20), residues: 732 sheet: 0.06 (0.19), residues: 726 loop : -1.48 (0.14), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.004 0.001 HIS A1064 PHE 0.031 0.001 PHE A 133 TYR 0.024 0.001 TYR B 453 ARG 0.005 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 200 time to evaluate : 2.779 Fit side-chains REVERT: A 241 LEU cc_start: 0.7373 (tt) cc_final: 0.6907 (mp) REVERT: A 305 SER cc_start: 0.8902 (t) cc_final: 0.8673 (t) REVERT: A 458 LYS cc_start: 0.7669 (mtmt) cc_final: 0.7365 (pttm) REVERT: B 374 PHE cc_start: 0.8600 (p90) cc_final: 0.8363 (p90) REVERT: B 571 ASP cc_start: 0.7337 (t0) cc_final: 0.6760 (t0) REVERT: B 592 PHE cc_start: 0.7492 (p90) cc_final: 0.7229 (p90) REVERT: B 1135 ASN cc_start: 0.7566 (t0) cc_final: 0.7257 (t0) REVERT: C 200 TYR cc_start: 0.7090 (m-80) cc_final: 0.6804 (m-80) REVERT: C 319 ARG cc_start: 0.8077 (ttm-80) cc_final: 0.7657 (ttm110) REVERT: C 564 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.6608 (tm-30) REVERT: C 574 ASP cc_start: 0.8205 (t0) cc_final: 0.7740 (t0) REVERT: C 1101 HIS cc_start: 0.7155 (m90) cc_final: 0.6589 (m90) REVERT: C 1142 GLN cc_start: 0.8279 (tp40) cc_final: 0.8003 (tp-100) outliers start: 17 outliers final: 10 residues processed: 211 average time/residue: 0.3507 time to fit residues: 123.2484 Evaluate side-chains 195 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 184 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 4.9990 chunk 211 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 chunk 282 optimal weight: 2.9990 chunk 298 optimal weight: 0.9980 chunk 147 optimal weight: 9.9990 chunk 267 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS A 644 GLN B1002 GLN C 644 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 25368 Z= 0.379 Angle : 0.592 9.712 34500 Z= 0.307 Chirality : 0.047 0.264 4029 Planarity : 0.004 0.042 4411 Dihedral : 5.834 56.122 4140 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.19 % Allowed : 10.86 % Favored : 87.95 % 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: -0.80 (0.15), residues: 3063 helix: 1.14 (0.19), residues: 725 sheet: -0.08 (0.19), residues: 719 loop : -1.58 (0.14), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 436 HIS 0.007 0.001 HIS B1048 PHE 0.032 0.002 PHE A 133 TYR 0.024 0.002 TYR B1067 ARG 0.004 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 189 time to evaluate : 2.556 Fit side-chains REVERT: A 241 LEU cc_start: 0.7546 (tt) cc_final: 0.7227 (mp) REVERT: A 305 SER cc_start: 0.8917 (t) cc_final: 0.8691 (t) REVERT: A 571 ASP cc_start: 0.7892 (t0) cc_final: 0.7420 (t0) REVERT: A 1072 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8546 (pm20) REVERT: B 190 ARG cc_start: 0.8100 (mmm160) cc_final: 0.7834 (mmm160) REVERT: B 493 GLN cc_start: 0.6759 (mp10) cc_final: 0.6557 (mp10) REVERT: B 571 ASP cc_start: 0.7684 (t0) cc_final: 0.6978 (t0) REVERT: B 994 ASP cc_start: 0.7952 (t0) cc_final: 0.7717 (t0) REVERT: B 1002 GLN cc_start: 0.7095 (tt0) cc_final: 0.6635 (tp-100) REVERT: B 1135 ASN cc_start: 0.7640 (t0) cc_final: 0.7350 (t0) REVERT: C 319 ARG cc_start: 0.8155 (ttm-80) cc_final: 0.7726 (ttm110) REVERT: C 564 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.6894 (tp40) REVERT: C 574 ASP cc_start: 0.8300 (t0) cc_final: 0.8091 (t0) REVERT: C 850 ILE cc_start: 0.7289 (mm) cc_final: 0.6928 (mt) REVERT: C 1101 HIS cc_start: 0.7184 (m90) cc_final: 0.6616 (m90) outliers start: 32 outliers final: 23 residues processed: 207 average time/residue: 0.3219 time to fit residues: 109.3927 Evaluate side-chains 205 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 180 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 8.9990 chunk 169 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 222 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 254 optimal weight: 0.7980 chunk 206 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25368 Z= 0.240 Angle : 0.514 9.675 34500 Z= 0.267 Chirality : 0.045 0.252 4029 Planarity : 0.003 0.041 4411 Dihedral : 5.563 55.931 4140 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.82 % Allowed : 12.01 % Favored : 87.18 % 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: -0.65 (0.15), residues: 3063 helix: 1.39 (0.19), residues: 728 sheet: -0.10 (0.19), residues: 721 loop : -1.49 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.003 0.001 HIS B1048 PHE 0.031 0.001 PHE A 133 TYR 0.027 0.001 TYR B 453 ARG 0.004 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 188 time to evaluate : 2.644 Fit side-chains revert: symmetry clash REVERT: A 237 ARG cc_start: 0.6630 (ttm-80) cc_final: 0.6361 (ttm-80) REVERT: A 305 SER cc_start: 0.8916 (t) cc_final: 0.8693 (t) REVERT: A 571 ASP cc_start: 0.7868 (t0) cc_final: 0.7397 (t0) REVERT: B 493 GLN cc_start: 0.6763 (mp10) cc_final: 0.6476 (mp10) REVERT: B 571 ASP cc_start: 0.7770 (t0) cc_final: 0.7096 (t0) REVERT: B 994 ASP cc_start: 0.7879 (t0) cc_final: 0.7647 (t0) REVERT: B 1002 GLN cc_start: 0.6957 (tt0) cc_final: 0.6518 (tp-100) REVERT: B 1135 ASN cc_start: 0.7641 (t0) cc_final: 0.7375 (t0) REVERT: C 200 TYR cc_start: 0.7279 (m-80) cc_final: 0.6877 (m-80) REVERT: C 319 ARG cc_start: 0.8120 (ttm-80) cc_final: 0.7714 (ttm110) REVERT: C 564 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.6948 (tp40) REVERT: C 1101 HIS cc_start: 0.7158 (m90) cc_final: 0.6597 (m90) REVERT: C 1142 GLN cc_start: 0.8086 (tp40) cc_final: 0.7427 (tm-30) outliers start: 22 outliers final: 18 residues processed: 200 average time/residue: 0.3285 time to fit residues: 108.8524 Evaluate side-chains 202 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 183 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 2.9990 chunk 268 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 175 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 298 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 98 optimal weight: 0.4980 chunk 156 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 25368 Z= 0.320 Angle : 0.554 9.745 34500 Z= 0.287 Chirality : 0.046 0.252 4029 Planarity : 0.004 0.041 4411 Dihedral : 5.625 55.865 4140 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.41 % Allowed : 12.82 % Favored : 85.77 % 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: -0.72 (0.15), residues: 3063 helix: 1.35 (0.19), residues: 726 sheet: -0.16 (0.18), residues: 734 loop : -1.55 (0.14), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.005 0.001 HIS B1048 PHE 0.034 0.002 PHE A 133 TYR 0.025 0.001 TYR B 453 ARG 0.003 0.000 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 195 time to evaluate : 2.992 Fit side-chains revert: symmetry clash REVERT: A 305 SER cc_start: 0.8924 (t) cc_final: 0.8697 (t) REVERT: A 571 ASP cc_start: 0.7780 (t0) cc_final: 0.7383 (t0) REVERT: B 191 GLU cc_start: 0.7789 (mp0) cc_final: 0.7468 (mp0) REVERT: B 269 TYR cc_start: 0.7125 (m-80) cc_final: 0.6842 (m-80) REVERT: B 493 GLN cc_start: 0.6721 (mp10) cc_final: 0.6367 (mp10) REVERT: B 571 ASP cc_start: 0.7810 (t0) cc_final: 0.7200 (t0) REVERT: B 994 ASP cc_start: 0.7899 (t0) cc_final: 0.7679 (t0) REVERT: B 1002 GLN cc_start: 0.6943 (tt0) cc_final: 0.6490 (tp-100) REVERT: B 1135 ASN cc_start: 0.7669 (t0) cc_final: 0.7413 (t0) REVERT: C 200 TYR cc_start: 0.7302 (m-80) cc_final: 0.7061 (m-80) REVERT: C 319 ARG cc_start: 0.8160 (ttm-80) cc_final: 0.7770 (ttm110) REVERT: C 564 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.6868 (tp40) REVERT: C 1101 HIS cc_start: 0.7237 (m90) cc_final: 0.6676 (m90) REVERT: C 1142 GLN cc_start: 0.8151 (tp40) cc_final: 0.7540 (tm-30) outliers start: 38 outliers final: 30 residues processed: 219 average time/residue: 0.3218 time to fit residues: 116.7726 Evaluate side-chains 223 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 192 time to evaluate : 2.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 170 optimal weight: 4.9990 chunk 218 optimal weight: 4.9990 chunk 169 optimal weight: 0.8980 chunk 251 optimal weight: 6.9990 chunk 166 optimal weight: 0.7980 chunk 297 optimal weight: 0.8980 chunk 186 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS C 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25368 Z= 0.175 Angle : 0.487 9.717 34500 Z= 0.252 Chirality : 0.044 0.255 4029 Planarity : 0.003 0.042 4411 Dihedral : 5.295 55.182 4140 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.26 % Allowed : 13.64 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 3063 helix: 1.65 (0.20), residues: 729 sheet: -0.09 (0.19), residues: 720 loop : -1.43 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.002 0.001 HIS B1101 PHE 0.034 0.001 PHE A 133 TYR 0.028 0.001 TYR B 453 ARG 0.002 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 195 time to evaluate : 2.856 Fit side-chains REVERT: A 237 ARG cc_start: 0.6995 (mtt-85) cc_final: 0.6437 (mtp-110) REVERT: A 571 ASP cc_start: 0.7716 (t0) cc_final: 0.7309 (t0) REVERT: A 902 MET cc_start: 0.8739 (tpt) cc_final: 0.8424 (tpt) REVERT: B 374 PHE cc_start: 0.8544 (p90) cc_final: 0.8239 (p90) REVERT: B 493 GLN cc_start: 0.6895 (mp10) cc_final: 0.6524 (mp10) REVERT: B 571 ASP cc_start: 0.7827 (t0) cc_final: 0.7209 (t0) REVERT: B 859 THR cc_start: 0.8566 (m) cc_final: 0.7999 (p) REVERT: B 1135 ASN cc_start: 0.7639 (t0) cc_final: 0.7390 (t0) REVERT: C 200 TYR cc_start: 0.7345 (m-80) cc_final: 0.7096 (m-80) REVERT: C 319 ARG cc_start: 0.8100 (ttm-80) cc_final: 0.7678 (ttm110) REVERT: C 564 GLN cc_start: 0.7694 (mm-40) cc_final: 0.6915 (tp40) REVERT: C 574 ASP cc_start: 0.8010 (t0) cc_final: 0.7772 (t0) REVERT: C 1101 HIS cc_start: 0.7201 (m90) cc_final: 0.6642 (m90) REVERT: C 1142 GLN cc_start: 0.8023 (tp40) cc_final: 0.7447 (tm-30) outliers start: 34 outliers final: 28 residues processed: 218 average time/residue: 0.3287 time to fit residues: 119.2197 Evaluate side-chains 219 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 191 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 0.9990 chunk 118 optimal weight: 0.6980 chunk 177 optimal weight: 0.0980 chunk 89 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 189 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 147 optimal weight: 0.4980 chunk 27 optimal weight: 10.0000 chunk 234 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS C 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25368 Z= 0.149 Angle : 0.468 9.752 34500 Z= 0.242 Chirality : 0.043 0.249 4029 Planarity : 0.003 0.042 4411 Dihedral : 5.021 55.587 4140 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.00 % Allowed : 14.38 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 3063 helix: 1.87 (0.20), residues: 729 sheet: 0.00 (0.19), residues: 721 loop : -1.35 (0.14), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.002 0.000 HIS A 207 PHE 0.036 0.001 PHE A 133 TYR 0.025 0.001 TYR B 453 ARG 0.003 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 195 time to evaluate : 3.038 Fit side-chains REVERT: A 237 ARG cc_start: 0.6935 (mtt-85) cc_final: 0.6408 (mtp-110) REVERT: A 571 ASP cc_start: 0.7587 (t0) cc_final: 0.7228 (t0) REVERT: A 902 MET cc_start: 0.8764 (tpt) cc_final: 0.8445 (tpt) REVERT: B 374 PHE cc_start: 0.8541 (p90) cc_final: 0.8295 (p90) REVERT: B 493 GLN cc_start: 0.6858 (mp10) cc_final: 0.6482 (mp10) REVERT: B 571 ASP cc_start: 0.7832 (t0) cc_final: 0.7124 (t0) REVERT: B 859 THR cc_start: 0.8553 (m) cc_final: 0.7979 (p) REVERT: B 1135 ASN cc_start: 0.7670 (t0) cc_final: 0.7414 (t0) REVERT: C 319 ARG cc_start: 0.8086 (ttm-80) cc_final: 0.7678 (ttm110) REVERT: C 564 GLN cc_start: 0.7668 (mm-40) cc_final: 0.6926 (tp40) REVERT: C 565 PHE cc_start: 0.6461 (m-80) cc_final: 0.6164 (m-80) REVERT: C 574 ASP cc_start: 0.7973 (t0) cc_final: 0.7727 (t0) REVERT: C 1101 HIS cc_start: 0.7172 (m90) cc_final: 0.6609 (m90) REVERT: C 1142 GLN cc_start: 0.8014 (tp40) cc_final: 0.7460 (tm-30) outliers start: 27 outliers final: 24 residues processed: 213 average time/residue: 0.3238 time to fit residues: 114.6354 Evaluate side-chains 208 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 184 time to evaluate : 2.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 0.8980 chunk 285 optimal weight: 1.9990 chunk 260 optimal weight: 3.9990 chunk 277 optimal weight: 4.9990 chunk 167 optimal weight: 0.7980 chunk 120 optimal weight: 8.9990 chunk 217 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 250 optimal weight: 1.9990 chunk 262 optimal weight: 0.9980 chunk 276 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A 505 HIS ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25368 Z= 0.230 Angle : 0.502 9.760 34500 Z= 0.260 Chirality : 0.044 0.244 4029 Planarity : 0.003 0.041 4411 Dihedral : 5.147 55.572 4140 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.11 % Allowed : 14.46 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 3063 helix: 1.71 (0.20), residues: 735 sheet: -0.03 (0.19), residues: 723 loop : -1.35 (0.14), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.003 0.001 HIS B1048 PHE 0.040 0.001 PHE A 133 TYR 0.026 0.001 TYR B 453 ARG 0.003 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 189 time to evaluate : 2.491 Fit side-chains REVERT: A 237 ARG cc_start: 0.6990 (mtt-85) cc_final: 0.6446 (mtp-110) REVERT: A 571 ASP cc_start: 0.7618 (t0) cc_final: 0.7285 (t0) REVERT: B 374 PHE cc_start: 0.8559 (p90) cc_final: 0.8299 (p90) REVERT: B 493 GLN cc_start: 0.6810 (mp10) cc_final: 0.6478 (mm110) REVERT: B 571 ASP cc_start: 0.7776 (t0) cc_final: 0.7133 (t0) REVERT: B 859 THR cc_start: 0.8572 (m) cc_final: 0.7972 (p) REVERT: B 1002 GLN cc_start: 0.6917 (tt0) cc_final: 0.6457 (tp-100) REVERT: B 1135 ASN cc_start: 0.7768 (t0) cc_final: 0.7503 (t0) REVERT: C 200 TYR cc_start: 0.7289 (m-80) cc_final: 0.6951 (m-80) REVERT: C 319 ARG cc_start: 0.8100 (ttm-80) cc_final: 0.7701 (ttm110) REVERT: C 564 GLN cc_start: 0.7717 (mm-40) cc_final: 0.6845 (tp40) REVERT: C 574 ASP cc_start: 0.8047 (t0) cc_final: 0.7795 (t0) REVERT: C 1101 HIS cc_start: 0.7188 (m90) cc_final: 0.6618 (m90) outliers start: 30 outliers final: 28 residues processed: 208 average time/residue: 0.3229 time to fit residues: 111.5105 Evaluate side-chains 216 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 188 time to evaluate : 2.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 0.1980 chunk 293 optimal weight: 0.9980 chunk 179 optimal weight: 0.6980 chunk 139 optimal weight: 8.9990 chunk 204 optimal weight: 0.8980 chunk 307 optimal weight: 6.9990 chunk 283 optimal weight: 3.9990 chunk 245 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 150 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A 422 ASN A 505 HIS C 405 ASN C 762 GLN C1142 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25368 Z= 0.161 Angle : 0.477 10.102 34500 Z= 0.245 Chirality : 0.043 0.248 4029 Planarity : 0.003 0.042 4411 Dihedral : 5.014 55.587 4140 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.15 % Allowed : 14.53 % Favored : 84.32 % 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: -0.27 (0.15), residues: 3063 helix: 1.85 (0.20), residues: 735 sheet: 0.04 (0.19), residues: 720 loop : -1.30 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.002 0.000 HIS A 207 PHE 0.036 0.001 PHE A 133 TYR 0.027 0.001 TYR B 453 ARG 0.002 0.000 ARG C 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 189 time to evaluate : 3.057 Fit side-chains REVERT: A 237 ARG cc_start: 0.6977 (mtt-85) cc_final: 0.6484 (mtp-110) REVERT: A 377 PHE cc_start: 0.8069 (t80) cc_final: 0.7658 (t80) REVERT: A 571 ASP cc_start: 0.7679 (t0) cc_final: 0.7374 (t0) REVERT: A 902 MET cc_start: 0.8735 (tpt) cc_final: 0.8513 (tpt) REVERT: B 374 PHE cc_start: 0.8499 (p90) cc_final: 0.8225 (p90) REVERT: B 471 GLU cc_start: 0.7474 (mp0) cc_final: 0.6714 (mp0) REVERT: B 493 GLN cc_start: 0.6841 (mp10) cc_final: 0.6483 (mm110) REVERT: B 571 ASP cc_start: 0.7767 (t0) cc_final: 0.7123 (t0) REVERT: B 859 THR cc_start: 0.8563 (m) cc_final: 0.7990 (p) REVERT: B 1135 ASN cc_start: 0.7819 (t0) cc_final: 0.7522 (t0) REVERT: C 200 TYR cc_start: 0.7149 (m-80) cc_final: 0.6812 (m-80) REVERT: C 319 ARG cc_start: 0.8059 (ttm-80) cc_final: 0.7659 (ttm110) REVERT: C 564 GLN cc_start: 0.7670 (mm-40) cc_final: 0.6836 (tp40) REVERT: C 574 ASP cc_start: 0.8012 (t0) cc_final: 0.7764 (t0) REVERT: C 1101 HIS cc_start: 0.7205 (m90) cc_final: 0.6637 (m90) REVERT: C 1142 GLN cc_start: 0.7867 (tp40) cc_final: 0.7377 (tm-30) outliers start: 31 outliers final: 28 residues processed: 208 average time/residue: 0.3634 time to fit residues: 126.1020 Evaluate side-chains 215 residues out of total 2698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 187 time to evaluate : 2.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 75 optimal weight: 0.0060 chunk 226 optimal weight: 0.6980 chunk 36 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 245 optimal weight: 20.0000 chunk 102 optimal weight: 0.7980 chunk 252 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A 505 HIS B 49 HIS C 762 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.155841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.120328 restraints weight = 32546.302| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.56 r_work: 0.3086 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25368 Z= 0.249 Angle : 0.517 10.548 34500 Z= 0.266 Chirality : 0.044 0.246 4029 Planarity : 0.003 0.041 4411 Dihedral : 5.172 55.711 4140 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.11 % Allowed : 14.49 % Favored : 84.40 % 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: -0.39 (0.15), residues: 3063 helix: 1.71 (0.20), residues: 736 sheet: -0.05 (0.19), residues: 709 loop : -1.32 (0.14), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.004 0.001 HIS B1048 PHE 0.035 0.001 PHE A 133 TYR 0.025 0.001 TYR B 453 ARG 0.003 0.000 ARG C 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4485.83 seconds wall clock time: 81 minutes 51.74 seconds (4911.74 seconds total)