Starting phenix.real_space_refine on Sun Jul 5 14:41:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fjo_31625/07_2026/7fjo_31625.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fjo_31625/07_2026/7fjo_31625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fjo_31625/07_2026/7fjo_31625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fjo_31625/07_2026/7fjo_31625.map" model { file = "/net/cci-nas-00/data/ceres_data/7fjo_31625/07_2026/7fjo_31625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fjo_31625/07_2026/7fjo_31625.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7fjo_31625/07_2026/7fjo_31625.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fjo_31625/07_2026/7fjo_31625.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 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 123 5.16 5 C 18207 2.51 5 N 4694 2.21 5 O 5523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28547 Number of models: 1 Model: "" Number of chains: 8 Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "G" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 886 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 108} Chain: "A" Number of atoms: 7696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7696 Classifications: {'peptide': 994} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 48, 'TRANS': 945} Chain breaks: 8 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'GLN:plan1': 4, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 7696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7696 Classifications: {'peptide': 994} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 48, 'TRANS': 945} Chain breaks: 8 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'GLN:plan1': 4, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 7678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7678 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 49, 'TRANS': 942} Chain breaks: 7 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 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 chiralities: 9 Restraints were copied for chains: H, J, K, L Time building chain proxies: 6.86, per 1000 atoms: 0.24 Number of scatterers: 28547 At special positions: 0 Unit cell: (193.23, 163.587, 157, 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 123 16.00 O 5523 8.00 N 4694 7.00 C 18207 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.05 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 94 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.05 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 94 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=6, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 717 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1134 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 717 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B1134 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1134 " Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.4 seconds 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6782 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 63 sheets defined 19.6% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.587A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.512A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.133A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.546A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.656A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.562A 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 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 963 removed outlier: 4.253A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 968 Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.820A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.482A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.581A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.677A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.056A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.502A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.868A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.580A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.589A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.549A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.869A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.870A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.615A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.587A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.667A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 759 removed outlier: 6.946A pdb=" N SER C 758 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE C 759 " --> pdb=" O TYR C 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 755 through 759' Processing helix chain 'C' and resid 760 through 783 removed outlier: 4.341A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.845A 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 866 through 885 removed outlier: 3.616A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.543A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.535A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.581A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (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 1033 removed outlier: 3.758A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1143 through 1147 Processing sheet with id=AA1, first strand: chain 'F' and resid 18 through 23 removed outlier: 3.589A pdb=" N CYS F 22 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR F 78 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP F 73 " --> pdb=" O THR F 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 59 through 60 removed outlier: 3.519A pdb=" N SER F 59 " --> pdb=" O ALA F 50 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE F 34 " --> pdb=" O ALA F 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.594A pdb=" N SER G 7 " --> pdb=" O SER G 22 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER G 22 " --> pdb=" O SER G 7 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.265A pdb=" N LEU G 11 " --> pdb=" O GLU G 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 30 through 31 removed outlier: 3.625A pdb=" N LYS G 36 " --> pdb=" O TYR G 31 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 59 through 60 removed outlier: 6.707A pdb=" N TRP G 41 " --> pdb=" O LEU G 53 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N HIS G 55 " --> pdb=" O LEU G 39 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU G 39 " --> pdb=" O HIS G 55 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 18 through 23 removed outlier: 3.589A pdb=" N CYS H 22 " --> pdb=" O ALA H 79 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 59 through 60 removed outlier: 3.519A pdb=" N SER H 59 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 18 through 23 removed outlier: 3.589A pdb=" N CYS J 22 " --> pdb=" O ALA J 79 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR J 78 " --> pdb=" O ASP J 73 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP J 73 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 59 through 60 removed outlier: 3.519A pdb=" N SER J 59 " --> pdb=" O ALA J 50 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE J 34 " --> pdb=" O ALA J 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.594A pdb=" N SER K 7 " --> pdb=" O SER K 22 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER K 22 " --> pdb=" O SER K 7 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.265A pdb=" N LEU K 11 " --> pdb=" O GLU K 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'K' and resid 30 through 31 removed outlier: 3.625A pdb=" N LYS K 36 " --> pdb=" O TYR K 31 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 59 through 60 removed outlier: 6.707A pdb=" N TRP K 41 " --> pdb=" O LEU K 53 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N HIS K 55 " --> pdb=" O LEU K 39 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU K 39 " --> pdb=" O HIS K 55 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.594A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.265A pdb=" N LEU L 11 " --> pdb=" O GLU L 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.625A pdb=" N LYS L 36 " --> pdb=" O TYR L 31 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 59 through 60 removed outlier: 6.707A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N HIS L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU L 39 " --> pdb=" O HIS L 55 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.794A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.672A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.823A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.646A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.292A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.006A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 354 through 355 removed outlier: 4.395A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 394 through 395 removed outlier: 3.864A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.648A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.999A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AD3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AD4, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.866A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.207A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.969A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.673A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.564A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AE3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.427A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.616A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 354 through 355 removed outlier: 4.394A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 394 through 395 removed outlier: 3.864A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.650A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.079A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AF1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.860A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 718 through 720 Processing sheet with id=AF3, first strand: chain 'B' and resid 718 through 720 removed outlier: 3.644A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AF5, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 4.919A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.533A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.343A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AF9, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.983A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 354 through 355 removed outlier: 4.394A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 394 through 395 removed outlier: 3.864A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.649A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.971A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AG6, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.862A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AG8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AG9, first strand: chain 'C' and resid 1094 through 1097 1063 hydrogen bonds defined for protein. 2868 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: 7.60 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 6982 1.33 - 1.47: 8667 1.47 - 1.61: 13383 1.61 - 1.75: 3 1.75 - 1.89: 153 Bond restraints: 29188 Sorted by residual: bond pdb=" CA GLY K 106 " pdb=" C GLY K 106 " ideal model delta sigma weight residual 1.518 1.627 -0.110 1.48e-02 4.57e+03 5.50e+01 bond pdb=" CA GLY L 106 " pdb=" C GLY L 106 " ideal model delta sigma weight residual 1.518 1.627 -0.109 1.48e-02 4.57e+03 5.44e+01 bond pdb=" CA GLY G 106 " pdb=" C GLY G 106 " ideal model delta sigma weight residual 1.518 1.626 -0.109 1.48e-02 4.57e+03 5.42e+01 bond pdb=" N GLY B 648 " pdb=" CA GLY B 648 " ideal model delta sigma weight residual 1.450 1.500 -0.049 1.01e-02 9.80e+03 2.37e+01 bond pdb=" CA CYS B 617 " pdb=" C CYS B 617 " ideal model delta sigma weight residual 1.522 1.589 -0.067 1.39e-02 5.18e+03 2.34e+01 ... (remaining 29183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 34742 2.46 - 4.92: 4779 4.92 - 7.37: 185 7.37 - 9.83: 14 9.83 - 12.29: 2 Bond angle restraints: 39722 Sorted by residual: angle pdb=" C CYS A 525 " pdb=" N GLY A 526 " pdb=" CA GLY A 526 " ideal model delta sigma weight residual 121.87 109.58 12.29 1.57e+00 4.06e-01 6.13e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 118.38 -7.68 1.22e+00 6.72e-01 3.97e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 118.35 -7.65 1.22e+00 6.72e-01 3.93e+01 angle pdb=" N GLY K 106 " pdb=" CA GLY K 106 " pdb=" C GLY K 106 " ideal model delta sigma weight residual 112.25 104.04 8.21 1.34e+00 5.57e-01 3.76e+01 angle pdb=" N GLY G 106 " pdb=" CA GLY G 106 " pdb=" C GLY G 106 " ideal model delta sigma weight residual 112.25 104.04 8.21 1.34e+00 5.57e-01 3.76e+01 ... (remaining 39717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 15795 17.36 - 34.71: 931 34.71 - 52.07: 160 52.07 - 69.43: 77 69.43 - 86.78: 21 Dihedral angle restraints: 16984 sinusoidal: 6417 harmonic: 10567 Sorted by residual: dihedral pdb=" CA PHE A 718 " pdb=" C PHE A 718 " pdb=" N THR A 719 " pdb=" CA THR A 719 " ideal model delta harmonic sigma weight residual 180.00 151.71 28.29 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA ASP B 198 " pdb=" C ASP B 198 " pdb=" N GLY B 199 " pdb=" CA GLY B 199 " ideal model delta harmonic sigma weight residual 180.00 151.74 28.26 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CB CYS F 22 " pdb=" SG CYS F 22 " pdb=" SG CYS F 96 " pdb=" CB CYS F 96 " ideal model delta sinusoidal sigma weight residual 93.00 45.98 47.02 1 1.00e+01 1.00e-02 3.06e+01 ... (remaining 16981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 3225 0.091 - 0.183: 1197 0.183 - 0.274: 153 0.274 - 0.366: 27 0.366 - 0.457: 4 Chirality restraints: 4606 Sorted by residual: chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C 801 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" CA CYS B 617 " pdb=" N CYS B 617 " pdb=" C CYS B 617 " pdb=" CB CYS B 617 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CA PRO B 986 " pdb=" N PRO B 986 " pdb=" C PRO B 986 " pdb=" CB PRO B 986 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 3.93e+00 ... (remaining 4603 not shown) Planarity restraints: 5088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1307 " 0.343 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG A1307 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG A1307 " 0.172 2.00e-02 2.50e+03 pdb=" N2 NAG A1307 " -0.515 2.00e-02 2.50e+03 pdb=" O7 NAG A1307 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1302 " -0.326 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG A1302 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG A1302 " -0.070 2.00e-02 2.50e+03 pdb=" N2 NAG A1302 " 0.504 2.00e-02 2.50e+03 pdb=" O7 NAG A1302 " -0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1304 " -0.333 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C7 NAG C1304 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG C1304 " -0.178 2.00e-02 2.50e+03 pdb=" N2 NAG C1304 " 0.497 2.00e-02 2.50e+03 pdb=" O7 NAG C1304 " -0.071 2.00e-02 2.50e+03 ... (remaining 5085 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 45 2.14 - 2.83: 7524 2.83 - 3.52: 37892 3.52 - 4.21: 67228 4.21 - 4.90: 114851 Nonbonded interactions: 227540 Sorted by model distance: nonbonded pdb=" CD PRO A 230 " pdb=" CD PRO C 521 " model vdw 1.446 3.840 nonbonded pdb=" CD2 TYR K 100 " pdb=" CD2 PHE B 486 " model vdw 1.536 3.640 nonbonded pdb=" CD2 TYR G 100 " pdb=" CD2 PHE C 486 " model vdw 1.536 3.640 nonbonded pdb=" CD2 TYR L 100 " pdb=" CD2 PHE A 486 " model vdw 1.537 3.640 nonbonded pdb=" OD1 ASP F 57 " pdb=" OH TYR C 489 " model vdw 1.662 3.040 ... (remaining 227535 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 27 through 87 or (resid 88 and (name N or name CA or name \ C or name O or name CB )) or resid 89 through 96 or (resid 97 and (name N or nam \ e CA or name C or name O or name CB )) or resid 98 through 109 or (resid 110 and \ (name N or name CA or name C or name O or name CB )) or resid 111 through 114 o \ r (resid 115 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 16 through 164 or resid 166 through 168 or (resid 169 and (name N or name CA or \ name C or name O or name CB )) or resid 170 through 190 or (resid 191 and (name \ N or name CA or name C or name O or name CB )) or resid 192 through 280 or (resi \ d 281 and (name N or name CA or name C or name O or name CB )) or resid 282 thro \ ugh 676 or resid 690 through 744 or (resid 745 and (name N or name CA or name C \ or name O or name CB )) or resid 746 through 747 or (resid 748 and (name N or na \ me CA or name C or name O or name CB )) or resid 749 through 810 or (resid 811 a \ nd (name N or name CA or name C or name O or name CB )) or resid 813 through 827 \ or resid 855 through 866 or (resid 867 through 868 and (name N or name CA or na \ me C or name O or name CB )) or resid 869 through 1308)) selection = (chain 'B' and (resid 27 through 87 or (resid 88 and (name N or name CA or name \ C or name O or name CB )) or resid 89 through 96 or (resid 97 and (name N or nam \ e CA or name C or name O or name CB )) or resid 98 through 109 or (resid 110 and \ (name N or name CA or name C or name O or name CB )) or resid 111 through 114 o \ r (resid 115 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 16 through 164 or resid 166 through 168 or (resid 169 and (name N or name CA or \ name C or name O or name CB )) or resid 170 through 190 or (resid 191 and (name \ N or name CA or name C or name O or name CB )) or resid 192 through 280 or (resi \ d 281 and (name N or name CA or name C or name O or name CB )) or resid 282 thro \ ugh 676 or resid 690 through 744 or (resid 745 and (name N or name CA or name C \ or name O or name CB )) or resid 746 through 747 or (resid 748 and (name N or na \ me CA or name C or name O or name CB )) or resid 749 through 810 or (resid 811 a \ nd (name N or name CA or name C or name O or name CB )) or resid 813 through 827 \ or resid 855 through 866 or (resid 867 through 868 and (name N or name CA or na \ me C or name O or name CB )) or resid 869 through 1308)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 95 or (resid 96 through 97 and (na \ me N or name CA or name C or name O or name CB )) or resid 98 through 143 or (re \ sid 165 and (name N or name CA or name C or name O or name CB )) or resid 166 th \ rough 196 or (resid 197 and (name N or name CA or name C or name O or name CB )) \ or resid 198 through 213 or (resid 214 and (name N or name CA or name C or name \ O or name CB )) or resid 215 through 217 or (resid 218 and (name N or name CA o \ r name C or name O or name CB )) or resid 219 through 238 or (resid 239 and (nam \ e N or name CA or name C or name O or name CB )) or resid 240 through 308 or (re \ sid 309 and (name N or name CA or name C or name O or name CB )) or resid 310 th \ rough 527 or (resid 528 and (name N or name CA or name C or name O or name CB )) \ or resid 529 through 811 or resid 813 through 1141 or (resid 1142 and (name N o \ r name CA or name C or name O or name CB )) or resid 1143 through 1144 or (resid \ 1145 through 1146 and (name N or name CA or name C or name O or name CB )) or r \ esid 1147 through 1308)) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'L' } 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: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 29.900 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3571 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 : 0.013 0.464 29225 Z= 0.901 Angle : 1.569 15.029 39809 Z= 1.077 Chirality : 0.089 0.457 4606 Planarity : 0.016 0.292 5063 Dihedral : 12.689 86.785 10184 Min Nonbonded Distance : 1.446 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.16 % Favored : 92.39 % Rotamer: Outliers : 3.26 % Allowed : 4.25 % Favored : 92.48 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.13), residues: 3576 helix: -0.31 (0.18), residues: 608 sheet: 0.43 (0.19), residues: 766 loop : -1.28 (0.12), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 102 TYR 0.096 0.009 TYR A 707 PHE 0.060 0.007 PHE B 927 TRP 0.050 0.005 TRP B 886 HIS 0.016 0.002 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01167 / 0.76 (29188) covalent geometry : angle 1.56489 / 1.08 (39722) SS BOND : bond 0.01665 / 0.85 ( 6) SS BOND : angle 2.09404 / 1.10 ( 12) hydrogen bonds : bond 0.16433 / 10.78 ( 1061) hydrogen bonds : angle 8.79292 / 5.97 ( 2868) Misc. bond : bond 0.34349 / 20.64 ( 6) link_NAG-ASN : bond 0.00934 / 0.68 ( 25) link_NAG-ASN : angle 2.87948 / 1.73 ( 75) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 535 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 22 CYS cc_start: 0.1615 (OUTLIER) cc_final: 0.0017 (p) REVERT: F 43 GLN cc_start: 0.1288 (OUTLIER) cc_final: 0.0209 (mt0) REVERT: F 78 THR cc_start: 0.2852 (OUTLIER) cc_final: 0.2643 (t) REVERT: F 86 LEU cc_start: 0.0172 (OUTLIER) cc_final: -0.0171 (mp) REVERT: G 93 TYR cc_start: -0.0724 (OUTLIER) cc_final: -0.1015 (m-80) REVERT: H 22 CYS cc_start: 0.2458 (OUTLIER) cc_final: 0.0381 (p) REVERT: H 43 GLN cc_start: -0.0031 (OUTLIER) cc_final: -0.0948 (mp10) REVERT: J 22 CYS cc_start: 0.1548 (OUTLIER) cc_final: 0.0098 (t) REVERT: J 51 ILE cc_start: -0.3377 (OUTLIER) cc_final: -0.3673 (mt) REVERT: J 109 GLN cc_start: 0.2176 (OUTLIER) cc_final: 0.1895 (mm110) REVERT: K 111 GLU cc_start: -0.2670 (OUTLIER) cc_final: -0.3640 (tp30) REVERT: K 112 ILE cc_start: 0.5508 (OUTLIER) cc_final: 0.5178 (mm) REVERT: L 21 LEU cc_start: 0.6184 (OUTLIER) cc_final: 0.5637 (tt) REVERT: A 320 VAL cc_start: 0.5664 (t) cc_final: 0.5342 (t) REVERT: A 1041 ASP cc_start: 0.5934 (t0) cc_final: 0.5680 (t0) REVERT: A 1048 HIS cc_start: 0.4012 (t70) cc_final: 0.3038 (t-170) REVERT: B 365 TYR cc_start: 0.8712 (m-80) cc_final: 0.8422 (m-80) REVERT: B 378 LYS cc_start: 0.8799 (pttt) cc_final: 0.8531 (ptpp) REVERT: B 390 LEU cc_start: 0.6878 (tp) cc_final: 0.6650 (mt) REVERT: B 392 PHE cc_start: 0.7530 (m-80) cc_final: 0.5661 (m-80) REVERT: B 519 HIS cc_start: 0.7322 (m90) cc_final: 0.7101 (m90) REVERT: C 389 ASP cc_start: 0.8205 (p0) cc_final: 0.7911 (t0) outliers start: 102 outliers final: 18 residues processed: 625 average time/residue: 0.1670 time to fit residues: 172.6108 Evaluate side-chains 322 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 291 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 93 TYR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 20 MET Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 109 GLN Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 6.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 102 ASN H 102 ASN H 109 GLN ** K 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN A 481 ASN A 493 GLN A 913 GLN A 955 ASN A1135 ASN B 394 ASN B 409 GLN B 493 GLN B 613 GLN B 913 GLN B 926 GLN B 935 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 409 GLN C 439 ASN C 481 ASN C 493 GLN C 519 HIS C 804 GLN C 901 GLN C 907 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.198198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.165553 restraints weight = 97041.540| |-----------------------------------------------------------------------------| r_work (start): 0.4400 rms_B_bonded: 5.24 r_work: 0.4166 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5811 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 29225 Z= 0.206 Angle : 0.801 14.679 39809 Z= 0.407 Chirality : 0.051 0.413 4606 Planarity : 0.005 0.071 5063 Dihedral : 6.356 65.675 3951 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.69 % Favored : 96.25 % Rotamer: Outliers : 3.36 % Allowed : 9.69 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.14), residues: 3576 helix: 0.94 (0.20), residues: 635 sheet: 0.19 (0.17), residues: 957 loop : -0.97 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 237 TYR 0.023 0.002 TYR B 789 PHE 0.025 0.003 PHE B 802 TRP 0.018 0.002 TRP B 64 HIS 0.013 0.002 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.21 (29188) covalent geometry : angle 0.78832 / 0.40 (39722) SS BOND : bond 0.00539 / 0.33 ( 6) SS BOND : angle 1.49732 / 0.77 ( 12) hydrogen bonds : bond 0.04789 / 3.29 ( 1061) hydrogen bonds : angle 6.58793 / 4.53 ( 2868) Misc. bond : bond 0.00184 / 0.11 ( 6) link_NAG-ASN : bond 0.00966 / 0.61 ( 25) link_NAG-ASN : angle 3.36551 / 2.45 ( 75) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 370 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 22 CYS cc_start: -0.1302 (OUTLIER) cc_final: -0.1596 (p) REVERT: J 22 CYS cc_start: 0.0709 (OUTLIER) cc_final: -0.0170 (t) REVERT: J 109 GLN cc_start: 0.3320 (OUTLIER) cc_final: 0.2826 (mp10) REVERT: K 44 GLN cc_start: 0.0307 (OUTLIER) cc_final: -0.0268 (mt0) REVERT: K 93 TYR cc_start: 0.4125 (OUTLIER) cc_final: 0.3115 (t80) REVERT: K 111 GLU cc_start: -0.3268 (OUTLIER) cc_final: -0.3960 (tp30) REVERT: A 619 GLU cc_start: 0.8551 (tp30) cc_final: 0.8134 (tp30) REVERT: A 654 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.7059 (tm-30) REVERT: A 656 VAL cc_start: 0.8228 (p) cc_final: 0.7460 (p) REVERT: A 716 THR cc_start: 0.4077 (p) cc_final: 0.3537 (m) REVERT: A 902 MET cc_start: 0.7611 (mmm) cc_final: 0.7239 (mmp) REVERT: B 200 TYR cc_start: 0.5115 (m-80) cc_final: 0.4604 (m-80) REVERT: B 329 PHE cc_start: 0.2030 (m-80) cc_final: 0.1817 (m-10) REVERT: B 392 PHE cc_start: 0.6678 (m-80) cc_final: 0.5555 (m-80) REVERT: B 453 TYR cc_start: 0.7605 (p90) cc_final: 0.7403 (p90) REVERT: B 703 ASN cc_start: 0.6554 (t0) cc_final: 0.6240 (m110) REVERT: B 884 SER cc_start: 0.8322 (p) cc_final: 0.8106 (t) REVERT: C 224 GLU cc_start: 0.7593 (pt0) cc_final: 0.6912 (pt0) REVERT: C 750 SER cc_start: 0.8208 (t) cc_final: 0.7801 (m) REVERT: C 1029 MET cc_start: 0.8279 (mmt) cc_final: 0.7961 (mmt) REVERT: C 1064 HIS cc_start: 0.6467 (OUTLIER) cc_final: 0.6172 (m90) outliers start: 105 outliers final: 50 residues processed: 456 average time/residue: 0.1681 time to fit residues: 127.8960 Evaluate side-chains 322 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 264 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 77 PHE Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 20 MET Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 109 GLN Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 44 GLN Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 93 TYR Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1102 TRP Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1064 HIS Chi-restraints excluded: chain C residue 1076 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 334 optimal weight: 3.9990 chunk 320 optimal weight: 0.6980 chunk 188 optimal weight: 8.9990 chunk 307 optimal weight: 6.9990 chunk 263 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 316 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 201 optimal weight: 7.9990 chunk 231 optimal weight: 3.9990 chunk 28 optimal weight: 20.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 762 GLN A1048 HIS B 481 ASN B1048 HIS ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN C 388 ASN C 751 ASN C 901 GLN C1048 HIS C1135 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.178783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.130193 restraints weight = 87876.462| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 4.86 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.8518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.138 29225 Z= 0.301 Angle : 0.995 20.295 39809 Z= 0.501 Chirality : 0.061 0.950 4606 Planarity : 0.006 0.072 5063 Dihedral : 6.275 71.118 3917 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.73 % Favored : 94.18 % Rotamer: Outliers : 3.61 % Allowed : 12.76 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.14), residues: 3576 helix: 0.28 (0.19), residues: 620 sheet: 0.04 (0.17), residues: 961 loop : -1.22 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1000 TYR 0.056 0.003 TYR B1067 PHE 0.056 0.003 PHE C 898 TRP 0.052 0.003 TRP C1102 HIS 0.017 0.003 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00671 / 0.30 (29188) covalent geometry : angle 0.97853 / 0.50 (39722) SS BOND : bond 0.01975 / 0.99 ( 6) SS BOND : angle 1.66955 / 0.94 ( 12) hydrogen bonds : bond 0.06538 / 4.39 ( 1061) hydrogen bonds : angle 6.89725 / 4.75 ( 2868) Misc. bond : bond 0.00105 / 0.05 ( 6) link_NAG-ASN : bond 0.02685 / 1.40 ( 25) link_NAG-ASN : angle 4.28030 / 2.99 ( 75) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 277 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 22 CYS cc_start: -0.0691 (OUTLIER) cc_final: -0.1694 (p) REVERT: G 108 THR cc_start: 0.1154 (OUTLIER) cc_final: 0.0863 (p) REVERT: J 81 MET cc_start: -0.0185 (ttm) cc_final: -0.0976 (tpp) REVERT: J 109 GLN cc_start: 0.2874 (OUTLIER) cc_final: 0.2243 (mp10) REVERT: K 76 ASP cc_start: 0.6370 (m-30) cc_final: 0.5804 (p0) REVERT: L 93 TYR cc_start: 0.2026 (OUTLIER) cc_final: 0.0683 (m-80) REVERT: A 189 LEU cc_start: 0.6345 (tt) cc_final: 0.5345 (tp) REVERT: A 289 VAL cc_start: 0.3893 (OUTLIER) cc_final: 0.3688 (m) REVERT: A 298 GLU cc_start: 0.7764 (tt0) cc_final: 0.7555 (mt-10) REVERT: A 587 ILE cc_start: 0.8445 (tp) cc_final: 0.8230 (mp) REVERT: A 758 SER cc_start: 0.8037 (m) cc_final: 0.7637 (p) REVERT: A 994 ASP cc_start: 0.7491 (t70) cc_final: 0.7289 (t0) REVERT: A 1031 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.7540 (mp0) REVERT: B 324 GLU cc_start: 0.5953 (pt0) cc_final: 0.5690 (pm20) REVERT: B 365 TYR cc_start: 0.7951 (m-80) cc_final: 0.7633 (m-80) REVERT: B 387 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8056 (pt) REVERT: B 392 PHE cc_start: 0.7741 (m-80) cc_final: 0.6446 (m-80) REVERT: B 559 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.6861 (t80) REVERT: B 1083 HIS cc_start: 0.3748 (t70) cc_final: 0.3537 (t70) REVERT: C 740 MET cc_start: 0.8115 (tmm) cc_final: 0.7859 (tpp) REVERT: C 750 SER cc_start: 0.8983 (t) cc_final: 0.8436 (m) REVERT: C 751 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8348 (p0) REVERT: C 762 GLN cc_start: 0.8141 (pp30) cc_final: 0.7905 (pp30) REVERT: C 904 TYR cc_start: 0.6952 (m-10) cc_final: 0.6680 (m-80) REVERT: C 990 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7072 (mt-10) outliers start: 113 outliers final: 54 residues processed: 368 average time/residue: 0.1763 time to fit residues: 107.5574 Evaluate side-chains 248 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 184 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain H residue 20 MET Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 109 GLN Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 256 optimal weight: 0.0030 chunk 207 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 166 optimal weight: 0.5980 chunk 205 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 239 optimal weight: 0.9980 chunk 231 optimal weight: 2.9990 chunk 27 optimal weight: 30.0000 chunk 113 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 ASN L 6 GLN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1125 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.176208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.127606 restraints weight = 86633.680| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 4.81 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.9096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29225 Z= 0.143 Angle : 0.617 16.934 39809 Z= 0.316 Chirality : 0.046 0.564 4606 Planarity : 0.004 0.055 5063 Dihedral : 5.196 68.789 3907 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.55 % Favored : 96.39 % Rotamer: Outliers : 2.50 % Allowed : 14.88 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.14), residues: 3576 helix: 1.27 (0.21), residues: 623 sheet: 0.21 (0.17), residues: 958 loop : -0.97 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1091 TYR 0.036 0.001 TYR B 351 PHE 0.042 0.002 PHE B1075 TRP 0.029 0.002 TRP C1102 HIS 0.006 0.001 HIS K 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (29188) covalent geometry : angle 0.60234 / 0.31 (39722) SS BOND : bond 0.00402 / 0.23 ( 6) SS BOND : angle 1.35668 / 0.64 ( 12) hydrogen bonds : bond 0.04220 / 2.88 ( 1061) hydrogen bonds : angle 5.97383 / 4.10 ( 2868) Misc. bond : bond 0.00051 / 0.02 ( 6) link_NAG-ASN : bond 0.00736 / 0.42 ( 25) link_NAG-ASN : angle 3.13591 / 1.88 ( 75) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 213 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 22 CYS cc_start: 0.0242 (OUTLIER) cc_final: -0.0913 (p) REVERT: H 81 MET cc_start: -0.4318 (ttt) cc_final: -0.4722 (mtt) REVERT: J 109 GLN cc_start: 0.1770 (OUTLIER) cc_final: 0.1468 (mp10) REVERT: K 76 ASP cc_start: 0.6170 (m-30) cc_final: 0.5599 (p0) REVERT: K 93 TYR cc_start: 0.4479 (OUTLIER) cc_final: 0.2786 (t80) REVERT: L 93 TYR cc_start: 0.1170 (OUTLIER) cc_final: -0.0051 (m-80) REVERT: A 91 TYR cc_start: 0.4385 (OUTLIER) cc_final: 0.3651 (t80) REVERT: A 586 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.7089 (t0) REVERT: A 740 MET cc_start: 0.8215 (tpp) cc_final: 0.7777 (ttt) REVERT: A 796 ASP cc_start: 0.7194 (p0) cc_final: 0.6748 (p0) REVERT: A 1100 THR cc_start: 0.2608 (p) cc_final: 0.2376 (p) REVERT: B 392 PHE cc_start: 0.6952 (m-80) cc_final: 0.6504 (m-80) REVERT: B 508 TYR cc_start: 0.7357 (m-80) cc_final: 0.7002 (m-80) REVERT: B 572 THR cc_start: 0.7383 (m) cc_final: 0.7176 (p) REVERT: B 693 ILE cc_start: 0.8241 (mp) cc_final: 0.8005 (mt) REVERT: B 781 VAL cc_start: 0.8893 (t) cc_final: 0.8671 (t) REVERT: C 201 PHE cc_start: 0.4542 (t80) cc_final: 0.3901 (t80) outliers start: 78 outliers final: 42 residues processed: 276 average time/residue: 0.1598 time to fit residues: 76.4370 Evaluate side-chains 222 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 174 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 20 MET Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain J residue 109 GLN Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 93 TYR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 350 optimal weight: 2.9990 chunk 12 optimal weight: 40.0000 chunk 238 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 180 optimal weight: 5.9990 chunk 18 optimal weight: 50.0000 chunk 127 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 343 optimal weight: 1.9990 chunk 279 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 ASN K 55 HIS L 44 GLN A 66 HIS A 388 ASN A 675 GLN A 955 ASN A 978 ASN B 655 HIS B 926 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 920 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.170907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.116798 restraints weight = 77817.078| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 4.17 r_work: 0.3317 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 1.0653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 29225 Z= 0.215 Angle : 0.698 11.951 39809 Z= 0.360 Chirality : 0.048 0.383 4606 Planarity : 0.005 0.101 5063 Dihedral : 5.201 69.597 3907 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.98 % Favored : 94.94 % Rotamer: Outliers : 3.29 % Allowed : 14.72 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.14), residues: 3576 helix: 1.05 (0.20), residues: 633 sheet: 0.13 (0.17), residues: 945 loop : -0.99 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 765 TYR 0.030 0.002 TYR J 32 PHE 0.042 0.002 PHE B1075 TRP 0.027 0.002 TRP B 64 HIS 0.013 0.002 HIS K 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 (29188) covalent geometry : angle 0.68920 / 0.36 (39722) SS BOND : bond 0.00450 / 0.24 ( 6) SS BOND : angle 0.64182 / 0.36 ( 12) hydrogen bonds : bond 0.04874 / 3.28 ( 1061) hydrogen bonds : angle 5.86213 / 4.01 ( 2868) Misc. bond : bond 0.00059 / 0.03 ( 6) link_NAG-ASN : bond 0.00850 / 0.48 ( 25) link_NAG-ASN : angle 2.61974 / 1.78 ( 75) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 187 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 36 TRP cc_start: 0.5455 (t-100) cc_final: 0.4941 (t-100) REVERT: J 81 MET cc_start: -0.1386 (tpp) cc_final: -0.2161 (tpp) REVERT: J 109 GLN cc_start: 0.3920 (OUTLIER) cc_final: 0.3315 (mp10) REVERT: K 76 ASP cc_start: 0.6306 (m-30) cc_final: 0.5721 (p0) REVERT: K 93 TYR cc_start: 0.4563 (OUTLIER) cc_final: 0.3530 (t80) REVERT: L 93 TYR cc_start: -0.0148 (OUTLIER) cc_final: -0.0923 (m-80) REVERT: A 104 TRP cc_start: 0.6339 (m-90) cc_final: 0.4643 (m-90) REVERT: A 306 PHE cc_start: 0.7558 (t80) cc_final: 0.7255 (t80) REVERT: A 796 ASP cc_start: 0.8059 (p0) cc_final: 0.7616 (p0) REVERT: A 858 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9197 (pp) REVERT: A 1082 CYS cc_start: 0.4564 (OUTLIER) cc_final: 0.4328 (t) REVERT: B 42 VAL cc_start: 0.8618 (t) cc_final: 0.8054 (t) REVERT: B 200 TYR cc_start: 0.6020 (m-80) cc_final: 0.5090 (m-80) REVERT: B 228 ASP cc_start: 0.5207 (OUTLIER) cc_final: 0.4831 (p0) REVERT: B 549 THR cc_start: 0.8386 (m) cc_final: 0.8011 (p) REVERT: B 559 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.7692 (t80) REVERT: B 588 THR cc_start: 0.8631 (m) cc_final: 0.8281 (p) REVERT: B 698 SER cc_start: 0.8842 (OUTLIER) cc_final: 0.8214 (p) REVERT: B 984 LEU cc_start: 0.7855 (tp) cc_final: 0.7525 (tt) REVERT: B 1119 ASN cc_start: 0.9191 (OUTLIER) cc_final: 0.8891 (t0) REVERT: C 90 VAL cc_start: 0.9080 (t) cc_final: 0.8839 (p) REVERT: C 950 ASP cc_start: 0.9334 (OUTLIER) cc_final: 0.9016 (t0) REVERT: C 990 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7416 (mt-10) outliers start: 103 outliers final: 62 residues processed: 266 average time/residue: 0.1573 time to fit residues: 72.7711 Evaluate side-chains 225 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 152 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 20 MET Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 109 GLN Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 93 TYR Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 6 optimal weight: 0.0270 chunk 260 optimal weight: 2.9990 chunk 15 optimal weight: 20.0000 chunk 327 optimal weight: 2.9990 chunk 214 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 219 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 291 optimal weight: 9.9990 overall best weight: 2.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 GLN ** K 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C 955 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.164687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.109927 restraints weight = 80648.550| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 4.21 r_work: 0.3264 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 1.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 29225 Z= 0.180 Angle : 0.609 11.016 39809 Z= 0.312 Chirality : 0.045 0.381 4606 Planarity : 0.004 0.063 5063 Dihedral : 4.993 68.687 3906 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.36 % Favored : 96.62 % Rotamer: Outliers : 2.62 % Allowed : 16.09 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.14), residues: 3576 helix: 1.41 (0.21), residues: 631 sheet: 0.17 (0.17), residues: 944 loop : -0.99 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 905 TYR 0.022 0.001 TYR A1067 PHE 0.044 0.002 PHE B 541 TRP 0.041 0.002 TRP H 36 HIS 0.016 0.002 HIS K 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (29188) covalent geometry : angle 0.60027 / 0.31 (39722) SS BOND : bond 0.00429 / 0.24 ( 6) SS BOND : angle 1.01818 / 0.47 ( 12) hydrogen bonds : bond 0.04313 / 2.91 ( 1061) hydrogen bonds : angle 5.65214 / 3.90 ( 2868) Misc. bond : bond 0.00047 / 0.02 ( 6) link_NAG-ASN : bond 0.00432 / 0.26 ( 25) link_NAG-ASN : angle 2.40012 / 1.63 ( 75) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 161 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 20 MET cc_start: -0.1716 (OUTLIER) cc_final: -0.1926 (mmm) REVERT: J 36 TRP cc_start: 0.5680 (t-100) cc_final: 0.5356 (t-100) REVERT: J 81 MET cc_start: -0.1316 (tpp) cc_final: -0.2020 (tpp) REVERT: J 109 GLN cc_start: 0.3954 (OUTLIER) cc_final: 0.3330 (mp10) REVERT: K 76 ASP cc_start: 0.5981 (m-30) cc_final: 0.5453 (p0) REVERT: K 93 TYR cc_start: 0.4356 (OUTLIER) cc_final: 0.3910 (m-80) REVERT: L 93 TYR cc_start: -0.0380 (OUTLIER) cc_final: -0.1056 (m-80) REVERT: A 104 TRP cc_start: 0.6288 (m-90) cc_final: 0.4588 (m-90) REVERT: A 796 ASP cc_start: 0.7936 (p0) cc_final: 0.7576 (p0) REVERT: A 858 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9184 (pp) REVERT: B 192 PHE cc_start: 0.6828 (m-80) cc_final: 0.6351 (t80) REVERT: B 200 TYR cc_start: 0.6255 (m-80) cc_final: 0.5747 (m-80) REVERT: B 559 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.7686 (t80) REVERT: C 90 VAL cc_start: 0.8980 (t) cc_final: 0.8678 (p) REVERT: C 238 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7628 (p90) REVERT: C 950 ASP cc_start: 0.9287 (m-30) cc_final: 0.9087 (t0) outliers start: 82 outliers final: 51 residues processed: 227 average time/residue: 0.1629 time to fit residues: 63.3887 Evaluate side-chains 195 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 137 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain H residue 20 MET Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain J residue 109 GLN Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 93 TYR Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1083 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 223 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 130 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 237 optimal weight: 0.9990 chunk 216 optimal weight: 0.7980 chunk 127 optimal weight: 0.7980 chunk 329 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 chunk 131 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS B 978 ASN B1002 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 913 GLN C 955 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.164087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.111285 restraints weight = 80696.903| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 4.14 r_work: 0.3290 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 1.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29225 Z= 0.135 Angle : 0.568 10.460 39809 Z= 0.291 Chirality : 0.044 0.341 4606 Planarity : 0.004 0.061 5063 Dihedral : 4.779 68.726 3906 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.05 % Favored : 95.89 % Rotamer: Outliers : 2.50 % Allowed : 16.47 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.14), residues: 3576 helix: 1.83 (0.22), residues: 613 sheet: 0.24 (0.17), residues: 948 loop : -0.92 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 328 TYR 0.023 0.001 TYR C 170 PHE 0.033 0.001 PHE C 823 TRP 0.017 0.001 TRP B 64 HIS 0.010 0.001 HIS K 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (29188) covalent geometry : angle 0.56076 / 0.29 (39722) SS BOND : bond 0.00338 / 0.21 ( 6) SS BOND : angle 0.72223 / 0.33 ( 12) hydrogen bonds : bond 0.03991 / 2.67 ( 1061) hydrogen bonds : angle 5.38335 / 3.72 ( 2868) Misc. bond : bond 0.00025 / 0.01 ( 6) link_NAG-ASN : bond 0.00353 / 0.20 ( 25) link_NAG-ASN : angle 2.21757 / 1.47 ( 75) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 144 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 20 MET cc_start: -0.1478 (OUTLIER) cc_final: -0.2338 (mmm) REVERT: H 81 MET cc_start: -0.5856 (ttt) cc_final: -0.6390 (mtt) REVERT: J 36 TRP cc_start: 0.5676 (t-100) cc_final: 0.5244 (t-100) REVERT: J 81 MET cc_start: -0.1048 (tpp) cc_final: -0.1849 (tpp) REVERT: J 109 GLN cc_start: 0.3690 (OUTLIER) cc_final: 0.3027 (mp10) REVERT: K 76 ASP cc_start: 0.5948 (m-30) cc_final: 0.5395 (p0) REVERT: K 93 TYR cc_start: 0.4691 (OUTLIER) cc_final: 0.4437 (m-80) REVERT: L 93 TYR cc_start: 0.0063 (OUTLIER) cc_final: -0.0749 (m-80) REVERT: A 104 TRP cc_start: 0.6554 (m-90) cc_final: 0.5949 (m-90) REVERT: A 796 ASP cc_start: 0.8006 (p0) cc_final: 0.7686 (p0) REVERT: A 858 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9167 (pp) REVERT: B 192 PHE cc_start: 0.6742 (m-80) cc_final: 0.6371 (t80) REVERT: B 200 TYR cc_start: 0.6472 (m-80) cc_final: 0.6042 (m-80) REVERT: B 984 LEU cc_start: 0.7920 (tp) cc_final: 0.7715 (tt) REVERT: C 238 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.7305 (p90) outliers start: 78 outliers final: 55 residues processed: 210 average time/residue: 0.1651 time to fit residues: 59.8816 Evaluate side-chains 192 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 131 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain H residue 20 MET Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 109 GLN Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 93 TYR Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1083 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 344 optimal weight: 4.9990 chunk 168 optimal weight: 20.0000 chunk 96 optimal weight: 0.0020 chunk 264 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 201 optimal weight: 5.9990 chunk 118 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 353 optimal weight: 2.9990 chunk 328 optimal weight: 1.9990 chunk 165 optimal weight: 7.9990 overall best weight: 1.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A1106 GLN B 978 ASN B1088 HIS C 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.161056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.105749 restraints weight = 78369.968| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.83 r_work: 0.3247 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 1.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 29225 Z= 0.184 Angle : 0.631 14.997 39809 Z= 0.320 Chirality : 0.045 0.386 4606 Planarity : 0.004 0.061 5063 Dihedral : 4.927 67.825 3906 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.78 % Favored : 96.17 % Rotamer: Outliers : 2.34 % Allowed : 16.54 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.14), residues: 3576 helix: 1.68 (0.21), residues: 618 sheet: 0.22 (0.17), residues: 917 loop : -0.96 (0.13), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 60 TYR 0.022 0.001 TYR A1138 PHE 0.028 0.002 PHE B 541 TRP 0.018 0.001 TRP B 64 HIS 0.009 0.001 HIS K 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (29188) covalent geometry : angle 0.62294 / 0.32 (39722) SS BOND : bond 0.00528 / 0.31 ( 6) SS BOND : angle 0.72855 / 0.34 ( 12) hydrogen bonds : bond 0.04497 / 3.03 ( 1061) hydrogen bonds : angle 5.45216 / 3.77 ( 2868) Misc. bond : bond 0.00035 / 0.02 ( 6) link_NAG-ASN : bond 0.00489 / 0.27 ( 25) link_NAG-ASN : angle 2.45867 / 1.65 ( 75) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 138 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 20 MET cc_start: -0.1772 (OUTLIER) cc_final: -0.2209 (mmm) REVERT: J 35 HIS cc_start: 0.2176 (m-70) cc_final: 0.1635 (m-70) REVERT: J 109 GLN cc_start: 0.3608 (OUTLIER) cc_final: 0.2809 (mp10) REVERT: K 41 TRP cc_start: 0.2374 (m100) cc_final: 0.1928 (m100) REVERT: K 76 ASP cc_start: 0.6010 (m-30) cc_final: 0.5427 (p0) REVERT: L 93 TYR cc_start: -0.0289 (OUTLIER) cc_final: -0.1012 (m-80) REVERT: A 104 TRP cc_start: 0.6614 (m-90) cc_final: 0.6024 (m-90) REVERT: A 796 ASP cc_start: 0.7862 (p0) cc_final: 0.7597 (p0) REVERT: A 858 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9142 (pp) REVERT: A 1106 GLN cc_start: 0.9305 (OUTLIER) cc_final: 0.9104 (pt0) REVERT: B 192 PHE cc_start: 0.6957 (m-80) cc_final: 0.6681 (t80) REVERT: C 197 ILE cc_start: 0.8817 (mt) cc_final: 0.8408 (pt) REVERT: C 200 TYR cc_start: 0.7917 (m-80) cc_final: 0.7422 (m-80) REVERT: C 740 MET cc_start: 0.9089 (tpp) cc_final: 0.8817 (ttp) REVERT: C 948 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8234 (pp) outliers start: 73 outliers final: 54 residues processed: 203 average time/residue: 0.1654 time to fit residues: 57.9492 Evaluate side-chains 178 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 118 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 20 MET Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 109 GLN Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 93 TYR Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 34 optimal weight: 9.9990 chunk 309 optimal weight: 3.9990 chunk 302 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 274 optimal weight: 8.9990 chunk 285 optimal weight: 20.0000 chunk 260 optimal weight: 0.4980 chunk 137 optimal weight: 0.5980 chunk 84 optimal weight: 0.1980 chunk 138 optimal weight: 0.8980 chunk 222 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 GLN A1106 GLN C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.161759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.109345 restraints weight = 78986.265| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 4.31 r_work: 0.3263 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 1.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 29225 Z= 0.110 Angle : 0.555 10.147 39809 Z= 0.281 Chirality : 0.044 0.342 4606 Planarity : 0.004 0.059 5063 Dihedral : 4.670 67.877 3906 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.34 % Rotamer: Outliers : 1.76 % Allowed : 17.24 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.14), residues: 3576 helix: 1.93 (0.22), residues: 613 sheet: 0.33 (0.17), residues: 944 loop : -0.91 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1107 TYR 0.049 0.001 TYR A 279 PHE 0.023 0.001 PHE B1075 TRP 0.020 0.001 TRP C 353 HIS 0.005 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (29188) covalent geometry : angle 0.54711 / 0.28 (39722) SS BOND : bond 0.00357 / 0.23 ( 6) SS BOND : angle 0.69524 / 0.34 ( 12) hydrogen bonds : bond 0.03850 / 2.59 ( 1061) hydrogen bonds : angle 5.20557 / 3.60 ( 2868) Misc. bond : bond 0.00021 / 0.01 ( 6) link_NAG-ASN : bond 0.00320 / 0.18 ( 25) link_NAG-ASN : angle 2.21343 / 1.48 ( 75) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 125 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 20 MET cc_start: -0.1266 (OUTLIER) cc_final: -0.1677 (mmm) REVERT: J 109 GLN cc_start: 0.3450 (OUTLIER) cc_final: 0.2686 (mp10) REVERT: K 76 ASP cc_start: 0.5989 (m-30) cc_final: 0.5417 (p0) REVERT: L 93 TYR cc_start: -0.0170 (OUTLIER) cc_final: -0.0895 (m-80) REVERT: A 104 TRP cc_start: 0.6684 (m-90) cc_final: 0.6085 (m-90) REVERT: A 796 ASP cc_start: 0.7947 (p0) cc_final: 0.7722 (p0) REVERT: A 858 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9066 (pp) REVERT: A 1106 GLN cc_start: 0.9352 (OUTLIER) cc_final: 0.9060 (pt0) REVERT: C 740 MET cc_start: 0.9088 (tpp) cc_final: 0.8754 (ttp) REVERT: C 948 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8221 (pp) outliers start: 55 outliers final: 43 residues processed: 173 average time/residue: 0.1663 time to fit residues: 49.8296 Evaluate side-chains 163 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 114 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain H residue 20 MET Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 109 GLN Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 93 TYR Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 951 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 166 optimal weight: 10.0000 chunk 152 optimal weight: 0.3980 chunk 136 optimal weight: 3.9990 chunk 39 optimal weight: 30.0000 chunk 214 optimal weight: 7.9990 chunk 43 optimal weight: 0.0470 chunk 4 optimal weight: 20.0000 chunk 270 optimal weight: 8.9990 chunk 332 optimal weight: 0.6980 chunk 352 optimal weight: 0.9980 chunk 22 optimal weight: 30.0000 overall best weight: 1.2280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.160654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.107705 restraints weight = 78919.072| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 4.31 r_work: 0.3240 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 1.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29225 Z= 0.131 Angle : 0.566 10.401 39809 Z= 0.287 Chirality : 0.044 0.363 4606 Planarity : 0.004 0.059 5063 Dihedral : 4.605 66.347 3906 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.78 % Favored : 96.20 % Rotamer: Outliers : 1.95 % Allowed : 17.24 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.14), residues: 3576 helix: 1.98 (0.21), residues: 616 sheet: 0.36 (0.17), residues: 933 loop : -0.89 (0.14), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1107 TYR 0.021 0.001 TYR B1138 PHE 0.026 0.001 PHE C 168 TRP 0.022 0.001 TRP K 41 HIS 0.005 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (29188) covalent geometry : angle 0.55847 / 0.29 (39722) SS BOND : bond 0.00334 / 0.22 ( 6) SS BOND : angle 0.63689 / 0.31 ( 12) hydrogen bonds : bond 0.03953 / 2.63 ( 1061) hydrogen bonds : angle 5.14601 / 3.55 ( 2868) Misc. bond : bond 0.00028 / 0.01 ( 6) link_NAG-ASN : bond 0.00333 / 0.19 ( 25) link_NAG-ASN : angle 2.25200 / 1.50 ( 75) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 124 time to evaluate : 2.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 20 MET cc_start: -0.1655 (OUTLIER) cc_final: -0.2092 (mmm) REVERT: J 36 TRP cc_start: 0.5542 (t-100) cc_final: 0.5211 (t-100) REVERT: J 109 GLN cc_start: 0.3257 (OUTLIER) cc_final: 0.2431 (mp10) REVERT: K 41 TRP cc_start: 0.1354 (m100) cc_final: 0.1056 (m100) REVERT: K 76 ASP cc_start: 0.5936 (m-30) cc_final: 0.5332 (p0) REVERT: K 92 TYR cc_start: 0.4892 (t80) cc_final: 0.4550 (t80) REVERT: K 93 TYR cc_start: 0.4772 (OUTLIER) cc_final: 0.4537 (t80) REVERT: L 93 TYR cc_start: -0.0006 (OUTLIER) cc_final: -0.0812 (m-80) REVERT: A 104 TRP cc_start: 0.6698 (m-90) cc_final: 0.6101 (m-90) REVERT: A 186 PHE cc_start: 0.3440 (t80) cc_final: 0.3166 (t80) REVERT: A 796 ASP cc_start: 0.7965 (p0) cc_final: 0.7748 (p0) REVERT: A 858 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9074 (pp) REVERT: B 41 LYS cc_start: 0.8376 (mttp) cc_final: 0.7952 (mmtm) REVERT: C 740 MET cc_start: 0.9085 (tpp) cc_final: 0.8763 (ttp) REVERT: C 948 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8147 (pp) REVERT: C 950 ASP cc_start: 0.9090 (t0) cc_final: 0.8818 (t0) outliers start: 61 outliers final: 46 residues processed: 176 average time/residue: 0.1689 time to fit residues: 51.2978 Evaluate side-chains 170 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 118 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 20 MET Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 109 GLN Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 93 TYR Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 951 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 135 optimal weight: 1.9990 chunk 262 optimal weight: 0.9980 chunk 307 optimal weight: 10.0000 chunk 208 optimal weight: 0.9990 chunk 49 optimal weight: 20.0000 chunk 102 optimal weight: 4.9990 chunk 234 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 230 optimal weight: 0.8980 chunk 202 optimal weight: 0.6980 chunk 238 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.161125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.109100 restraints weight = 79228.456| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 4.08 r_work: 0.3246 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 1.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29225 Z= 0.106 Angle : 0.553 12.972 39809 Z= 0.277 Chirality : 0.044 0.346 4606 Planarity : 0.004 0.058 5063 Dihedral : 4.480 64.398 3906 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.86 % Favored : 96.11 % Rotamer: Outliers : 1.76 % Allowed : 17.63 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.14), residues: 3576 helix: 2.02 (0.21), residues: 622 sheet: 0.42 (0.17), residues: 933 loop : -0.83 (0.14), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 765 TYR 0.020 0.001 TYR B 170 PHE 0.024 0.001 PHE C 168 TRP 0.020 0.001 TRP C 353 HIS 0.006 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (29188) covalent geometry : angle 0.54578 / 0.28 (39722) SS BOND : bond 0.00342 / 0.23 ( 6) SS BOND : angle 0.56778 / 0.28 ( 12) hydrogen bonds : bond 0.03654 / 2.46 ( 1061) hydrogen bonds : angle 5.02069 / 3.48 ( 2868) Misc. bond : bond 0.00026 / 0.01 ( 6) link_NAG-ASN : bond 0.00300 / 0.17 ( 25) link_NAG-ASN : angle 2.13306 / 1.42 ( 75) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9156.83 seconds wall clock time: 157 minutes 26.09 seconds (9446.09 seconds total)