Starting phenix.real_space_refine on Sun Feb 18 06:25:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crv_7573/02_2024/6crv_7573.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crv_7573/02_2024/6crv_7573.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crv_7573/02_2024/6crv_7573.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crv_7573/02_2024/6crv_7573.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crv_7573/02_2024/6crv_7573.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crv_7573/02_2024/6crv_7573.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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 111 5.16 5 C 13362 2.51 5 N 3438 2.21 5 O 4125 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21036 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 6833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 6833 Classifications: {'peptide': 881} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 841} Chain breaks: 5 Chain: "B" Number of atoms: 6833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 6833 Classifications: {'peptide': 881} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 841} Chain breaks: 5 Chain: "C" Number of atoms: 6833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 6833 Classifications: {'peptide': 881} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 841} Chain breaks: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 11.03, per 1000 atoms: 0.52 Number of scatterers: 21036 At special positions: 0 Unit cell: (146.26, 149.35, 144.2, 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 111 16.00 O 4125 8.00 N 3438 7.00 C 13362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 133 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.02 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.02 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.04 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.03 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.00 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.02 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.02 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.00 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.02 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 133 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.02 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.02 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.00 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 65 " " NAG A1304 " - " ASN A 691 " " NAG A1308 " - " ASN A1080 " " NAG A1309 " - " ASN A1116 " " NAG A1310 " - " ASN A1056 " " NAG A1311 " - " ASN A 602 " " NAG B1301 " - " ASN B 65 " " NAG B1304 " - " ASN B 691 " " NAG B1308 " - " ASN B1080 " " NAG B1309 " - " ASN B1116 " " NAG B1310 " - " ASN B1056 " " NAG B1311 " - " ASN B 602 " " NAG C1301 " - " ASN C 65 " " NAG C1304 " - " ASN C 691 " " NAG C1308 " - " ASN C1080 " " NAG C1309 " - " ASN C1116 " " NAG C1310 " - " ASN C1056 " " NAG C1311 " - " ASN C 602 " " NAG D 1 " - " ASN A 269 " " NAG E 1 " - " ASN A 783 " " NAG F 1 " - " ASN A 699 " " NAG G 1 " - " ASN B 269 " " NAG H 1 " - " ASN B 783 " " NAG I 1 " - " ASN B 699 " " NAG J 1 " - " ASN C 269 " " NAG K 1 " - " ASN C 783 " " NAG L 1 " - " ASN C 699 " Time building additional restraints: 9.01 Conformation dependent library (CDL) restraints added in 4.0 seconds 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4950 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 45 sheets defined 24.9% alpha, 42.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 602 through 612 Processing helix chain 'A' and resid 719 through 724 Processing helix chain 'A' and resid 728 through 735 Processing helix chain 'A' and resid 736 through 739 Processing helix chain 'A' and resid 740 through 765 removed outlier: 3.534A pdb=" N GLN A 744 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 763 " --> pdb=" O ASN A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 805 removed outlier: 3.584A pdb=" N LEU A 803 " --> pdb=" O PHE A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 866 removed outlier: 3.536A pdb=" N THR A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 removed outlier: 3.550A pdb=" N PHE A 870 " --> pdb=" O GLY A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 890 Processing helix chain 'A' and resid 895 through 900 removed outlier: 3.576A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 923 Processing helix chain 'A' and resid 927 through 947 removed outlier: 3.587A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN A 937 " --> pdb=" O VAL A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 967 through 1013 removed outlier: 3.569A pdb=" N THR A 980 " --> pdb=" O ASP A 976 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 998 " --> pdb=" O LEU A 994 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU A 999 " --> pdb=" O ILE A 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 602 through 612 Processing helix chain 'B' and resid 719 through 724 Processing helix chain 'B' and resid 728 through 735 Processing helix chain 'B' and resid 736 through 739 Processing helix chain 'B' and resid 740 through 765 removed outlier: 3.534A pdb=" N GLN B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 763 " --> pdb=" O ASN B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 805 removed outlier: 3.584A pdb=" N LEU B 803 " --> pdb=" O PHE B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 866 removed outlier: 3.536A pdb=" N THR B 865 " --> pdb=" O SER B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 871 removed outlier: 3.550A pdb=" N PHE B 870 " --> pdb=" O GLY B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 890 Processing helix chain 'B' and resid 895 through 900 removed outlier: 3.576A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 923 Processing helix chain 'B' and resid 927 through 947 removed outlier: 3.588A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN B 937 " --> pdb=" O VAL B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 958 through 966 Processing helix chain 'B' and resid 967 through 1013 removed outlier: 3.569A pdb=" N THR B 980 " --> pdb=" O ASP B 976 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 998 " --> pdb=" O LEU B 994 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU B 999 " --> pdb=" O ILE B 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 602 through 612 Processing helix chain 'C' and resid 719 through 724 Processing helix chain 'C' and resid 728 through 735 Processing helix chain 'C' and resid 736 through 739 Processing helix chain 'C' and resid 740 through 765 removed outlier: 3.534A pdb=" N GLN C 744 " --> pdb=" O SER C 740 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR C 760 " --> pdb=" O GLN C 756 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 763 " --> pdb=" O ASN C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 805 removed outlier: 3.584A pdb=" N LEU C 803 " --> pdb=" O PHE C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 866 removed outlier: 3.536A pdb=" N THR C 865 " --> pdb=" O SER C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 871 removed outlier: 3.550A pdb=" N PHE C 870 " --> pdb=" O GLY C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 890 Processing helix chain 'C' and resid 895 through 900 removed outlier: 3.575A pdb=" N TYR C 899 " --> pdb=" O GLN C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 923 Processing helix chain 'C' and resid 927 through 947 removed outlier: 3.587A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN C 937 " --> pdb=" O VAL C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 948 through 950 No H-bonds generated for 'chain 'C' and resid 948 through 950' Processing helix chain 'C' and resid 958 through 966 Processing helix chain 'C' and resid 967 through 1013 removed outlier: 3.568A pdb=" N THR C 980 " --> pdb=" O ASP C 976 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA C 998 " --> pdb=" O LEU C 994 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU C 999 " --> pdb=" O ILE C 995 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 35 removed outlier: 7.800A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 251 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N HIS A 181 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE A 203 " --> pdb=" O HIS A 181 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ARG A 183 " --> pdb=" O GLN A 201 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLN A 201 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N PHE A 185 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLY A 199 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N PHE A 187 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N TYR A 197 " --> pdb=" O PHE A 187 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ASN A 189 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR A 195 " --> pdb=" O ASN A 189 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 46 through 47 removed outlier: 6.490A pdb=" N PHE A 47 " --> pdb=" O ARG C 553 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER C 561 " --> pdb=" O GLY C 552 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL C 313 " --> pdb=" O ASN C 528 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 59 removed outlier: 3.813A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 82 removed outlier: 6.587A pdb=" N VAL A 123 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE A 164 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE A 125 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU A 162 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA A 127 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN A 129 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASN A 158 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU A 131 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA A 156 " --> pdb=" O GLU A 131 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N CYS A 133 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N ASP A 154 " --> pdb=" O CYS A 133 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A 135 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE A 152 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE A 137 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR A 150 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA A 139 " --> pdb=" O THR A 148 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 81 through 82 removed outlier: 13.934A pdb=" N PHE A 231 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 13.514A pdb=" N LEU A 132 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 13.118A pdb=" N ALA A 233 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 10.294A pdb=" N ASP A 134 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 9.998A pdb=" N LEU A 235 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ALA A 237 " --> pdb=" O PRO A 136 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE A 138 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N SER A 239 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL A 140 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL A 123 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE A 164 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE A 125 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU A 162 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA A 127 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN A 129 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASN A 158 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU A 131 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA A 156 " --> pdb=" O GLU A 131 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N CYS A 133 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N ASP A 154 " --> pdb=" O CYS A 133 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A 135 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE A 152 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE A 137 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR A 150 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA A 139 " --> pdb=" O THR A 148 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 615 through 616 removed outlier: 3.952A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN A 304 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY A 579 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY A 580 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 314 removed outlier: 6.550A pdb=" N VAL A 313 " --> pdb=" O ASN A 528 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER A 561 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE A 551 " --> pdb=" O PHE B 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 640 through 646 removed outlier: 6.060A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N VAL A 642 " --> pdb=" O THR A 678 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 683 through 685 removed outlier: 6.225A pdb=" N ALA A 683 " --> pdb=" O MET B 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.627A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY A1041 " --> pdb=" O ALA A1038 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.627A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A1060 " --> pdb=" O PHE A1077 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AB5, first strand: chain 'A' and resid 769 through 771 Processing sheet with id=AB6, first strand: chain 'A' and resid 778 through 779 removed outlier: 3.678A pdb=" N PHE A 782 " --> pdb=" O PHE A 779 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 821 through 823 Processing sheet with id=AB8, first strand: chain 'A' and resid 1102 through 1107 removed outlier: 4.366A pdb=" N ALA A1069 " --> pdb=" O SER A1105 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 31 through 35 Processing sheet with id=AC1, first strand: chain 'B' and resid 31 through 35 removed outlier: 7.801A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N HIS B 181 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE B 203 " --> pdb=" O HIS B 181 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ARG B 183 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLN B 201 " --> pdb=" O ARG B 183 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N PHE B 185 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLY B 199 " --> pdb=" O PHE B 185 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N PHE B 187 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N TYR B 197 " --> pdb=" O PHE B 187 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ASN B 189 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR B 195 " --> pdb=" O ASN B 189 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LEU B 194 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 51 through 59 removed outlier: 3.813A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 81 through 82 removed outlier: 6.587A pdb=" N VAL B 123 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE B 164 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE B 125 " --> pdb=" O GLU B 162 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU B 162 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA B 127 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN B 129 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASN B 158 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU B 131 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA B 156 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N CYS B 133 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ASP B 154 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN B 135 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE B 152 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N PHE B 137 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR B 150 " --> pdb=" O PHE B 137 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 139 " --> pdb=" O THR B 148 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 81 through 82 removed outlier: 13.934A pdb=" N PHE B 231 " --> pdb=" O PHE B 130 " (cutoff:3.500A) removed outlier: 13.515A pdb=" N LEU B 132 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 13.119A pdb=" N ALA B 233 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 10.294A pdb=" N ASP B 134 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N LEU B 235 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ALA B 237 " --> pdb=" O PRO B 136 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE B 138 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N SER B 239 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL B 140 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL B 123 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE B 164 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE B 125 " --> pdb=" O GLU B 162 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU B 162 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA B 127 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN B 129 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASN B 158 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU B 131 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA B 156 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N CYS B 133 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ASP B 154 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN B 135 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE B 152 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N PHE B 137 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR B 150 " --> pdb=" O PHE B 137 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 139 " --> pdb=" O THR B 148 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 615 through 616 removed outlier: 3.952A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN B 304 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY B 579 " --> pdb=" O ASN B 304 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 312 through 314 removed outlier: 6.550A pdb=" N VAL B 313 " --> pdb=" O ASN B 528 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER B 561 " --> pdb=" O GLY B 552 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 640 through 646 removed outlier: 6.060A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N VAL B 642 " --> pdb=" O THR B 678 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 683 through 685 removed outlier: 6.196A pdb=" N ALA B 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.627A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B1041 " --> pdb=" O ALA B1038 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.627A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA B1060 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AD3, first strand: chain 'B' and resid 778 through 779 removed outlier: 3.678A pdb=" N PHE B 782 " --> pdb=" O PHE B 779 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 821 through 823 Processing sheet with id=AD5, first strand: chain 'B' and resid 1102 through 1107 removed outlier: 4.366A pdb=" N ALA B1069 " --> pdb=" O SER B1105 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 31 through 35 Processing sheet with id=AD7, first strand: chain 'C' and resid 31 through 35 removed outlier: 7.801A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N HIS C 181 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE C 203 " --> pdb=" O HIS C 181 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ARG C 183 " --> pdb=" O GLN C 201 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLN C 201 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N PHE C 185 " --> pdb=" O GLY C 199 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLY C 199 " --> pdb=" O PHE C 185 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N PHE C 187 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N TYR C 197 " --> pdb=" O PHE C 187 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ASN C 189 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR C 195 " --> pdb=" O ASN C 189 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU C 194 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 51 through 59 removed outlier: 3.813A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 81 through 82 removed outlier: 6.587A pdb=" N VAL C 123 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE C 164 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE C 125 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU C 162 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA C 127 " --> pdb=" O THR C 160 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN C 129 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASN C 158 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU C 131 " --> pdb=" O ALA C 156 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA C 156 " --> pdb=" O GLU C 131 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N CYS C 133 " --> pdb=" O ASP C 154 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ASP C 154 " --> pdb=" O CYS C 133 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN C 135 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE C 152 " --> pdb=" O ASN C 135 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE C 137 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR C 150 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA C 139 " --> pdb=" O THR C 148 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 81 through 82 removed outlier: 13.935A pdb=" N PHE C 231 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 13.514A pdb=" N LEU C 132 " --> pdb=" O PHE C 231 " (cutoff:3.500A) removed outlier: 13.119A pdb=" N ALA C 233 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N ASP C 134 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 9.998A pdb=" N LEU C 235 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ALA C 237 " --> pdb=" O PRO C 136 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE C 138 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N SER C 239 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL C 140 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL C 123 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE C 164 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE C 125 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU C 162 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA C 127 " --> pdb=" O THR C 160 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN C 129 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASN C 158 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU C 131 " --> pdb=" O ALA C 156 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA C 156 " --> pdb=" O GLU C 131 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N CYS C 133 " --> pdb=" O ASP C 154 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ASP C 154 " --> pdb=" O CYS C 133 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN C 135 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE C 152 " --> pdb=" O ASN C 135 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE C 137 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR C 150 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA C 139 " --> pdb=" O THR C 148 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 615 through 616 removed outlier: 3.953A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN C 304 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY C 579 " --> pdb=" O ASN C 304 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY C 580 " --> pdb=" O GLN C 599 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 640 through 646 removed outlier: 6.060A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N VAL C 642 " --> pdb=" O THR C 678 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.627A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY C1041 " --> pdb=" O ALA C1038 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.627A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA C1060 " --> pdb=" O PHE C1077 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE C1077 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 716 through 718 Processing sheet with id=AE7, first strand: chain 'C' and resid 778 through 779 removed outlier: 3.678A pdb=" N PHE C 782 " --> pdb=" O PHE C 779 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 821 through 823 Processing sheet with id=AE9, first strand: chain 'C' and resid 1102 through 1107 removed outlier: 4.367A pdb=" N ALA C1069 " --> pdb=" O SER C1105 " (cutoff:3.500A) 955 hydrogen bonds defined for protein. 2604 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.45 Time building geometry restraints manager: 9.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6362 1.33 - 1.46: 5223 1.46 - 1.58: 9742 1.58 - 1.71: 3 1.71 - 1.83: 153 Bond restraints: 21483 Sorted by residual: bond pdb=" CB CYS B1014 " pdb=" SG CYS B1014 " ideal model delta sigma weight residual 1.808 1.658 0.150 3.30e-02 9.18e+02 2.06e+01 bond pdb=" CB CYS C1014 " pdb=" SG CYS C1014 " ideal model delta sigma weight residual 1.808 1.658 0.150 3.30e-02 9.18e+02 2.06e+01 bond pdb=" CB CYS A1014 " pdb=" SG CYS A1014 " ideal model delta sigma weight residual 1.808 1.658 0.150 3.30e-02 9.18e+02 2.06e+01 bond pdb=" CA TYR A 300 " pdb=" CB TYR A 300 " ideal model delta sigma weight residual 1.532 1.483 0.048 1.58e-02 4.01e+03 9.42e+00 bond pdb=" CA TYR C 300 " pdb=" CB TYR C 300 " ideal model delta sigma weight residual 1.532 1.484 0.048 1.58e-02 4.01e+03 9.38e+00 ... (remaining 21478 not shown) Histogram of bond angle deviations from ideal: 95.51 - 103.22: 201 103.22 - 110.93: 7925 110.93 - 118.64: 9013 118.64 - 126.35: 11829 126.35 - 134.06: 243 Bond angle restraints: 29211 Sorted by residual: angle pdb=" N GLY C 867 " pdb=" CA GLY C 867 " pdb=" C GLY C 867 " ideal model delta sigma weight residual 110.95 119.29 -8.34 1.70e+00 3.46e-01 2.40e+01 angle pdb=" N GLY B 867 " pdb=" CA GLY B 867 " pdb=" C GLY B 867 " ideal model delta sigma weight residual 110.95 119.27 -8.32 1.70e+00 3.46e-01 2.40e+01 angle pdb=" N GLY A 867 " pdb=" CA GLY A 867 " pdb=" C GLY A 867 " ideal model delta sigma weight residual 110.95 119.26 -8.31 1.70e+00 3.46e-01 2.39e+01 angle pdb=" C PHE C 83 " pdb=" N LYS C 84 " pdb=" CA LYS C 84 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 angle pdb=" C PHE A 83 " pdb=" N LYS A 84 " pdb=" CA LYS A 84 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 ... (remaining 29206 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.45: 12941 21.45 - 42.89: 256 42.89 - 64.34: 69 64.34 - 85.78: 27 85.78 - 107.23: 12 Dihedral angle restraints: 13305 sinusoidal: 5631 harmonic: 7674 Sorted by residual: dihedral pdb=" CB CYS B1014 " pdb=" SG CYS B1014 " pdb=" SG CYS B1025 " pdb=" CB CYS B1025 " ideal model delta sinusoidal sigma weight residual -86.00 -169.27 83.27 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CB CYS A1014 " pdb=" SG CYS A1014 " pdb=" SG CYS A1025 " pdb=" CB CYS A1025 " ideal model delta sinusoidal sigma weight residual -86.00 -169.26 83.26 1 1.00e+01 1.00e-02 8.47e+01 dihedral pdb=" CB CYS C1014 " pdb=" SG CYS C1014 " pdb=" SG CYS C1025 " pdb=" CB CYS C1025 " ideal model delta sinusoidal sigma weight residual -86.00 -169.25 83.25 1 1.00e+01 1.00e-02 8.47e+01 ... (remaining 13302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2221 0.057 - 0.115: 1021 0.115 - 0.172: 180 0.172 - 0.230: 31 0.230 - 0.287: 12 Chirality restraints: 3465 Sorted by residual: chirality pdb=" CB VAL A 711 " pdb=" CA VAL A 711 " pdb=" CG1 VAL A 711 " pdb=" CG2 VAL A 711 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB VAL C 711 " pdb=" CA VAL C 711 " pdb=" CG1 VAL C 711 " pdb=" CG2 VAL C 711 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CB VAL B 711 " pdb=" CA VAL B 711 " pdb=" CG1 VAL B 711 " pdb=" CG2 VAL B 711 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 3462 not shown) Planarity restraints: 3753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 868 " 0.017 2.00e-02 2.50e+03 1.95e-02 9.50e+00 pdb=" CG TRP B 868 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP B 868 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP B 868 " -0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP B 868 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 868 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 868 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 868 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 868 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 868 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 868 " 0.017 2.00e-02 2.50e+03 1.94e-02 9.38e+00 pdb=" CG TRP A 868 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A 868 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP A 868 " -0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP A 868 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 868 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 868 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 868 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 868 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 868 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 868 " 0.017 2.00e-02 2.50e+03 1.93e-02 9.31e+00 pdb=" CG TRP C 868 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP C 868 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP C 868 " -0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP C 868 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C 868 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP C 868 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 868 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 868 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP C 868 " 0.005 2.00e-02 2.50e+03 ... (remaining 3750 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1339 2.72 - 3.26: 18996 3.26 - 3.81: 32848 3.81 - 4.35: 40034 4.35 - 4.90: 71121 Nonbonded interactions: 164338 Sorted by model distance: nonbonded pdb=" NH2 ARG A 306 " pdb=" OD1 ASP B 727 " model vdw 2.170 2.520 nonbonded pdb=" NH2 ARG B 306 " pdb=" OD1 ASP C 727 " model vdw 2.183 2.520 nonbonded pdb=" OE1 GLU B 999 " pdb=" NH2 ARG C1001 " model vdw 2.209 2.520 nonbonded pdb=" OE1 GLU A 999 " pdb=" NH2 ARG B1001 " model vdw 2.278 2.520 nonbonded pdb=" O GLY C 77 " pdb=" OH TYR C 252 " model vdw 2.302 2.440 ... (remaining 164333 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'K' } 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: 2.520 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: 0.040 Extract box with map and model: 8.220 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 59.220 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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 0.150 21483 Z= 0.834 Angle : 1.091 11.019 29211 Z= 0.597 Chirality : 0.064 0.287 3465 Planarity : 0.007 0.073 3726 Dihedral : 11.023 107.227 8256 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.26 % Allowed : 0.66 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.13), residues: 2607 helix: -3.57 (0.10), residues: 600 sheet: -0.70 (0.19), residues: 642 loop : -1.98 (0.14), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.008 TRP B 868 HIS 0.017 0.004 HIS A 33 PHE 0.051 0.005 PHE C 870 TYR 0.051 0.006 TYR C 197 ARG 0.013 0.002 ARG B1089 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 339 time to evaluate : 2.376 Fit side-chains revert: symmetry clash REVERT: A 67 THR cc_start: 0.7688 (m) cc_final: 0.7314 (p) REVERT: A 89 PHE cc_start: 0.6290 (t80) cc_final: 0.5806 (t80) REVERT: A 868 TRP cc_start: 0.5200 (t-100) cc_final: 0.4887 (t-100) REVERT: A 932 ASP cc_start: 0.7695 (t70) cc_final: 0.7483 (t0) REVERT: B 78 ASN cc_start: 0.6603 (p0) cc_final: 0.6034 (m110) REVERT: B 89 PHE cc_start: 0.6198 (t80) cc_final: 0.5882 (t80) REVERT: B 932 ASP cc_start: 0.7793 (t70) cc_final: 0.7519 (t0) REVERT: C 87 ILE cc_start: 0.8520 (pt) cc_final: 0.8314 (mm) REVERT: C 932 ASP cc_start: 0.7957 (t70) cc_final: 0.7666 (t0) outliers start: 6 outliers final: 2 residues processed: 345 average time/residue: 0.3718 time to fit residues: 188.9327 Evaluate side-chains 181 residues out of total 2283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 179 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain B residue 1022 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 206 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 154 optimal weight: 0.5980 chunk 239 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 GLN A 818 GLN A 883 GLN A1030 HIS A1046 HIS B 599 GLN B 721 ASN B 756 GLN B 818 GLN B1030 HIS B1046 HIS C 599 GLN C 818 GLN C1030 HIS C1046 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 21483 Z= 0.206 Angle : 0.635 7.462 29211 Z= 0.340 Chirality : 0.046 0.269 3465 Planarity : 0.005 0.050 3726 Dihedral : 9.841 72.597 3623 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.18 % Allowed : 4.99 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.15), residues: 2607 helix: -0.18 (0.19), residues: 609 sheet: -0.49 (0.19), residues: 660 loop : -1.73 (0.14), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 868 HIS 0.005 0.001 HIS A 33 PHE 0.022 0.002 PHE C 83 TYR 0.014 0.002 TYR A 266 ARG 0.004 0.000 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 210 time to evaluate : 2.344 Fit side-chains revert: symmetry clash REVERT: A 67 THR cc_start: 0.7294 (m) cc_final: 0.6787 (p) REVERT: A 99 ARG cc_start: 0.6212 (mmt90) cc_final: 0.5912 (mmt90) REVERT: A 721 ASN cc_start: 0.7247 (m-40) cc_final: 0.7031 (m-40) REVERT: A 819 TYR cc_start: 0.7964 (p90) cc_final: 0.7563 (p90) REVERT: B 78 ASN cc_start: 0.6824 (p0) cc_final: 0.6257 (m110) REVERT: B 89 PHE cc_start: 0.6439 (t80) cc_final: 0.6077 (t80) REVERT: B 99 ARG cc_start: 0.6022 (mmt90) cc_final: 0.5768 (mtt90) REVERT: B 758 ARG cc_start: 0.7604 (tmm160) cc_final: 0.7348 (ttp80) REVERT: B 762 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7204 (mm-30) REVERT: C 89 PHE cc_start: 0.6299 (t80) cc_final: 0.6072 (t80) REVERT: C 99 ARG cc_start: 0.6233 (mmt90) cc_final: 0.5695 (mtt90) REVERT: C 294 GLU cc_start: 0.7183 (pm20) cc_final: 0.6971 (pm20) REVERT: C 758 ARG cc_start: 0.7384 (tmm160) cc_final: 0.7143 (ttp80) outliers start: 27 outliers final: 18 residues processed: 232 average time/residue: 0.3687 time to fit residues: 128.7470 Evaluate side-chains 177 residues out of total 2283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 159 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain B residue 937 ASN Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 198 LYS Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1098 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 240 optimal weight: 2.9990 chunk 259 optimal weight: 4.9990 chunk 213 optimal weight: 3.9990 chunk 238 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 192 optimal weight: 10.0000 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 21483 Z= 0.259 Angle : 0.601 7.888 29211 Z= 0.320 Chirality : 0.047 0.291 3465 Planarity : 0.004 0.043 3726 Dihedral : 8.346 59.830 3623 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.84 % Allowed : 6.18 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 2607 helix: 1.08 (0.21), residues: 615 sheet: -0.33 (0.20), residues: 645 loop : -1.48 (0.15), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 868 HIS 0.005 0.001 HIS C1030 PHE 0.026 0.002 PHE A 83 TYR 0.017 0.002 TYR C 886 ARG 0.003 0.000 ARG C 306 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 180 time to evaluate : 2.444 Fit side-chains REVERT: A 67 THR cc_start: 0.7323 (m) cc_final: 0.6811 (p) REVERT: A 89 PHE cc_start: 0.6494 (t80) cc_final: 0.5953 (t80) REVERT: A 99 ARG cc_start: 0.6346 (mmt90) cc_final: 0.5808 (mtt90) REVERT: A 819 TYR cc_start: 0.7943 (p90) cc_final: 0.7489 (p90) REVERT: B 78 ASN cc_start: 0.6953 (p0) cc_final: 0.6599 (m110) REVERT: B 89 PHE cc_start: 0.6513 (t80) cc_final: 0.6025 (t80) REVERT: B 99 ARG cc_start: 0.6047 (mmt90) cc_final: 0.5779 (mtt90) REVERT: B 758 ARG cc_start: 0.7461 (tmm160) cc_final: 0.7168 (ttp80) REVERT: C 89 PHE cc_start: 0.6566 (t80) cc_final: 0.6201 (t80) REVERT: C 99 ARG cc_start: 0.6304 (mmt90) cc_final: 0.5933 (mtt90) REVERT: C 750 SER cc_start: 0.8810 (t) cc_final: 0.8591 (m) outliers start: 42 outliers final: 28 residues processed: 216 average time/residue: 0.3470 time to fit residues: 116.3049 Evaluate side-chains 188 residues out of total 2283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 160 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 198 LYS Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 707 GLU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1098 THR Chi-restraints excluded: chain C residue 1111 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 0.9990 chunk 180 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 241 optimal weight: 1.9990 chunk 255 optimal weight: 0.7980 chunk 125 optimal weight: 0.4980 chunk 228 optimal weight: 0.9990 chunk 68 optimal weight: 0.1980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 721 ASN C 786 GLN C 917 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21483 Z= 0.167 Angle : 0.543 7.087 29211 Z= 0.289 Chirality : 0.045 0.237 3465 Planarity : 0.003 0.036 3726 Dihedral : 7.180 59.977 3623 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.84 % Allowed : 6.92 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.16), residues: 2607 helix: 1.80 (0.21), residues: 606 sheet: -0.21 (0.20), residues: 642 loop : -1.36 (0.15), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 868 HIS 0.007 0.001 HIS C 33 PHE 0.025 0.001 PHE A 83 TYR 0.015 0.001 TYR A 886 ARG 0.003 0.000 ARG C 758 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 189 time to evaluate : 2.292 Fit side-chains revert: symmetry clash REVERT: A 67 THR cc_start: 0.7303 (m) cc_final: 0.6730 (p) REVERT: A 89 PHE cc_start: 0.6470 (t80) cc_final: 0.5966 (t80) REVERT: A 819 TYR cc_start: 0.7926 (p90) cc_final: 0.7454 (p90) REVERT: B 52 LEU cc_start: 0.8529 (mt) cc_final: 0.8308 (mp) REVERT: B 78 ASN cc_start: 0.6945 (p0) cc_final: 0.6721 (m110) REVERT: B 87 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7897 (mp) REVERT: B 89 PHE cc_start: 0.6534 (t80) cc_final: 0.6027 (t80) REVERT: B 99 ARG cc_start: 0.6092 (mmt90) cc_final: 0.5773 (mtt90) REVERT: C 89 PHE cc_start: 0.6392 (t80) cc_final: 0.6048 (t80) REVERT: C 99 ARG cc_start: 0.6431 (mmt90) cc_final: 0.6033 (mtt90) outliers start: 42 outliers final: 25 residues processed: 222 average time/residue: 0.3144 time to fit residues: 110.0619 Evaluate side-chains 190 residues out of total 2283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 164 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 999 GLU Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1111 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 217 optimal weight: 4.9990 chunk 176 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 130 optimal weight: 5.9990 chunk 229 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS A 661 HIS A 786 GLN A 818 GLN A 917 GLN B 661 HIS B 756 GLN C 33 HIS C 189 ASN C 304 ASN C 661 HIS C 756 GLN ** C 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 818 GLN ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 947 GLN C1095 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 21483 Z= 0.454 Angle : 0.681 7.313 29211 Z= 0.360 Chirality : 0.050 0.259 3465 Planarity : 0.004 0.039 3726 Dihedral : 7.048 59.836 3623 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.54 % Allowed : 7.45 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.16), residues: 2607 helix: 1.50 (0.21), residues: 609 sheet: -0.34 (0.20), residues: 645 loop : -1.48 (0.15), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 868 HIS 0.007 0.001 HIS C 33 PHE 0.030 0.002 PHE B 83 TYR 0.017 0.003 TYR B 738 ARG 0.006 0.001 ARG C 977 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 184 time to evaluate : 2.373 Fit side-chains REVERT: A 67 THR cc_start: 0.7369 (m) cc_final: 0.6829 (p) REVERT: A 99 ARG cc_start: 0.6320 (mmt90) cc_final: 0.6012 (mmt90) REVERT: B 67 THR cc_start: 0.7298 (m) cc_final: 0.6737 (p) REVERT: B 87 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8303 (mp) REVERT: B 99 ARG cc_start: 0.6422 (mmt90) cc_final: 0.6074 (mtt90) REVERT: B 198 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8041 (tttp) REVERT: B 1053 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7784 (mp10) REVERT: C 67 THR cc_start: 0.7316 (m) cc_final: 0.6858 (p) REVERT: C 99 ARG cc_start: 0.6540 (mmt90) cc_final: 0.6006 (mtt90) REVERT: C 756 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.7969 (mp-120) outliers start: 58 outliers final: 44 residues processed: 231 average time/residue: 0.3517 time to fit residues: 125.4530 Evaluate side-chains 210 residues out of total 2283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 162 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 635 CYS Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 937 ASN Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1053 GLN Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 756 GLN Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1033 SER Chi-restraints excluded: chain C residue 1098 THR Chi-restraints excluded: chain C residue 1111 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 0.6980 chunk 229 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 255 optimal weight: 0.7980 chunk 212 optimal weight: 0.6980 chunk 118 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 818 GLN A 877 GLN A1088 GLN ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN B1088 GLN ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN C 818 GLN C1053 GLN C1095 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 21483 Z= 0.180 Angle : 0.544 6.834 29211 Z= 0.290 Chirality : 0.045 0.257 3465 Planarity : 0.004 0.034 3726 Dihedral : 6.437 59.931 3623 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.88 % Allowed : 8.63 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.16), residues: 2607 helix: 2.02 (0.22), residues: 609 sheet: -0.16 (0.20), residues: 627 loop : -1.28 (0.15), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 868 HIS 0.003 0.001 HIS B 33 PHE 0.027 0.001 PHE C 551 TYR 0.015 0.001 TYR A 886 ARG 0.005 0.000 ARG C 758 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 177 time to evaluate : 2.330 Fit side-chains REVERT: A 67 THR cc_start: 0.7343 (m) cc_final: 0.6794 (p) REVERT: A 99 ARG cc_start: 0.6225 (mmt90) cc_final: 0.5895 (mmt90) REVERT: B 67 THR cc_start: 0.7270 (m) cc_final: 0.6756 (p) REVERT: B 87 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8143 (mp) REVERT: B 99 ARG cc_start: 0.6284 (mmt90) cc_final: 0.5861 (mtt90) REVERT: B 198 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8013 (tttp) REVERT: C 67 THR cc_start: 0.7309 (m) cc_final: 0.6874 (p) REVERT: C 99 ARG cc_start: 0.6504 (mmt90) cc_final: 0.6049 (mtt90) REVERT: C 107 MET cc_start: 0.3982 (mpp) cc_final: 0.3474 (mtp) REVERT: C 151 MET cc_start: 0.3891 (mmm) cc_final: 0.2718 (mtm) outliers start: 43 outliers final: 32 residues processed: 212 average time/residue: 0.3359 time to fit residues: 111.4926 Evaluate side-chains 191 residues out of total 2283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 157 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 937 ASN Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 756 GLN Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1023 ASP Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1111 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 144 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 254 optimal weight: 4.9990 chunk 159 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 GLN A 877 GLN ** A 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 ASN B 818 GLN B1095 GLN C 189 ASN C 756 GLN C 818 GLN C1053 GLN C1095 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 21483 Z= 0.516 Angle : 0.694 8.108 29211 Z= 0.367 Chirality : 0.051 0.284 3465 Planarity : 0.004 0.038 3726 Dihedral : 6.736 58.417 3623 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.67 % Allowed : 9.07 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.16), residues: 2607 helix: 1.66 (0.21), residues: 606 sheet: -0.36 (0.20), residues: 648 loop : -1.47 (0.15), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 868 HIS 0.007 0.001 HIS C1040 PHE 0.030 0.002 PHE C 83 TYR 0.016 0.002 TYR B 266 ARG 0.004 0.001 ARG C 996 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 167 time to evaluate : 2.363 Fit side-chains REVERT: A 67 THR cc_start: 0.7326 (m) cc_final: 0.6868 (p) REVERT: A 99 ARG cc_start: 0.6268 (mmt90) cc_final: 0.5932 (mmt90) REVERT: A 107 MET cc_start: 0.4975 (mpp) cc_final: 0.4303 (mtt) REVERT: B 67 THR cc_start: 0.7398 (m) cc_final: 0.6874 (p) REVERT: B 87 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8329 (mp) REVERT: B 99 ARG cc_start: 0.6430 (mmt90) cc_final: 0.6062 (mtt90) REVERT: B 107 MET cc_start: 0.4636 (mpp) cc_final: 0.3494 (mtt) REVERT: B 198 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8046 (tttp) REVERT: C 67 THR cc_start: 0.7410 (m) cc_final: 0.6997 (p) REVERT: C 99 ARG cc_start: 0.6656 (mmt90) cc_final: 0.6200 (mtt90) REVERT: C 107 MET cc_start: 0.4363 (mpp) cc_final: 0.3760 (mtp) REVERT: C 151 MET cc_start: 0.4512 (mmm) cc_final: 0.3047 (ttm) outliers start: 61 outliers final: 48 residues processed: 215 average time/residue: 0.3295 time to fit residues: 110.3529 Evaluate side-chains 211 residues out of total 2283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 161 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 635 CYS Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 937 ASN Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 756 GLN Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1023 ASP Chi-restraints excluded: chain C residue 1033 SER Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1098 THR Chi-restraints excluded: chain C residue 1111 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 0.9990 chunk 101 optimal weight: 0.2980 chunk 151 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 161 optimal weight: 0.7980 chunk 173 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 200 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 GLN ** A 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 GLN ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 818 GLN B 877 GLN C 189 ASN C 756 GLN C1088 GLN C1095 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21483 Z= 0.167 Angle : 0.545 6.879 29211 Z= 0.291 Chirality : 0.044 0.231 3465 Planarity : 0.004 0.035 3726 Dihedral : 6.228 59.793 3623 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.10 % Allowed : 10.07 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.16), residues: 2607 helix: 2.11 (0.21), residues: 606 sheet: -0.20 (0.20), residues: 633 loop : -1.28 (0.15), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 868 HIS 0.003 0.001 HIS B1030 PHE 0.026 0.001 PHE B 83 TYR 0.017 0.001 TYR A 886 ARG 0.004 0.000 ARG C 758 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 173 time to evaluate : 2.262 Fit side-chains REVERT: A 67 THR cc_start: 0.7367 (m) cc_final: 0.6826 (p) REVERT: A 99 ARG cc_start: 0.6204 (mmt90) cc_final: 0.5859 (mmt90) REVERT: A 107 MET cc_start: 0.5063 (mpp) cc_final: 0.4370 (mtt) REVERT: A 965 ARG cc_start: 0.7642 (mmm-85) cc_final: 0.7440 (tpp-160) REVERT: B 67 THR cc_start: 0.7341 (m) cc_final: 0.6828 (p) REVERT: B 87 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8157 (mp) REVERT: B 99 ARG cc_start: 0.6395 (mmt90) cc_final: 0.5977 (mtt90) REVERT: B 107 MET cc_start: 0.4560 (mpp) cc_final: 0.3487 (mtp) REVERT: C 67 THR cc_start: 0.7356 (m) cc_final: 0.6956 (p) REVERT: C 99 ARG cc_start: 0.6520 (mmt90) cc_final: 0.5971 (mtt90) REVERT: C 107 MET cc_start: 0.4222 (mpp) cc_final: 0.3741 (mtp) REVERT: C 151 MET cc_start: 0.4455 (mmm) cc_final: 0.3046 (ttm) outliers start: 48 outliers final: 35 residues processed: 212 average time/residue: 0.3240 time to fit residues: 107.7982 Evaluate side-chains 195 residues out of total 2283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 159 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 756 GLN Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1023 ASP Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 0.7980 chunk 222 optimal weight: 4.9990 chunk 237 optimal weight: 3.9990 chunk 142 optimal weight: 0.5980 chunk 103 optimal weight: 0.0060 chunk 186 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 214 optimal weight: 0.8980 chunk 224 optimal weight: 0.9990 chunk 236 optimal weight: 0.0170 chunk 155 optimal weight: 3.9990 overall best weight: 0.4634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 GLN ** A 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN C 818 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 21483 Z= 0.141 Angle : 0.520 6.782 29211 Z= 0.276 Chirality : 0.044 0.219 3465 Planarity : 0.003 0.036 3726 Dihedral : 5.787 59.645 3623 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.88 % Allowed : 10.51 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.16), residues: 2607 helix: 2.49 (0.22), residues: 603 sheet: -0.10 (0.20), residues: 645 loop : -1.20 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 868 HIS 0.002 0.000 HIS B1030 PHE 0.027 0.001 PHE B 83 TYR 0.018 0.001 TYR A 886 ARG 0.003 0.000 ARG C 758 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 169 time to evaluate : 2.405 Fit side-chains REVERT: A 67 THR cc_start: 0.7349 (m) cc_final: 0.6799 (p) REVERT: A 99 ARG cc_start: 0.6179 (mmt90) cc_final: 0.5855 (mmt90) REVERT: A 107 MET cc_start: 0.5060 (mpp) cc_final: 0.4349 (mtt) REVERT: B 67 THR cc_start: 0.7353 (m) cc_final: 0.6825 (p) REVERT: B 87 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8090 (mp) REVERT: B 99 ARG cc_start: 0.6389 (mmt90) cc_final: 0.5971 (mtt90) REVERT: B 107 MET cc_start: 0.4525 (mpp) cc_final: 0.3478 (mtp) REVERT: C 67 THR cc_start: 0.7345 (m) cc_final: 0.6948 (p) REVERT: C 99 ARG cc_start: 0.6542 (mmt90) cc_final: 0.5987 (mtt90) REVERT: C 107 MET cc_start: 0.4191 (mpp) cc_final: 0.3771 (mtp) REVERT: C 151 MET cc_start: 0.4411 (mmm) cc_final: 0.3046 (ttm) REVERT: C 643 ASP cc_start: 0.7166 (OUTLIER) cc_final: 0.6942 (p0) outliers start: 43 outliers final: 32 residues processed: 202 average time/residue: 0.3262 time to fit residues: 104.1132 Evaluate side-chains 191 residues out of total 2283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 157 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 263 optimal weight: 4.9990 chunk 242 optimal weight: 2.9990 chunk 209 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 128 optimal weight: 0.4980 chunk 166 optimal weight: 0.0470 overall best weight: 1.2482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 ASN C 189 ASN C 756 GLN C 818 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21483 Z= 0.221 Angle : 0.549 7.452 29211 Z= 0.292 Chirality : 0.045 0.220 3465 Planarity : 0.003 0.036 3726 Dihedral : 5.699 59.571 3623 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.71 % Allowed : 10.82 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.16), residues: 2607 helix: 2.46 (0.21), residues: 606 sheet: -0.16 (0.20), residues: 648 loop : -1.17 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 868 HIS 0.003 0.001 HIS C1040 PHE 0.027 0.001 PHE B 83 TYR 0.019 0.001 TYR B 163 ARG 0.004 0.000 ARG C 758 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 165 time to evaluate : 2.590 Fit side-chains REVERT: A 67 THR cc_start: 0.7392 (m) cc_final: 0.6835 (p) REVERT: A 99 ARG cc_start: 0.6198 (mmt90) cc_final: 0.5870 (mmt90) REVERT: B 67 THR cc_start: 0.7396 (m) cc_final: 0.6867 (p) REVERT: B 87 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8138 (mp) REVERT: B 99 ARG cc_start: 0.6425 (mmt90) cc_final: 0.6009 (mtt90) REVERT: B 107 MET cc_start: 0.4508 (mpp) cc_final: 0.3401 (mtp) REVERT: C 67 THR cc_start: 0.7383 (m) cc_final: 0.6993 (p) REVERT: C 99 ARG cc_start: 0.6571 (mmt90) cc_final: 0.6014 (mtt90) REVERT: C 107 MET cc_start: 0.4137 (mpp) cc_final: 0.3482 (mtp) REVERT: C 151 MET cc_start: 0.4453 (mmm) cc_final: 0.2985 (ttm) outliers start: 39 outliers final: 34 residues processed: 195 average time/residue: 0.3346 time to fit residues: 102.8404 Evaluate side-chains 198 residues out of total 2283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 163 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 999 GLU Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 193 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 209 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 26 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 chunk 184 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 GLN ** A 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 189 ASN B1088 GLN C 189 ASN C 756 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.156864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.118439 restraints weight = 31004.693| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.15 r_work: 0.3137 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 21483 Z= 0.292 Angle : 0.583 6.846 29211 Z= 0.309 Chirality : 0.046 0.231 3465 Planarity : 0.004 0.035 3726 Dihedral : 5.773 59.988 3623 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.01 % Allowed : 10.56 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.16), residues: 2607 helix: 2.27 (0.21), residues: 606 sheet: -0.23 (0.20), residues: 633 loop : -1.20 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 868 HIS 0.004 0.001 HIS B1046 PHE 0.027 0.002 PHE B 83 TYR 0.019 0.002 TYR A 886 ARG 0.003 0.000 ARG C 758 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4023.30 seconds wall clock time: 74 minutes 18.55 seconds (4458.55 seconds total)