Starting phenix.real_space_refine on Thu Oct 29 19:24:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rde_4815/10_2026/6rde_4815.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rde_4815/10_2026/6rde_4815.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6rde_4815/10_2026/6rde_4815.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rde_4815/10_2026/6rde_4815.cif" model { file = "/net/cci-nas-00/data/ceres_data/6rde_4815/10_2026/6rde_4815.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rde_4815/10_2026/6rde_4815.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rde_4815/10_2026/6rde_4815.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rde_4815/10_2026/6rde_4815.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 116 5.16 5 C 21548 2.51 5 N 5795 2.21 5 O 6449 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 256 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33926 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "P" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 886 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3649 Classifications: {'peptide': 483} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 461} Chain: "U" Number of atoms: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3978 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 3961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3961 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4087 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 513} Chain: "Y" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3952 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 497} Chain: "Z" Number of atoms: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4095 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 514} Chain breaks: 1 Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "U" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "V" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "X" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "Y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 7.25, per 1000 atoms: 0.21 Number of scatterers: 33926 At special positions: 0 Unit cell: (164.268, 129.519, 208.494, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 116 16.00 P 13 15.00 Mg 5 11.99 O 6449 8.00 N 5795 7.00 C 21548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.5 seconds 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8158 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 27 sheets defined 53.2% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 54 through 67 removed outlier: 3.872A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA A 64 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 92 removed outlier: 4.195A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 104 removed outlier: 4.207A pdb=" N GLY A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 125 removed outlier: 3.751A pdb=" N SER A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 120 " --> pdb=" O PHE A 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 67 removed outlier: 3.544A pdb=" N LYS B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 92 removed outlier: 3.947A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 112 Processing helix chain 'B' and resid 113 through 126 removed outlier: 4.017A pdb=" N LEU B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 66 removed outlier: 3.752A pdb=" N LYS C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C 64 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 92 removed outlier: 4.224A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY C 75 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 126 removed outlier: 3.979A pdb=" N GLY C 101 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL C 120 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 removed outlier: 4.531A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY D 65 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 92 removed outlier: 3.675A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG D 91 " --> pdb=" O ASN D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 117 removed outlier: 3.626A pdb=" N VAL D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY D 101 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER D 112 " --> pdb=" O ALA D 108 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 126 removed outlier: 3.523A pdb=" N PHE D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 67 removed outlier: 3.514A pdb=" N LYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA E 64 " --> pdb=" O LYS E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 92 removed outlier: 4.012A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU E 85 " --> pdb=" O MET E 81 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA E 90 " --> pdb=" O ILE E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 112 removed outlier: 3.988A pdb=" N VAL E 100 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY E 101 " --> pdb=" O LYS E 97 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 125 removed outlier: 3.880A pdb=" N VAL E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU E 125 " --> pdb=" O VAL E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 3.918A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 92 removed outlier: 4.078A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY F 79 " --> pdb=" O GLY F 75 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL F 80 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 96 Processing helix chain 'F' and resid 97 through 111 removed outlier: 3.538A pdb=" N GLY F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU F 111 " --> pdb=" O PHE F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.882A pdb=" N LEU F 118 " --> pdb=" O ALA F 114 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU F 119 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE F 126 " --> pdb=" O PHE F 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 68 removed outlier: 4.201A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 92 removed outlier: 4.373A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY G 79 " --> pdb=" O GLY G 75 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE G 86 " --> pdb=" O PHE G 82 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG G 91 " --> pdb=" O ASN G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 126 removed outlier: 3.527A pdb=" N VAL G 100 " --> pdb=" O ALA G 96 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLY G 101 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR G 102 " --> pdb=" O GLN G 98 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL G 120 " --> pdb=" O PHE G 116 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE G 126 " --> pdb=" O PHE G 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 68 removed outlier: 4.340A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY H 65 " --> pdb=" O MET H 61 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA H 67 " --> pdb=" O GLY H 63 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 90 removed outlier: 3.695A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 94 No H-bonds generated for 'chain 'H' and resid 92 through 94' Processing helix chain 'H' and resid 95 through 126 removed outlier: 3.984A pdb=" N GLY H 101 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA H 108 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 68 removed outlier: 3.621A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL I 62 " --> pdb=" O ALA I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 92 removed outlier: 3.615A pdb=" N GLY I 79 " --> pdb=" O GLY I 75 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG I 91 " --> pdb=" O ASN I 87 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN I 92 " --> pdb=" O GLY I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 111 removed outlier: 3.957A pdb=" N GLY I 101 " --> pdb=" O LYS I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 126 removed outlier: 3.668A pdb=" N LEU I 118 " --> pdb=" O ALA I 114 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL I 120 " --> pdb=" O PHE I 116 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE I 126 " --> pdb=" O PHE I 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 removed outlier: 3.517A pdb=" N SER J 59 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA J 64 " --> pdb=" O LYS J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 92 removed outlier: 4.030A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY J 75 " --> pdb=" O LEU J 71 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 125 removed outlier: 3.697A pdb=" N LEU J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER J 112 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU J 125 " --> pdb=" O VAL J 121 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 64 Processing helix chain 'P' and resid 68 through 84 removed outlier: 3.630A pdb=" N HIS P 84 " --> pdb=" O LEU P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 93 removed outlier: 3.830A pdb=" N ARG P 88 " --> pdb=" O HIS P 84 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 109 Processing helix chain 'P' and resid 115 through 129 Processing helix chain 'P' and resid 130 through 132 No H-bonds generated for 'chain 'P' and resid 130 through 132' Processing helix chain 'P' and resid 133 through 147 removed outlier: 4.157A pdb=" N VAL P 139 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN P 140 " --> pdb=" O GLU P 136 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU P 143 " --> pdb=" O VAL P 139 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 13 removed outlier: 3.651A pdb=" N GLY Q 13 " --> pdb=" O ARG Q 10 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 29 removed outlier: 3.543A pdb=" N LEU Q 27 " --> pdb=" O CYS Q 23 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN Q 29 " --> pdb=" O ASP Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 40 removed outlier: 3.658A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 44 removed outlier: 3.763A pdb=" N ALA Q 44 " --> pdb=" O ALA Q 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 41 through 44' Processing helix chain 'R' and resid 31 through 41 removed outlier: 3.897A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS R 40 " --> pdb=" O VAL R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 55 removed outlier: 3.610A pdb=" N THR R 55 " --> pdb=" O SER R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 159 through 170 removed outlier: 3.712A pdb=" N LEU R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA R 165 " --> pdb=" O LYS R 161 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 193 removed outlier: 3.534A pdb=" N GLU R 186 " --> pdb=" O ARG R 182 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU R 187 " --> pdb=" O ALA R 183 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA R 190 " --> pdb=" O GLU R 186 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER R 193 " --> pdb=" O SER R 189 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 89 removed outlier: 3.646A pdb=" N ARG S 48 " --> pdb=" O LYS S 44 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS S 55 " --> pdb=" O LYS S 51 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN S 70 " --> pdb=" O SER S 66 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA S 74 " --> pdb=" O ASN S 70 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU S 76 " --> pdb=" O GLN S 72 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN S 77 " --> pdb=" O ILE S 73 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY S 80 " --> pdb=" O GLU S 76 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU S 81 " --> pdb=" O GLN S 77 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL S 82 " --> pdb=" O SER S 78 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP S 83 " --> pdb=" O ARG S 79 " (cutoff:3.500A) Proline residue: S 84 - end of helix Processing helix chain 'S' and resid 117 through 127 Processing helix chain 'S' and resid 143 through 151 removed outlier: 3.706A pdb=" N ARG S 147 " --> pdb=" O GLY S 143 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER S 148 " --> pdb=" O ASP S 144 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN S 149 " --> pdb=" O LYS S 145 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 185 removed outlier: 3.887A pdb=" N HIS S 185 " --> pdb=" O GLU S 181 " (cutoff:3.500A) Processing helix chain 'S' and resid 216 through 221 removed outlier: 3.594A pdb=" N GLU S 221 " --> pdb=" O GLU S 217 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 274 removed outlier: 3.791A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) Processing helix chain 'S' and resid 276 through 315 removed outlier: 3.572A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU S 290 " --> pdb=" O GLY S 286 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU S 314 " --> pdb=" O GLY S 310 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 138 removed outlier: 3.924A pdb=" N VAL T 137 " --> pdb=" O ASN T 134 " (cutoff:3.500A) Processing helix chain 'T' and resid 156 through 160 Processing helix chain 'T' and resid 206 through 213 Processing helix chain 'T' and resid 230 through 247 removed outlier: 3.532A pdb=" N LYS T 243 " --> pdb=" O ILE T 239 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN T 244 " --> pdb=" O ILE T 240 " (cutoff:3.500A) Processing helix chain 'T' and resid 250 through 253 Processing helix chain 'T' and resid 265 through 280 Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 295 through 316 Proline residue: T 303 - end of helix removed outlier: 4.412A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 341 removed outlier: 3.550A pdb=" N VAL T 332 " --> pdb=" O SER T 328 " (cutoff:3.500A) Processing helix chain 'T' and resid 346 through 350 Processing helix chain 'T' and resid 353 through 363 removed outlier: 3.853A pdb=" N HIS T 358 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (cutoff:3.500A) Processing helix chain 'T' and resid 392 through 400 Processing helix chain 'T' and resid 409 through 415 Processing helix chain 'T' and resid 430 through 435 removed outlier: 4.055A pdb=" N GLN T 435 " --> pdb=" O SER T 432 " (cutoff:3.500A) Processing helix chain 'T' and resid 436 through 441 removed outlier: 3.579A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) Processing helix chain 'T' and resid 443 through 460 removed outlier: 3.611A pdb=" N PHE T 459 " --> pdb=" O GLU T 455 " (cutoff:3.500A) Processing helix chain 'T' and resid 469 through 484 removed outlier: 3.652A pdb=" N ARG T 479 " --> pdb=" O GLU T 475 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU T 482 " --> pdb=" O ALA T 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 493 through 506 removed outlier: 3.831A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 516 through 528 removed outlier: 3.555A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) Processing helix chain 'T' and resid 529 through 540 removed outlier: 4.219A pdb=" N PHE T 533 " --> pdb=" O ASN T 529 " (cutoff:3.500A) Processing helix chain 'T' and resid 543 through 556 removed outlier: 3.573A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA T 552 " --> pdb=" O ALA T 548 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 49 removed outlier: 3.571A pdb=" N LEU U 48 " --> pdb=" O LEU U 45 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG U 49 " --> pdb=" O ASP U 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 45 through 49' Processing helix chain 'U' and resid 58 through 63 removed outlier: 3.632A pdb=" N SER U 63 " --> pdb=" O ILE U 59 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 72 removed outlier: 3.899A pdb=" N ALA U 69 " --> pdb=" O LYS U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 134 through 138 removed outlier: 4.063A pdb=" N VAL U 137 " --> pdb=" O ASN U 134 " (cutoff:3.500A) Processing helix chain 'U' and resid 156 through 160 removed outlier: 3.624A pdb=" N THR U 159 " --> pdb=" O GLY U 156 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU U 160 " --> pdb=" O PRO U 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 156 through 160' Processing helix chain 'U' and resid 206 through 213 Processing helix chain 'U' and resid 230 through 247 removed outlier: 3.867A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 280 Processing helix chain 'U' and resid 281 through 283 No H-bonds generated for 'chain 'U' and resid 281 through 283' Processing helix chain 'U' and resid 295 through 316 Proline residue: U 303 - end of helix removed outlier: 3.610A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG U 314 " --> pdb=" O ALA U 310 " (cutoff:3.500A) Processing helix chain 'U' and resid 326 through 341 removed outlier: 3.928A pdb=" N VAL U 332 " --> pdb=" O SER U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 346 through 350 Processing helix chain 'U' and resid 353 through 363 removed outlier: 3.555A pdb=" N HIS U 358 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) Processing helix chain 'U' and resid 369 through 373 removed outlier: 3.523A pdb=" N GLY U 373 " --> pdb=" O LYS U 370 " (cutoff:3.500A) Processing helix chain 'U' and resid 392 through 402 Processing helix chain 'U' and resid 409 through 415 removed outlier: 3.617A pdb=" N TYR U 414 " --> pdb=" O THR U 410 " (cutoff:3.500A) Processing helix chain 'U' and resid 436 through 450 removed outlier: 4.078A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) Processing helix chain 'U' and resid 450 through 458 removed outlier: 3.824A pdb=" N GLU U 455 " --> pdb=" O ALA U 451 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL U 456 " --> pdb=" O GLN U 452 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA U 458 " --> pdb=" O ARG U 454 " (cutoff:3.500A) Processing helix chain 'U' and resid 469 through 485 removed outlier: 3.637A pdb=" N VAL U 473 " --> pdb=" O ALA U 469 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA U 478 " --> pdb=" O LEU U 474 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU U 482 " --> pdb=" O ALA U 478 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET U 483 " --> pdb=" O ARG U 479 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU U 484 " --> pdb=" O LEU U 480 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS U 485 " --> pdb=" O THR U 481 " (cutoff:3.500A) Processing helix chain 'U' and resid 493 through 506 removed outlier: 3.781A pdb=" N VAL U 499 " --> pdb=" O GLU U 495 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) Processing helix chain 'U' and resid 516 through 528 removed outlier: 3.739A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 531 through 540 removed outlier: 3.686A pdb=" N ILE U 535 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 543 through 554 Processing helix chain 'V' and resid 44 through 49 Processing helix chain 'V' and resid 58 through 67 removed outlier: 3.864A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 68 through 70 No H-bonds generated for 'chain 'V' and resid 68 through 70' Processing helix chain 'V' and resid 134 through 138 removed outlier: 3.927A pdb=" N VAL V 137 " --> pdb=" O ASN V 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 160 removed outlier: 3.563A pdb=" N THR V 159 " --> pdb=" O GLY V 156 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU V 160 " --> pdb=" O PRO V 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 156 through 160' Processing helix chain 'V' and resid 206 through 212 Processing helix chain 'V' and resid 230 through 247 removed outlier: 3.548A pdb=" N GLN V 242 " --> pdb=" O ALA V 238 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS V 243 " --> pdb=" O ILE V 239 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) Processing helix chain 'V' and resid 248 through 249 No H-bonds generated for 'chain 'V' and resid 248 through 249' Processing helix chain 'V' and resid 250 through 253 Processing helix chain 'V' and resid 265 through 280 Processing helix chain 'V' and resid 281 through 283 No H-bonds generated for 'chain 'V' and resid 281 through 283' Processing helix chain 'V' and resid 295 through 316 Proline residue: V 303 - end of helix removed outlier: 3.571A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG V 314 " --> pdb=" O ALA V 310 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 341 removed outlier: 3.583A pdb=" N LEU V 341 " --> pdb=" O MET V 337 " (cutoff:3.500A) Processing helix chain 'V' and resid 346 through 350 Processing helix chain 'V' and resid 351 through 352 No H-bonds generated for 'chain 'V' and resid 351 through 352' Processing helix chain 'V' and resid 353 through 363 removed outlier: 3.660A pdb=" N HIS V 358 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU V 361 " --> pdb=" O LEU V 357 " (cutoff:3.500A) Processing helix chain 'V' and resid 369 through 373 removed outlier: 3.734A pdb=" N GLY V 373 " --> pdb=" O LYS V 370 " (cutoff:3.500A) Processing helix chain 'V' and resid 392 through 402 Processing helix chain 'V' and resid 409 through 414 removed outlier: 3.693A pdb=" N TYR V 414 " --> pdb=" O THR V 410 " (cutoff:3.500A) Processing helix chain 'V' and resid 430 through 435 removed outlier: 3.657A pdb=" N ALA V 433 " --> pdb=" O VAL V 430 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA V 434 " --> pdb=" O GLY V 431 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN V 435 " --> pdb=" O SER V 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 430 through 435' Processing helix chain 'V' and resid 438 through 457 removed outlier: 3.888A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU V 455 " --> pdb=" O ALA V 451 " (cutoff:3.500A) Processing helix chain 'V' and resid 469 through 482 removed outlier: 3.877A pdb=" N ALA V 478 " --> pdb=" O LEU V 474 " (cutoff:3.500A) Processing helix chain 'V' and resid 493 through 506 removed outlier: 3.608A pdb=" N ALA V 504 " --> pdb=" O ALA V 500 " (cutoff:3.500A) Processing helix chain 'V' and resid 507 through 511 removed outlier: 4.457A pdb=" N LYS V 511 " --> pdb=" O PHE V 508 " (cutoff:3.500A) Processing helix chain 'V' and resid 513 through 516 removed outlier: 3.706A pdb=" N ASP V 516 " --> pdb=" O ARG V 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 513 through 516' Processing helix chain 'V' and resid 517 through 528 removed outlier: 3.698A pdb=" N GLU V 522 " --> pdb=" O VAL V 518 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN V 527 " --> pdb=" O ALA V 523 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL V 528 " --> pdb=" O VAL V 524 " (cutoff:3.500A) Processing helix chain 'V' and resid 531 through 540 removed outlier: 3.558A pdb=" N ALA V 538 " --> pdb=" O LYS V 534 " (cutoff:3.500A) Processing helix chain 'V' and resid 548 through 554 removed outlier: 3.657A pdb=" N ALA V 552 " --> pdb=" O ALA V 548 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 118 Processing helix chain 'X' and resid 149 through 153 Processing helix chain 'X' and resid 164 through 171 Processing helix chain 'X' and resid 188 through 204 Processing helix chain 'X' and resid 216 through 231 Processing helix chain 'X' and resid 235 through 242 removed outlier: 3.788A pdb=" N GLU X 238 " --> pdb=" O LEU X 235 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 254 through 259 Processing helix chain 'X' and resid 260 through 275 removed outlier: 3.727A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 286 through 301 removed outlier: 3.574A pdb=" N PHE X 290 " --> pdb=" O ASN X 286 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 323 Processing helix chain 'X' and resid 341 through 345 removed outlier: 3.593A pdb=" N ASP X 344 " --> pdb=" O VAL X 341 " (cutoff:3.500A) Processing helix chain 'X' and resid 348 through 355 Processing helix chain 'X' and resid 365 through 371 removed outlier: 3.799A pdb=" N LEU X 371 " --> pdb=" O SER X 367 " (cutoff:3.500A) Processing helix chain 'X' and resid 393 through 413 removed outlier: 3.545A pdb=" N VAL X 399 " --> pdb=" O GLU X 395 " (cutoff:3.500A) Processing helix chain 'X' and resid 428 through 441 Processing helix chain 'X' and resid 450 through 455 Processing helix chain 'X' and resid 462 through 475 removed outlier: 3.517A pdb=" N SER X 468 " --> pdb=" O ALA X 464 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY X 472 " --> pdb=" O SER X 468 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL X 473 " --> pdb=" O GLY X 469 " (cutoff:3.500A) Processing helix chain 'X' and resid 482 through 486 Processing helix chain 'X' and resid 491 through 503 removed outlier: 3.520A pdb=" N VAL X 495 " --> pdb=" O ASP X 491 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) Processing helix chain 'X' and resid 504 through 507 Processing helix chain 'X' and resid 526 through 532 Processing helix chain 'Y' and resid 114 through 118 removed outlier: 3.526A pdb=" N LEU Y 118 " --> pdb=" O ARG Y 115 " (cutoff:3.500A) Processing helix chain 'Y' and resid 149 through 153 Processing helix chain 'Y' and resid 164 through 171 Processing helix chain 'Y' and resid 190 through 200 Processing helix chain 'Y' and resid 201 through 204 Processing helix chain 'Y' and resid 216 through 230 Processing helix chain 'Y' and resid 235 through 242 removed outlier: 3.951A pdb=" N GLU Y 238 " --> pdb=" O LEU Y 235 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG Y 239 " --> pdb=" O GLY Y 236 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 254 through 259 Processing helix chain 'Y' and resid 260 through 275 removed outlier: 3.546A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 298 removed outlier: 3.715A pdb=" N THR Y 291 " --> pdb=" O ILE Y 287 " (cutoff:3.500A) Processing helix chain 'Y' and resid 313 through 323 Processing helix chain 'Y' and resid 342 through 345 Processing helix chain 'Y' and resid 348 through 355 removed outlier: 3.637A pdb=" N THR Y 354 " --> pdb=" O ALA Y 350 " (cutoff:3.500A) Processing helix chain 'Y' and resid 356 through 358 No H-bonds generated for 'chain 'Y' and resid 356 through 358' Processing helix chain 'Y' and resid 365 through 370 Processing helix chain 'Y' and resid 393 through 413 Processing helix chain 'Y' and resid 413 through 420 Processing helix chain 'Y' and resid 421 through 425 removed outlier: 3.892A pdb=" N GLU Y 424 " --> pdb=" O GLY Y 421 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU Y 425 " --> pdb=" O MET Y 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 421 through 425' Processing helix chain 'Y' and resid 426 through 443 removed outlier: 3.648A pdb=" N THR Y 432 " --> pdb=" O GLU Y 428 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA Y 434 " --> pdb=" O LYS Y 430 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG Y 441 " --> pdb=" O ARG Y 437 " (cutoff:3.500A) Processing helix chain 'Y' and resid 450 through 455 Processing helix chain 'Y' and resid 462 through 476 removed outlier: 3.840A pdb=" N VAL Y 473 " --> pdb=" O GLY Y 469 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU Y 474 " --> pdb=" O PHE Y 470 " (cutoff:3.500A) Processing helix chain 'Y' and resid 482 through 486 removed outlier: 3.597A pdb=" N ALA Y 485 " --> pdb=" O PRO Y 482 " (cutoff:3.500A) Processing helix chain 'Y' and resid 491 through 508 removed outlier: 3.867A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) Processing helix chain 'Y' and resid 526 through 533 Processing helix chain 'Z' and resid 114 through 118 removed outlier: 3.576A pdb=" N THR Z 117 " --> pdb=" O GLY Z 114 " (cutoff:3.500A) Processing helix chain 'Z' and resid 164 through 171 Processing helix chain 'Z' and resid 188 through 200 Processing helix chain 'Z' and resid 217 through 230 Processing helix chain 'Z' and resid 235 through 242 removed outlier: 3.581A pdb=" N GLU Z 238 " --> pdb=" O LEU Z 235 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 254 through 275 removed outlier: 3.619A pdb=" N ARG Z 260 " --> pdb=" O GLY Z 256 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 299 removed outlier: 3.822A pdb=" N THR Z 291 " --> pdb=" O ILE Z 287 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL Z 297 " --> pdb=" O ALA Z 293 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA Z 299 " --> pdb=" O SER Z 295 " (cutoff:3.500A) Processing helix chain 'Z' and resid 313 through 323 Processing helix chain 'Z' and resid 342 through 345 Processing helix chain 'Z' and resid 348 through 354 removed outlier: 3.909A pdb=" N THR Z 354 " --> pdb=" O ALA Z 350 " (cutoff:3.500A) Processing helix chain 'Z' and resid 365 through 371 removed outlier: 3.556A pdb=" N ALA Z 369 " --> pdb=" O SER Z 365 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU Z 371 " --> pdb=" O SER Z 367 " (cutoff:3.500A) Processing helix chain 'Z' and resid 388 through 393 Processing helix chain 'Z' and resid 393 through 418 removed outlier: 3.849A pdb=" N VAL Z 399 " --> pdb=" O GLU Z 395 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP Z 415 " --> pdb=" O LYS Z 411 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ILE Z 416 " --> pdb=" O ASN Z 412 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA Z 418 " --> pdb=" O GLN Z 414 " (cutoff:3.500A) Processing helix chain 'Z' and resid 430 through 444 removed outlier: 3.723A pdb=" N LYS Z 438 " --> pdb=" O ALA Z 434 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG Z 441 " --> pdb=" O ARG Z 437 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER Z 444 " --> pdb=" O GLN Z 440 " (cutoff:3.500A) Processing helix chain 'Z' and resid 448 through 452 removed outlier: 3.922A pdb=" N VAL Z 452 " --> pdb=" O VAL Z 449 " (cutoff:3.500A) Processing helix chain 'Z' and resid 462 through 476 removed outlier: 3.716A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) Processing helix chain 'Z' and resid 482 through 486 Processing helix chain 'Z' and resid 491 through 508 removed outlier: 3.892A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS Z 501 " --> pdb=" O GLU Z 497 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA Z 507 " --> pdb=" O ALA Z 503 " (cutoff:3.500A) Processing helix chain 'Z' and resid 526 through 534 removed outlier: 3.599A pdb=" N LEU Z 530 " --> pdb=" O SER Z 526 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL Z 531 " --> pdb=" O LEU Z 527 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER Z 532 " --> pdb=" O ASP Z 528 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE Z 534 " --> pdb=" O LEU Z 530 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Q' and resid 61 through 63 removed outlier: 10.396A pdb=" N VAL S 137 " --> pdb=" O TYR S 158 " (cutoff:3.500A) removed outlier: 9.240A pdb=" N LEU S 160 " --> pdb=" O VAL S 137 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL S 139 " --> pdb=" O LEU S 160 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ILE S 162 " --> pdb=" O VAL S 139 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N SER S 141 " --> pdb=" O ILE S 162 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER S 189 " --> pdb=" O LYS S 99 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 80 through 82 removed outlier: 6.416A pdb=" N PHE R 74 " --> pdb=" O LEU R 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 80 through 82 removed outlier: 6.416A pdb=" N PHE R 74 " --> pdb=" O LEU R 81 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE R 144 " --> pdb=" O PRO R 71 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASN R 73 " --> pdb=" O ILE R 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 97 through 100 removed outlier: 3.582A pdb=" N THR R 88 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'T' and resid 87 through 89 removed outlier: 6.769A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLY T 117 " --> pdb=" O PHE T 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 37 through 44 current: chain 'T' and resid 144 through 150 Processing sheet with id=AA6, first strand: chain 'T' and resid 87 through 89 removed outlier: 6.769A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLY T 117 " --> pdb=" O PHE T 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 116 through 122 current: chain 'Y' and resid 61 through 65 removed outlier: 4.386A pdb=" N SER Y 61 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG Y 86 " --> pdb=" O ALA Y 77 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N HIS Y 79 " --> pdb=" O THR Y 84 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR Y 84 " --> pdb=" O HIS Y 79 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 37 through 44 current: chain 'T' and resid 144 through 150 Processing sheet with id=AA7, first strand: chain 'T' and resid 152 through 155 Processing sheet with id=AA8, first strand: chain 'T' and resid 163 through 164 removed outlier: 8.949A pdb=" N ILE T 286 " --> pdb=" O VAL T 255 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N CYS T 257 " --> pdb=" O ILE T 286 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N VAL T 288 " --> pdb=" O CYS T 257 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TYR T 259 " --> pdb=" O VAL T 288 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ALA T 290 " --> pdb=" O TYR T 259 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ALA T 261 " --> pdb=" O ALA T 290 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU T 222 " --> pdb=" O ILE T 406 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU T 408 " --> pdb=" O LEU T 222 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE T 224 " --> pdb=" O LEU T 408 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'T' and resid 201 through 202 removed outlier: 4.439A pdb=" N ILE T 215 " --> pdb=" O LEU T 202 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'U' and resid 116 through 122 removed outlier: 3.503A pdb=" N VAL U 109 " --> pdb=" O GLY U 117 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU U 107 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU U 108 " --> pdb=" O THR U 147 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N PHE U 132 " --> pdb=" O GLY U 117 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY U 117 " --> pdb=" O PHE U 132 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ARG X 86 " --> pdb=" O ALA X 77 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N HIS X 79 " --> pdb=" O THR X 84 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR X 84 " --> pdb=" O HIS X 79 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'U' and resid 152 through 155 Processing sheet with id=AB3, first strand: chain 'U' and resid 163 through 165 removed outlier: 6.573A pdb=" N THR U 164 " --> pdb=" O SER U 289 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU U 222 " --> pdb=" O ILE U 406 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU U 408 " --> pdb=" O LEU U 222 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE U 224 " --> pdb=" O LEU U 408 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'U' and resid 201 through 202 removed outlier: 4.278A pdb=" N ILE U 215 " --> pdb=" O LEU U 202 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'V' and resid 116 through 122 removed outlier: 3.747A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N LEU V 108 " --> pdb=" O THR V 147 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ALA V 119 " --> pdb=" O VAL V 130 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ARG Z 86 " --> pdb=" O ALA Z 77 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N HIS Z 79 " --> pdb=" O THR Z 84 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR Z 84 " --> pdb=" O HIS Z 79 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'V' and resid 152 through 155 Processing sheet with id=AB7, first strand: chain 'V' and resid 163 through 164 removed outlier: 6.681A pdb=" N LEU V 222 " --> pdb=" O ILE V 406 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LEU V 408 " --> pdb=" O LEU V 222 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE V 224 " --> pdb=" O LEU V 408 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'X' and resid 110 through 113 Processing sheet with id=AB9, first strand: chain 'X' and resid 121 through 122 removed outlier: 6.291A pdb=" N MET X 122 " --> pdb=" O TYR X 248 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N GLN X 250 " --> pdb=" O MET X 122 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL X 247 " --> pdb=" O SER X 208 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE X 210 " --> pdb=" O VAL X 247 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N GLY X 249 " --> pdb=" O PHE X 210 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLY X 212 " --> pdb=" O GLY X 249 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL X 213 " --> pdb=" O ASP X 285 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL X 280 " --> pdb=" O THR X 334 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL X 336 " --> pdb=" O VAL X 280 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU X 282 " --> pdb=" O VAL X 336 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ALA X 338 " --> pdb=" O LEU X 282 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL X 284 " --> pdb=" O ALA X 338 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE X 179 " --> pdb=" O GLN X 337 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS X 178 " --> pdb=" O ASP X 359 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N THR X 361 " --> pdb=" O LYS X 178 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLY X 180 " --> pdb=" O THR X 361 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N VAL X 363 " --> pdb=" O GLY X 180 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE X 182 " --> pdb=" O VAL X 363 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'X' and resid 159 through 160 removed outlier: 4.443A pdb=" N TYR X 173 " --> pdb=" O LEU X 160 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'X' and resid 559 through 561 Processing sheet with id=AC3, first strand: chain 'Y' and resid 110 through 113 Processing sheet with id=AC4, first strand: chain 'Y' and resid 121 through 122 removed outlier: 6.291A pdb=" N MET Y 122 " --> pdb=" O TYR Y 248 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER Y 208 " --> pdb=" O THR Y 245 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL Y 247 " --> pdb=" O SER Y 208 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE Y 210 " --> pdb=" O VAL Y 247 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLY Y 249 " --> pdb=" O PHE Y 210 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLY Y 212 " --> pdb=" O GLY Y 249 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE Y 207 " --> pdb=" O ASP Y 279 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL Y 280 " --> pdb=" O THR Y 334 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL Y 336 " --> pdb=" O VAL Y 280 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU Y 282 " --> pdb=" O VAL Y 336 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ALA Y 338 " --> pdb=" O LEU Y 282 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL Y 284 " --> pdb=" O ALA Y 338 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N TYR Y 340 " --> pdb=" O VAL Y 284 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Y' and resid 159 through 160 removed outlier: 4.230A pdb=" N TYR Y 173 " --> pdb=" O LEU Y 160 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Z' and resid 110 through 113 Processing sheet with id=AC7, first strand: chain 'Z' and resid 121 through 122 removed outlier: 6.412A pdb=" N ILE Z 179 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL Z 339 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU Z 181 " --> pdb=" O VAL Z 339 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LYS Z 178 " --> pdb=" O ALA Z 360 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N THR Z 362 " --> pdb=" O LYS Z 178 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLY Z 180 " --> pdb=" O THR Z 362 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Z' and resid 159 through 160 removed outlier: 4.255A pdb=" N TYR Z 173 " --> pdb=" O LEU Z 160 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Z' and resid 559 through 561 1631 hydrogen bonds defined for protein. 4674 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.02 Time building geometry restraints manager: 3.77 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: 10105 1.33 - 1.45: 5348 1.45 - 1.57: 18742 1.57 - 1.69: 21 1.69 - 1.81: 200 Bond restraints: 34416 Sorted by residual: bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.40e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.89e+01 bond pdb=" C5 ATP U1001 " pdb=" N7 ATP U1001 " ideal model delta sigma weight residual 1.387 1.334 0.053 1.00e-02 1.00e+04 2.78e+01 bond pdb=" C4 ATP U1001 " pdb=" N9 ATP U1001 " ideal model delta sigma weight residual 1.374 1.331 0.043 1.00e-02 1.00e+04 1.87e+01 bond pdb=" C8 ATP U1001 " pdb=" N7 ATP U1001 " ideal model delta sigma weight residual 1.310 1.348 -0.038 1.00e-02 1.00e+04 1.42e+01 ... (remaining 34411 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.04: 46300 4.04 - 8.08: 317 8.08 - 12.12: 24 12.12 - 16.16: 0 16.16 - 20.20: 1 Bond angle restraints: 46642 Sorted by residual: angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 119.67 20.20 1.00e+00 1.00e+00 4.08e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 126.00 10.83 1.00e+00 1.00e+00 1.17e+02 angle pdb=" C5 ATP U1001 " pdb=" C4 ATP U1001 " pdb=" N3 ATP U1001 " ideal model delta sigma weight residual 126.80 118.34 8.46 1.00e+00 1.00e+00 7.16e+01 angle pdb=" N3 ATP U1001 " pdb=" C4 ATP U1001 " pdb=" N9 ATP U1001 " ideal model delta sigma weight residual 127.04 135.33 -8.29 1.15e+00 7.59e-01 5.21e+01 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 132.66 7.21 1.00e+00 1.00e+00 5.20e+01 ... (remaining 46637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.15: 20130 32.15 - 64.31: 538 64.31 - 96.46: 56 96.46 - 128.62: 2 128.62 - 160.77: 1 Dihedral angle restraints: 20727 sinusoidal: 7973 harmonic: 12754 Sorted by residual: dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -127.83 -52.17 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual -180.00 -129.31 -50.69 0 5.00e+00 4.00e-02 1.03e+02 dihedral pdb=" C5' ADP Z 601 " pdb=" O5' ADP Z 601 " pdb=" PA ADP Z 601 " pdb=" O2A ADP Z 601 " ideal model delta sinusoidal sigma weight residual 300.00 139.23 160.77 1 2.00e+01 2.50e-03 4.67e+01 ... (remaining 20724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 4221 0.068 - 0.137: 1153 0.137 - 0.205: 127 0.205 - 0.273: 17 0.273 - 0.341: 2 Chirality restraints: 5520 Sorted by residual: chirality pdb=" CB VAL T 180 " pdb=" CA VAL T 180 " pdb=" CG1 VAL T 180 " pdb=" CG2 VAL T 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB VAL U 180 " pdb=" CA VAL U 180 " pdb=" CG1 VAL U 180 " pdb=" CG2 VAL U 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA ASP Y 513 " pdb=" N ASP Y 513 " pdb=" C ASP Y 513 " pdb=" CB ASP Y 513 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 5517 not shown) Planarity restraints: 5995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.031 2.00e-02 2.50e+03 6.01e-02 3.61e+01 pdb=" C ALA Z 503 " -0.104 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.039 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA X 307 " 0.016 2.00e-02 2.50e+03 3.08e-02 9.46e+00 pdb=" C ALA X 307 " -0.053 2.00e-02 2.50e+03 pdb=" O ALA X 307 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL X 308 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU Q 33 " -0.048 5.00e-02 4.00e+02 7.22e-02 8.33e+00 pdb=" N PRO Q 34 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO Q 34 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO Q 34 " -0.040 5.00e-02 4.00e+02 ... (remaining 5992 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 46 2.33 - 2.97: 15617 2.97 - 3.62: 50515 3.62 - 4.26: 87311 4.26 - 4.90: 141433 Nonbonded interactions: 294922 Sorted by model distance: nonbonded pdb="MG MG U1002 " pdb=" O HOH U1104 " model vdw 1.688 2.170 nonbonded pdb="MG MG V1002 " pdb=" O HOH V1104 " model vdw 1.706 2.170 nonbonded pdb=" OG1 THR V 232 " pdb="MG MG V1002 " model vdw 2.046 2.170 nonbonded pdb=" O3B ADP Y 601 " pdb="MG MG Y 602 " model vdw 2.053 2.170 nonbonded pdb=" OG1 THR Y 190 " pdb="MG MG Y 602 " model vdw 2.057 2.170 ... (remaining 294917 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'T' selection = (chain 'U' and resid 80 through 1002) selection = (chain 'V' and resid 80 through 1002) } ncs_group { reference = (chain 'X' and resid 37 through 552) selection = (chain 'Y' and resid 37 through 552) selection = (chain 'Z' and resid 37 through 552) } 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: 11.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 30.880 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 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 : 0.011 0.784 34418 Z= 0.659 Angle : 0.992 20.204 46642 Z= 0.555 Chirality : 0.060 0.341 5520 Planarity : 0.007 0.072 5995 Dihedral : 14.766 160.771 12569 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.69 % Favored : 95.16 % Rotamer: Outliers : 0.39 % Allowed : 5.53 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.69 (0.10), residues: 4459 helix: -4.19 (0.05), residues: 2128 sheet: -1.42 (0.20), residues: 616 loop : -1.93 (0.13), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG U 454 TYR 0.021 0.003 TYR X 310 PHE 0.031 0.003 PHE S 249 TRP 0.024 0.003 TRP R 37 HIS 0.008 0.002 HIS Z 144 Details of bonding type rmsd/Z covalent geometry : bond 0.01033 / 0.44 (34416) covalent geometry : angle 0.99163 / 0.56 (46642) hydrogen bonds : bond 0.27827 / 18.40 ( 1622) hydrogen bonds : angle 10.39416 / 7.16 ( 4674) Misc. bond : bond 0.64152 / 32.98 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 582 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 117 SER cc_start: 0.8546 (p) cc_final: 0.8332 (p) REVERT: G 61 MET cc_start: 0.7264 (mmt) cc_final: 0.7050 (mmm) REVERT: G 113 ILE cc_start: 0.7666 (mt) cc_final: 0.7276 (mt) REVERT: J 61 MET cc_start: 0.7676 (mpp) cc_final: 0.7198 (mtp) REVERT: J 119 LEU cc_start: 0.7307 (tt) cc_final: 0.7037 (tp) REVERT: S 68 MET cc_start: 0.7606 (ttp) cc_final: 0.7312 (ttt) REVERT: S 271 MET cc_start: 0.7645 (ttp) cc_final: 0.7407 (ttt) REVERT: T 479 ARG cc_start: 0.8372 (mtt90) cc_final: 0.8076 (mtt90) REVERT: T 489 PHE cc_start: 0.8270 (m-80) cc_final: 0.8006 (m-80) REVERT: T 537 LYS cc_start: 0.8041 (tptt) cc_final: 0.7595 (ttpp) REVERT: U 309 MET cc_start: 0.8712 (mtt) cc_final: 0.8395 (mtt) REVERT: U 509 LEU cc_start: 0.7876 (mt) cc_final: 0.7656 (mp) REVERT: V 488 GLN cc_start: 0.8086 (pt0) cc_final: 0.7762 (pt0) REVERT: X 90 MET cc_start: 0.8912 (mmt) cc_final: 0.8709 (mmt) REVERT: X 408 GLN cc_start: 0.7372 (tp40) cc_final: 0.7138 (tp40) REVERT: X 412 ASN cc_start: 0.8213 (m-40) cc_final: 0.7940 (m-40) REVERT: Y 359 ASP cc_start: 0.7662 (m-30) cc_final: 0.7428 (m-30) REVERT: Y 415 ASP cc_start: 0.7484 (p0) cc_final: 0.7265 (p0) REVERT: Y 451 GLU cc_start: 0.7166 (pt0) cc_final: 0.6962 (pt0) REVERT: Y 501 LYS cc_start: 0.7764 (tptt) cc_final: 0.7377 (mtpm) REVERT: Z 317 ASP cc_start: 0.7610 (m-30) cc_final: 0.7134 (m-30) REVERT: Z 401 ARG cc_start: 0.7652 (mmm160) cc_final: 0.7303 (mtp180) REVERT: Z 405 LYS cc_start: 0.8541 (tptt) cc_final: 0.7677 (mtpt) outliers start: 14 outliers final: 5 residues processed: 591 average time/residue: 0.6665 time to fit residues: 471.8743 Evaluate side-chains 406 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 401 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain Y residue 371 LEU Chi-restraints excluded: chain Z residue 280 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: [432, 197, 388, 215, 20, 132, 261, 248, 207, 401, 424] chunk 432 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 0.3980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 0.9990 chunk 424 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN A 94 ASN B 92 ASN C 94 ASN E 87 ASN F 87 ASN J 87 ASN J 92 ASN J 94 ASN P 71 GLN Q 43 GLN Q 46 HIS R 38 ASN R 73 ASN R 137 HIS R 154 GLN S 98 ASN ** S 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 262 ASN S 267 HIS T 121 ASN T 152 ASN T 196 GLN ** T 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 386 GLN T 435 GLN T 539 ASN T 549 HIS U 152 ASN U 241 HIS U 246 ASN U 248 GLN U 264 GLN U 271 GLN U 319 HIS U 386 GLN U 422 ASN V 61 HIS V 121 ASN V 126 HIS V 139 HIS ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 242 GLN V 271 GLN V 386 GLN V 486 GLN V 497 GLN ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 199 ASN X 278 GLN X 294 ASN X 448 GLN X 514 ASN Y 157 GLN Y 174 GLN Y 199 ASN Y 278 GLN Y 390 ASN Y 412 ASN Z 100 GLN Z 123 ASN Z 174 GLN Z 408 GLN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.142874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.104078 restraints weight = 46710.961| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.68 r_work: 0.3086 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34418 Z= 0.142 Angle : 0.605 9.155 46642 Z= 0.318 Chirality : 0.043 0.174 5520 Planarity : 0.005 0.063 5995 Dihedral : 6.805 123.344 4829 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.01 % Favored : 96.82 % Rotamer: Outliers : 2.16 % Allowed : 12.12 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.11), residues: 4459 helix: -2.04 (0.09), residues: 2145 sheet: -1.18 (0.21), residues: 579 loop : -1.27 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 385 TYR 0.018 0.002 TYR E 102 PHE 0.021 0.001 PHE U 508 TRP 0.017 0.002 TRP U 73 HIS 0.007 0.001 HIS V 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (34416) covalent geometry : angle 0.60493 / 0.32 (46642) hydrogen bonds : bond 0.04393 / 2.90 ( 1622) hydrogen bonds : angle 5.38347 / 3.76 ( 4674) Misc. bond : bond 0.00151 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 498 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.6054 (OUTLIER) cc_final: 0.5388 (ptp) REVERT: B 82 PHE cc_start: 0.7719 (m-80) cc_final: 0.7391 (m-80) REVERT: C 61 MET cc_start: 0.7017 (OUTLIER) cc_final: 0.6490 (mtp) REVERT: C 111 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6996 (mm-30) REVERT: E 61 MET cc_start: 0.7859 (mtm) cc_final: 0.7199 (ttp) REVERT: E 95 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.7956 (mt) REVERT: F 124 ILE cc_start: 0.7663 (mm) cc_final: 0.7455 (mm) REVERT: G 61 MET cc_start: 0.6863 (mmt) cc_final: 0.6519 (mmm) REVERT: I 118 LEU cc_start: 0.6979 (mt) cc_final: 0.6714 (mt) REVERT: P 106 SER cc_start: 0.8475 (m) cc_final: 0.8137 (p) REVERT: P 108 VAL cc_start: 0.8441 (t) cc_final: 0.8067 (p) REVERT: Q 43 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.6846 (mm-40) REVERT: Q 48 ARG cc_start: 0.7426 (ptt90) cc_final: 0.7223 (ptt90) REVERT: Q 61 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7629 (tttm) REVERT: R 154 GLN cc_start: 0.6413 (OUTLIER) cc_final: 0.6165 (pt0) REVERT: S 55 LYS cc_start: 0.8118 (tttm) cc_final: 0.7852 (tptt) REVERT: S 181 GLU cc_start: 0.7609 (tp30) cc_final: 0.7302 (mp0) REVERT: S 234 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8248 (tm-30) REVERT: S 271 MET cc_start: 0.8362 (ttp) cc_final: 0.7960 (ttt) REVERT: S 275 GLU cc_start: 0.7922 (tp30) cc_final: 0.7673 (tp30) REVERT: S 283 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7821 (mt-10) REVERT: T 179 ASN cc_start: 0.8887 (t0) cc_final: 0.8633 (t0) REVERT: T 476 ARG cc_start: 0.7807 (tpp80) cc_final: 0.7534 (tpp80) REVERT: T 508 PHE cc_start: 0.8833 (m-80) cc_final: 0.8502 (m-80) REVERT: T 537 LYS cc_start: 0.8069 (tptt) cc_final: 0.7213 (ttpp) REVERT: U 309 MET cc_start: 0.9264 (mtt) cc_final: 0.8928 (mtt) REVERT: U 474 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7698 (mt) REVERT: V 101 LYS cc_start: 0.8715 (mmtp) cc_final: 0.8303 (mmmt) REVERT: V 314 ARG cc_start: 0.9174 (ttp80) cc_final: 0.8726 (ttp-170) REVERT: V 425 LEU cc_start: 0.8585 (mt) cc_final: 0.8382 (mt) REVERT: V 447 LYS cc_start: 0.6890 (tppt) cc_final: 0.6678 (tppt) REVERT: V 488 GLN cc_start: 0.8301 (pt0) cc_final: 0.8045 (pt0) REVERT: V 492 ILE cc_start: 0.8752 (mt) cc_final: 0.8549 (mm) REVERT: X 219 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8279 (mm-30) REVERT: X 408 GLN cc_start: 0.7549 (tp40) cc_final: 0.7013 (tp40) REVERT: X 412 ASN cc_start: 0.8590 (m-40) cc_final: 0.8127 (m-40) REVERT: X 441 ARG cc_start: 0.8127 (mpt180) cc_final: 0.7855 (tpp-160) REVERT: X 448 GLN cc_start: 0.8172 (tt0) cc_final: 0.7669 (mt0) REVERT: Y 195 GLU cc_start: 0.8869 (tp30) cc_final: 0.8630 (tp30) REVERT: Y 266 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8546 (tt) REVERT: Y 279 ASP cc_start: 0.8726 (OUTLIER) cc_final: 0.8506 (m-30) REVERT: Y 359 ASP cc_start: 0.8440 (m-30) cc_final: 0.8102 (m-30) REVERT: Y 501 LYS cc_start: 0.7347 (tptt) cc_final: 0.6697 (ttpp) REVERT: Z 317 ASP cc_start: 0.7995 (m-30) cc_final: 0.7410 (m-30) REVERT: Z 405 LYS cc_start: 0.8321 (tptt) cc_final: 0.7923 (tptm) REVERT: Z 429 ASP cc_start: 0.6697 (OUTLIER) cc_final: 0.6476 (p0) REVERT: Z 502 MET cc_start: 0.6275 (mtp) cc_final: 0.6049 (ptp) outliers start: 77 outliers final: 18 residues processed: 537 average time/residue: 0.6376 time to fit residues: 415.2118 Evaluate side-chains 453 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 425 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain Q residue 43 GLN Chi-restraints excluded: chain Q residue 61 LYS Chi-restraints excluded: chain R residue 154 GLN Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 204 LYS Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 395 GLU Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 279 ASP Chi-restraints excluded: chain Z residue 414 GLN Chi-restraints excluded: chain Z residue 429 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: [346, 25, 371, 318, 228, 121, 174, 220, 387, 86, 183] chunk 346 optimal weight: 0.0770 chunk 25 optimal weight: 3.9990 chunk 371 optimal weight: 1.9990 chunk 318 optimal weight: 3.9990 chunk 228 optimal weight: 0.9990 chunk 121 optimal weight: 0.1980 chunk 174 optimal weight: 0.6980 chunk 220 optimal weight: 0.5980 chunk 387 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 overall best weight: 0.5140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN B 87 ASN E 87 ASN J 87 ASN J 92 ASN P 71 GLN ** P 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 358 HIS T 405 GLN T 539 ASN U 152 ASN U 422 ASN ** U 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS V 64 GLN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 83 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.145284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.108416 restraints weight = 46694.520| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.61 r_work: 0.3121 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34418 Z= 0.116 Angle : 0.547 8.971 46642 Z= 0.283 Chirality : 0.042 0.161 5520 Planarity : 0.004 0.062 5995 Dihedral : 6.125 98.016 4825 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.16 % Favored : 96.68 % Rotamer: Outliers : 2.36 % Allowed : 14.14 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.12), residues: 4459 helix: -0.88 (0.11), residues: 2143 sheet: -1.13 (0.21), residues: 589 loop : -1.03 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 86 TYR 0.025 0.001 TYR I 102 PHE 0.023 0.001 PHE U 508 TRP 0.015 0.001 TRP U 73 HIS 0.004 0.001 HIS V 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (34416) covalent geometry : angle 0.54701 / 0.28 (46642) hydrogen bonds : bond 0.03697 / 2.44 ( 1622) hydrogen bonds : angle 4.75040 / 3.34 ( 4674) Misc. bond : bond 0.00116 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 489 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.5868 (mpp) cc_final: 0.5367 (ptp) REVERT: A 87 ASN cc_start: 0.7845 (OUTLIER) cc_final: 0.7422 (m-40) REVERT: D 109 LEU cc_start: 0.7572 (mm) cc_final: 0.6919 (tt) REVERT: E 61 MET cc_start: 0.8026 (mtm) cc_final: 0.7543 (ttm) REVERT: E 95 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7874 (pp) REVERT: F 124 ILE cc_start: 0.7642 (mm) cc_final: 0.7119 (mm) REVERT: G 60 LYS cc_start: 0.7114 (ptpt) cc_final: 0.6786 (ptpt) REVERT: G 61 MET cc_start: 0.6764 (mmt) cc_final: 0.6466 (mmm) REVERT: G 113 ILE cc_start: 0.7426 (OUTLIER) cc_final: 0.7224 (mt) REVERT: H 124 ILE cc_start: 0.7841 (mp) cc_final: 0.7630 (mp) REVERT: H 125 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.6199 (mp) REVERT: I 102 TYR cc_start: 0.7382 (m-80) cc_final: 0.7085 (m-80) REVERT: I 118 LEU cc_start: 0.7092 (mt) cc_final: 0.6881 (mt) REVERT: P 64 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: P 106 SER cc_start: 0.8482 (m) cc_final: 0.8101 (p) REVERT: P 108 VAL cc_start: 0.8472 (t) cc_final: 0.8065 (p) REVERT: Q 61 LYS cc_start: 0.7935 (tttm) cc_final: 0.7651 (tttm) REVERT: S 55 LYS cc_start: 0.8198 (tttm) cc_final: 0.7874 (tptt) REVERT: S 68 MET cc_start: 0.7523 (ttt) cc_final: 0.7300 (ttp) REVERT: S 181 GLU cc_start: 0.7439 (tp30) cc_final: 0.7218 (mp0) REVERT: S 216 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6825 (mp) REVERT: S 234 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8084 (tm-30) REVERT: S 245 ASP cc_start: 0.8336 (m-30) cc_final: 0.8135 (m-30) REVERT: S 271 MET cc_start: 0.8322 (ttp) cc_final: 0.7884 (ttt) REVERT: S 275 GLU cc_start: 0.7916 (tp30) cc_final: 0.7598 (tp30) REVERT: T 179 ASN cc_start: 0.8744 (t0) cc_final: 0.8483 (t0) REVERT: T 508 PHE cc_start: 0.8760 (m-80) cc_final: 0.8352 (m-80) REVERT: T 537 LYS cc_start: 0.8037 (tptt) cc_final: 0.7296 (ttpp) REVERT: T 541 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7966 (tttp) REVERT: U 251 LYS cc_start: 0.8355 (ttpp) cc_final: 0.8021 (ttpt) REVERT: U 287 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8792 (tpp) REVERT: U 309 MET cc_start: 0.9282 (mtt) cc_final: 0.8973 (mtt) REVERT: U 447 LYS cc_start: 0.8045 (mmtt) cc_final: 0.7815 (mmtt) REVERT: U 474 LEU cc_start: 0.7745 (mp) cc_final: 0.7536 (mt) REVERT: V 488 GLN cc_start: 0.8214 (pt0) cc_final: 0.8011 (pt0) REVERT: V 502 TYR cc_start: 0.7662 (t80) cc_final: 0.7416 (t80) REVERT: V 547 ASP cc_start: 0.7330 (p0) cc_final: 0.6548 (t0) REVERT: X 408 GLN cc_start: 0.7558 (tp40) cc_final: 0.7032 (tp40) REVERT: X 412 ASN cc_start: 0.8448 (m-40) cc_final: 0.8002 (m-40) REVERT: X 448 GLN cc_start: 0.8084 (tt0) cc_final: 0.7625 (mt0) REVERT: X 471 GLN cc_start: 0.7385 (mt0) cc_final: 0.6946 (mm-40) REVERT: X 497 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6704 (mp0) REVERT: Y 195 GLU cc_start: 0.8904 (tp30) cc_final: 0.8674 (tp30) REVERT: Y 359 ASP cc_start: 0.8313 (m-30) cc_final: 0.8061 (m-30) REVERT: Y 501 LYS cc_start: 0.7302 (tptt) cc_final: 0.6635 (ttpp) REVERT: Z 194 MET cc_start: 0.8244 (mmt) cc_final: 0.8032 (mmm) REVERT: Z 317 ASP cc_start: 0.7800 (m-30) cc_final: 0.7321 (m-30) REVERT: Z 405 LYS cc_start: 0.8218 (tptt) cc_final: 0.6911 (mtmm) REVERT: Z 429 ASP cc_start: 0.6451 (OUTLIER) cc_final: 0.6183 (p0) REVERT: Z 430 LYS cc_start: 0.7146 (mttp) cc_final: 0.6886 (mtmt) REVERT: Z 453 PHE cc_start: 0.6329 (m-10) cc_final: 0.6082 (m-80) REVERT: Z 488 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8132 (tpp) outliers start: 84 outliers final: 24 residues processed: 536 average time/residue: 0.6238 time to fit residues: 404.0196 Evaluate side-chains 439 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 405 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 102 TYR Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 541 LYS Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 282 MET Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Z residue 414 GLN Chi-restraints excluded: chain Z residue 429 ASP Chi-restraints excluded: chain Z residue 488 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: [154, 191, 102, 373, 63, 300, 247, 425, 181, 31, 293] chunk 154 optimal weight: 0.8980 chunk 191 optimal weight: 0.7980 chunk 102 optimal weight: 0.0980 chunk 373 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 300 optimal weight: 2.9990 chunk 247 optimal weight: 0.0670 chunk 425 optimal weight: 0.5980 chunk 181 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 293 optimal weight: 1.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN B 87 ASN C 94 ASN J 87 ASN ** P 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN R 83 GLN R 154 GLN S 98 ASN ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 241 HIS T 488 GLN T 539 ASN U 253 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 549 HIS V 61 HIS V 196 GLN ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 390 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.145629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.108928 restraints weight = 46224.945| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.62 r_work: 0.3139 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 34418 Z= 0.109 Angle : 0.538 9.193 46642 Z= 0.274 Chirality : 0.042 0.182 5520 Planarity : 0.004 0.058 5995 Dihedral : 5.827 97.954 4825 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.07 % Favored : 96.79 % Rotamer: Outliers : 2.89 % Allowed : 15.46 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.12), residues: 4459 helix: -0.31 (0.11), residues: 2165 sheet: -1.02 (0.21), residues: 581 loop : -0.80 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 48 TYR 0.020 0.001 TYR I 102 PHE 0.018 0.001 PHE U 508 TRP 0.017 0.001 TRP U 73 HIS 0.005 0.001 HIS V 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (34416) covalent geometry : angle 0.53750 / 0.27 (46642) hydrogen bonds : bond 0.03392 / 2.25 ( 1622) hydrogen bonds : angle 4.46935 / 3.14 ( 4674) Misc. bond : bond 0.00087 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 453 time to evaluate : 1.145 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.5917 (OUTLIER) cc_final: 0.5578 (ptp) REVERT: A 87 ASN cc_start: 0.7774 (m110) cc_final: 0.7370 (m-40) REVERT: B 82 PHE cc_start: 0.7701 (m-80) cc_final: 0.7466 (m-80) REVERT: B 102 TYR cc_start: 0.7096 (m-80) cc_final: 0.6833 (m-80) REVERT: E 61 MET cc_start: 0.8020 (mtm) cc_final: 0.7631 (ttm) REVERT: E 78 LEU cc_start: 0.7219 (pp) cc_final: 0.6577 (mt) REVERT: E 95 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7924 (mt) REVERT: F 124 ILE cc_start: 0.7589 (mm) cc_final: 0.7014 (mm) REVERT: G 61 MET cc_start: 0.6804 (mmt) cc_final: 0.6553 (mmm) REVERT: G 113 ILE cc_start: 0.7575 (OUTLIER) cc_final: 0.7365 (mt) REVERT: J 82 PHE cc_start: 0.7906 (m-80) cc_final: 0.7509 (m-80) REVERT: J 119 LEU cc_start: 0.6966 (tt) cc_final: 0.6697 (tp) REVERT: P 64 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8043 (mp0) REVERT: P 106 SER cc_start: 0.8449 (m) cc_final: 0.8042 (p) REVERT: P 108 VAL cc_start: 0.8510 (t) cc_final: 0.8114 (p) REVERT: Q 61 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7698 (tttm) REVERT: S 55 LYS cc_start: 0.8155 (tttm) cc_final: 0.7888 (tptt) REVERT: S 68 MET cc_start: 0.7578 (ttt) cc_final: 0.7332 (ttp) REVERT: S 198 ARG cc_start: 0.7344 (mmp80) cc_final: 0.7128 (mmp80) REVERT: S 216 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6854 (mp) REVERT: S 245 ASP cc_start: 0.8384 (m-30) cc_final: 0.8164 (m-30) REVERT: S 266 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8306 (tt0) REVERT: S 271 MET cc_start: 0.8272 (ttp) cc_final: 0.7848 (ttt) REVERT: S 275 GLU cc_start: 0.7943 (tp30) cc_final: 0.7631 (tp30) REVERT: T 237 ASP cc_start: 0.8040 (m-30) cc_final: 0.7828 (m-30) REVERT: T 475 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7581 (mm-30) REVERT: T 508 PHE cc_start: 0.8718 (m-80) cc_final: 0.8344 (m-80) REVERT: T 537 LYS cc_start: 0.8006 (tptt) cc_final: 0.7298 (ttpp) REVERT: T 541 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7876 (tttp) REVERT: U 92 ASP cc_start: 0.8793 (m-30) cc_final: 0.8420 (m-30) REVERT: U 251 LYS cc_start: 0.8216 (ttpp) cc_final: 0.7683 (ttmm) REVERT: U 309 MET cc_start: 0.9266 (mtt) cc_final: 0.8947 (mtt) REVERT: U 447 LYS cc_start: 0.7929 (mmtt) cc_final: 0.7628 (mmtt) REVERT: U 474 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7579 (mt) REVERT: V 502 TYR cc_start: 0.7648 (t80) cc_final: 0.7405 (t80) REVERT: V 518 VAL cc_start: 0.7725 (OUTLIER) cc_final: 0.7444 (t) REVERT: V 547 ASP cc_start: 0.7238 (p0) cc_final: 0.6447 (t0) REVERT: X 276 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8424 (mm-30) REVERT: X 408 GLN cc_start: 0.7593 (tp40) cc_final: 0.7090 (tp40) REVERT: X 412 ASN cc_start: 0.8465 (m-40) cc_final: 0.8032 (m-40) REVERT: X 448 GLN cc_start: 0.8107 (tt0) cc_final: 0.7661 (mt0) REVERT: X 471 GLN cc_start: 0.7375 (mt0) cc_final: 0.7033 (mm-40) REVERT: X 497 GLU cc_start: 0.7554 (mt-10) cc_final: 0.6851 (mp0) REVERT: Y 66 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: Y 195 GLU cc_start: 0.8915 (tp30) cc_final: 0.8695 (tp30) REVERT: Y 266 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8570 (tt) REVERT: Y 359 ASP cc_start: 0.8181 (m-30) cc_final: 0.7900 (m-30) REVERT: Y 501 LYS cc_start: 0.7298 (tptt) cc_final: 0.6634 (ttpp) REVERT: Z 317 ASP cc_start: 0.7612 (m-30) cc_final: 0.7172 (m-30) REVERT: Z 398 ASN cc_start: 0.8508 (m-40) cc_final: 0.8275 (m110) REVERT: Z 401 ARG cc_start: 0.6970 (mtp180) cc_final: 0.6194 (mmt90) REVERT: Z 405 LYS cc_start: 0.8173 (tptt) cc_final: 0.7894 (tptm) REVERT: Z 414 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7295 (mt0) REVERT: Z 429 ASP cc_start: 0.6359 (OUTLIER) cc_final: 0.6099 (p0) REVERT: Z 430 LYS cc_start: 0.7150 (mttp) cc_final: 0.6924 (mtmt) REVERT: Z 453 PHE cc_start: 0.6216 (m-10) cc_final: 0.5962 (m-80) outliers start: 103 outliers final: 33 residues processed: 515 average time/residue: 0.6243 time to fit residues: 391.4751 Evaluate side-chains 452 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 405 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain G residue 102 TYR Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 61 LYS Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 233 ILE Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 479 ARG Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 541 LYS Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 395 GLU Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Z residue 414 GLN Chi-restraints excluded: chain Z residue 429 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: [330, 314, 417, 110, 13, 440, 26, 429, 340, 134, 159] chunk 330 optimal weight: 4.9990 chunk 314 optimal weight: 2.9990 chunk 417 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 440 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 429 optimal weight: 0.0070 chunk 340 optimal weight: 1.9990 chunk 134 optimal weight: 0.0870 chunk 159 optimal weight: 0.0770 overall best weight: 0.3734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN I 98 GLN J 87 ASN P 65 ASN P 140 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 GLN R 154 GLN ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 188 GLN T 121 ASN T 539 ASN U 61 HIS U 422 ASN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS ** Y 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.146943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.110252 restraints weight = 46478.972| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.69 r_work: 0.3151 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 34418 Z= 0.100 Angle : 0.527 9.465 46642 Z= 0.268 Chirality : 0.042 0.245 5520 Planarity : 0.004 0.052 5995 Dihedral : 5.544 94.521 4825 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.16 % Favored : 96.70 % Rotamer: Outliers : 2.69 % Allowed : 16.52 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.13), residues: 4459 helix: 0.12 (0.11), residues: 2150 sheet: -0.84 (0.21), residues: 562 loop : -0.64 (0.15), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 115 TYR 0.028 0.001 TYR I 102 PHE 0.026 0.001 PHE U 508 TRP 0.022 0.001 TRP U 73 HIS 0.005 0.001 HIS R 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (34416) covalent geometry : angle 0.52656 / 0.27 (46642) hydrogen bonds : bond 0.03162 / 2.10 ( 1622) hydrogen bonds : angle 4.29014 / 3.02 ( 4674) Misc. bond : bond 0.00060 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 465 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.5882 (OUTLIER) cc_final: 0.5582 (ptp) REVERT: A 87 ASN cc_start: 0.7844 (OUTLIER) cc_final: 0.7411 (m-40) REVERT: B 102 TYR cc_start: 0.7137 (m-80) cc_final: 0.6846 (m-80) REVERT: E 61 MET cc_start: 0.7944 (mtm) cc_final: 0.7631 (ttm) REVERT: E 78 LEU cc_start: 0.7258 (pp) cc_final: 0.6670 (mt) REVERT: E 95 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7864 (mt) REVERT: F 124 ILE cc_start: 0.7533 (mm) cc_final: 0.6931 (mm) REVERT: G 61 MET cc_start: 0.6788 (mmt) cc_final: 0.6465 (mmm) REVERT: P 63 LYS cc_start: 0.8010 (tptm) cc_final: 0.7790 (tttm) REVERT: P 64 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8151 (mp0) REVERT: P 106 SER cc_start: 0.8323 (m) cc_final: 0.7913 (p) REVERT: P 149 LYS cc_start: 0.7041 (ptpp) cc_final: 0.6236 (pptt) REVERT: S 48 ARG cc_start: 0.7740 (ttt180) cc_final: 0.7432 (ttp80) REVERT: S 68 MET cc_start: 0.7623 (ttt) cc_final: 0.7381 (ttp) REVERT: S 180 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7362 (mt-10) REVERT: S 232 ASP cc_start: 0.8085 (m-30) cc_final: 0.7852 (p0) REVERT: S 234 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7949 (tm-30) REVERT: S 266 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8288 (tt0) REVERT: S 271 MET cc_start: 0.8283 (ttp) cc_final: 0.7854 (ttt) REVERT: S 275 GLU cc_start: 0.7951 (tp30) cc_final: 0.7656 (tp30) REVERT: T 300 PHE cc_start: 0.9353 (OUTLIER) cc_final: 0.8268 (t80) REVERT: T 508 PHE cc_start: 0.8700 (m-80) cc_final: 0.8344 (m-80) REVERT: T 537 LYS cc_start: 0.8017 (tptt) cc_final: 0.7244 (ttpp) REVERT: T 541 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7835 (tttp) REVERT: U 92 ASP cc_start: 0.8769 (m-30) cc_final: 0.8354 (m-30) REVERT: U 149 GLN cc_start: 0.8257 (mm110) cc_final: 0.8023 (pt0) REVERT: U 251 LYS cc_start: 0.8066 (ttpp) cc_final: 0.7594 (ttmm) REVERT: U 309 MET cc_start: 0.9285 (mtt) cc_final: 0.8981 (mtt) REVERT: U 447 LYS cc_start: 0.7884 (mmtt) cc_final: 0.7618 (mmtt) REVERT: U 474 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7370 (mt) REVERT: V 73 TRP cc_start: 0.7141 (m-10) cc_final: 0.6423 (m-10) REVERT: V 502 TYR cc_start: 0.7633 (t80) cc_final: 0.7402 (t80) REVERT: V 518 VAL cc_start: 0.7464 (OUTLIER) cc_final: 0.7203 (t) REVERT: V 522 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7559 (mp0) REVERT: V 547 ASP cc_start: 0.7216 (p0) cc_final: 0.6484 (t0) REVERT: V 549 HIS cc_start: 0.6703 (OUTLIER) cc_final: 0.5867 (m170) REVERT: X 276 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8470 (mm-30) REVERT: X 408 GLN cc_start: 0.7648 (tp40) cc_final: 0.7220 (tp40) REVERT: X 412 ASN cc_start: 0.8421 (m-40) cc_final: 0.8025 (m-40) REVERT: X 440 GLN cc_start: 0.8424 (mt0) cc_final: 0.8172 (mt0) REVERT: X 448 GLN cc_start: 0.8065 (tt0) cc_final: 0.7643 (mt0) REVERT: X 471 GLN cc_start: 0.7336 (mt0) cc_final: 0.7034 (mm-40) REVERT: X 497 GLU cc_start: 0.7569 (mt-10) cc_final: 0.6962 (mp0) REVERT: Y 195 GLU cc_start: 0.8915 (tp30) cc_final: 0.8695 (tp30) REVERT: Y 266 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8554 (tt) REVERT: Y 359 ASP cc_start: 0.8139 (m-30) cc_final: 0.7862 (m-30) REVERT: Y 501 LYS cc_start: 0.7269 (tptt) cc_final: 0.6597 (ttpp) REVERT: Z 317 ASP cc_start: 0.7714 (m-30) cc_final: 0.7286 (m-30) REVERT: Z 381 ASP cc_start: 0.8502 (t0) cc_final: 0.8281 (t0) REVERT: Z 398 ASN cc_start: 0.8474 (m-40) cc_final: 0.8239 (m110) REVERT: Z 401 ARG cc_start: 0.6904 (mtp180) cc_final: 0.6245 (mmp80) REVERT: Z 429 ASP cc_start: 0.6266 (OUTLIER) cc_final: 0.6013 (p0) REVERT: Z 484 MET cc_start: 0.7481 (mmm) cc_final: 0.6055 (pmm) outliers start: 96 outliers final: 37 residues processed: 526 average time/residue: 0.6151 time to fit residues: 393.6822 Evaluate side-chains 459 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 410 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 102 TYR Chi-restraints excluded: chain G residue 102 TYR Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 541 LYS Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 272 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 282 MET Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 549 HIS Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Z residue 429 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: [294, 219, 306, 195, 330, 70, 136, 369, 91, 137, 288] chunk 294 optimal weight: 4.9990 chunk 219 optimal weight: 0.7980 chunk 306 optimal weight: 1.9990 chunk 195 optimal weight: 0.8980 chunk 330 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 369 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 137 optimal weight: 0.0980 chunk 288 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN C 94 ASN J 87 ASN P 65 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 GLN R 154 GLN S 98 ASN ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN U 515 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS V 244 ASN ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 241 ASN X 278 GLN ** Y 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 390 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.143453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.106119 restraints weight = 46105.798| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.66 r_work: 0.3090 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 34418 Z= 0.156 Angle : 0.572 9.929 46642 Z= 0.291 Chirality : 0.044 0.273 5520 Planarity : 0.004 0.049 5995 Dihedral : 5.786 97.609 4825 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.54 % Favored : 96.34 % Rotamer: Outliers : 2.92 % Allowed : 17.59 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.13), residues: 4459 helix: 0.18 (0.11), residues: 2152 sheet: -0.92 (0.21), residues: 580 loop : -0.60 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 435 TYR 0.033 0.002 TYR I 102 PHE 0.026 0.001 PHE U 508 TRP 0.013 0.001 TRP U 73 HIS 0.006 0.001 HIS V 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (34416) covalent geometry : angle 0.57181 / 0.29 (46642) hydrogen bonds : bond 0.03574 / 2.38 ( 1622) hydrogen bonds : angle 4.41349 / 3.11 ( 4674) Misc. bond : bond 0.00166 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 410 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.5867 (OUTLIER) cc_final: 0.5539 (ptp) REVERT: A 87 ASN cc_start: 0.7890 (m110) cc_final: 0.7477 (m-40) REVERT: B 102 TYR cc_start: 0.7277 (m-80) cc_final: 0.7065 (m-80) REVERT: E 61 MET cc_start: 0.8027 (mtm) cc_final: 0.7640 (ttm) REVERT: E 78 LEU cc_start: 0.7209 (pp) cc_final: 0.6604 (mt) REVERT: E 95 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8011 (pp) REVERT: G 61 MET cc_start: 0.6848 (mmt) cc_final: 0.6567 (mmm) REVERT: H 120 VAL cc_start: 0.6739 (t) cc_final: 0.6527 (t) REVERT: J 126 PHE cc_start: 0.7167 (m-80) cc_final: 0.6884 (m-80) REVERT: P 64 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7964 (mp0) REVERT: P 106 SER cc_start: 0.8487 (m) cc_final: 0.8060 (p) REVERT: P 136 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7861 (pt0) REVERT: Q 61 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7673 (tttm) REVERT: R 58 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7476 (mmtp) REVERT: S 48 ARG cc_start: 0.7887 (ttt180) cc_final: 0.7578 (ttp80) REVERT: S 68 MET cc_start: 0.7591 (ttt) cc_final: 0.7336 (ttp) REVERT: S 198 ARG cc_start: 0.7330 (mmp80) cc_final: 0.7118 (mmp80) REVERT: S 234 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7877 (tm-30) REVERT: S 266 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8303 (tt0) REVERT: S 271 MET cc_start: 0.8210 (ttp) cc_final: 0.7766 (ttt) REVERT: S 275 GLU cc_start: 0.7897 (tp30) cc_final: 0.7620 (tp30) REVERT: T 407 PHE cc_start: 0.8205 (t80) cc_final: 0.7575 (m-80) REVERT: T 475 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7441 (mm-30) REVERT: T 508 PHE cc_start: 0.8747 (m-80) cc_final: 0.8330 (m-80) REVERT: T 537 LYS cc_start: 0.8036 (tptt) cc_final: 0.7225 (ttpp) REVERT: T 541 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7908 (tttp) REVERT: U 92 ASP cc_start: 0.8796 (m-30) cc_final: 0.8329 (m-30) REVERT: U 447 LYS cc_start: 0.8083 (mmtt) cc_final: 0.7753 (mmtt) REVERT: U 449 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.8015 (mm-30) REVERT: U 474 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7364 (mt) REVERT: V 50 LYS cc_start: 0.7332 (mmtp) cc_final: 0.7080 (mmmm) REVERT: V 488 GLN cc_start: 0.8189 (pt0) cc_final: 0.7749 (pt0) REVERT: V 502 TYR cc_start: 0.7630 (t80) cc_final: 0.7392 (t80) REVERT: V 518 VAL cc_start: 0.7588 (OUTLIER) cc_final: 0.7329 (t) REVERT: V 547 ASP cc_start: 0.7240 (p0) cc_final: 0.6473 (t0) REVERT: X 226 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7955 (tp30) REVERT: X 368 ILE cc_start: 0.8768 (mm) cc_final: 0.8433 (mp) REVERT: X 408 GLN cc_start: 0.7683 (tp40) cc_final: 0.7179 (tp40) REVERT: X 412 ASN cc_start: 0.8451 (m-40) cc_final: 0.8026 (m-40) REVERT: X 440 GLN cc_start: 0.8417 (mt0) cc_final: 0.8165 (mt0) REVERT: X 448 GLN cc_start: 0.8119 (tt0) cc_final: 0.7669 (mt0) REVERT: X 497 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7038 (mp0) REVERT: Y 66 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.6906 (mp0) REVERT: Y 195 GLU cc_start: 0.8978 (tp30) cc_final: 0.8733 (tp30) REVERT: Y 359 ASP cc_start: 0.8331 (m-30) cc_final: 0.8011 (m-30) REVERT: Y 501 LYS cc_start: 0.7286 (tptt) cc_final: 0.6606 (ttpp) REVERT: Z 152 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8166 (pm20) REVERT: Z 401 ARG cc_start: 0.6977 (mtp180) cc_final: 0.6130 (mmt90) outliers start: 104 outliers final: 47 residues processed: 480 average time/residue: 0.6125 time to fit residues: 356.9291 Evaluate side-chains 441 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 380 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 102 TYR Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 61 LYS Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 479 ARG Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 541 LYS Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 272 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 449 GLU Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 282 MET Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain X residue 226 GLU Chi-restraints excluded: chain X residue 298 SER Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Z residue 152 GLU Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 325 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: [200, 150, 46, 10, 357, 287, 184, 93, 199, 94, 82] chunk 200 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 357 optimal weight: 1.9990 chunk 287 optimal weight: 4.9990 chunk 184 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 199 optimal weight: 0.6980 chunk 94 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN A 98 GLN C 94 ASN F 94 ASN J 87 ASN P 65 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN V 61 HIS V 405 GLN ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 198 ASN Z 390 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.143551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.106089 restraints weight = 46320.021| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.69 r_work: 0.3087 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 34418 Z= 0.147 Angle : 0.571 10.139 46642 Z= 0.291 Chirality : 0.044 0.281 5520 Planarity : 0.004 0.052 5995 Dihedral : 5.783 100.159 4825 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.52 % Favored : 96.37 % Rotamer: Outliers : 2.83 % Allowed : 17.84 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.13), residues: 4459 helix: 0.28 (0.11), residues: 2157 sheet: -0.90 (0.21), residues: 571 loop : -0.52 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 435 TYR 0.031 0.002 TYR I 102 PHE 0.023 0.001 PHE A 107 TRP 0.016 0.001 TRP V 73 HIS 0.007 0.001 HIS V 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (34416) covalent geometry : angle 0.57144 / 0.29 (46642) hydrogen bonds : bond 0.03508 / 2.33 ( 1622) hydrogen bonds : angle 4.40087 / 3.10 ( 4674) Misc. bond : bond 0.00146 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 393 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.5916 (OUTLIER) cc_final: 0.5556 (ptp) REVERT: A 87 ASN cc_start: 0.7852 (OUTLIER) cc_final: 0.7442 (m-40) REVERT: B 102 TYR cc_start: 0.7256 (m-80) cc_final: 0.7045 (m-80) REVERT: E 61 MET cc_start: 0.8033 (mtm) cc_final: 0.7652 (ttm) REVERT: E 86 ILE cc_start: 0.7831 (mm) cc_final: 0.7477 (tt) REVERT: E 95 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8084 (pp) REVERT: F 124 ILE cc_start: 0.7722 (mm) cc_final: 0.6854 (mm) REVERT: G 61 MET cc_start: 0.6790 (mmt) cc_final: 0.6493 (mmm) REVERT: J 119 LEU cc_start: 0.6994 (tt) cc_final: 0.6719 (tp) REVERT: J 126 PHE cc_start: 0.7060 (m-80) cc_final: 0.6772 (m-80) REVERT: P 64 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8106 (mp0) REVERT: P 106 SER cc_start: 0.8498 (m) cc_final: 0.8069 (p) REVERT: Q 42 ARG cc_start: 0.7624 (ptp-170) cc_final: 0.7166 (pmm-80) REVERT: Q 61 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7724 (tttm) REVERT: R 58 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7519 (mmtp) REVERT: S 48 ARG cc_start: 0.7963 (ttt180) cc_final: 0.7614 (ttp80) REVERT: S 68 MET cc_start: 0.7625 (ttt) cc_final: 0.7376 (ttp) REVERT: S 204 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8139 (mppt) REVERT: S 234 GLU cc_start: 0.8469 (tm-30) cc_final: 0.7976 (tm-30) REVERT: S 266 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8374 (tt0) REVERT: S 271 MET cc_start: 0.8259 (ttp) cc_final: 0.7831 (ttt) REVERT: S 275 GLU cc_start: 0.7917 (tp30) cc_final: 0.7651 (tp30) REVERT: T 300 PHE cc_start: 0.9408 (OUTLIER) cc_final: 0.8279 (t80) REVERT: T 407 PHE cc_start: 0.8302 (t80) cc_final: 0.7671 (m-80) REVERT: T 508 PHE cc_start: 0.8748 (m-80) cc_final: 0.8258 (m-80) REVERT: T 537 LYS cc_start: 0.8065 (tptt) cc_final: 0.7261 (ttpp) REVERT: T 541 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7897 (tttp) REVERT: U 447 LYS cc_start: 0.8090 (mmtt) cc_final: 0.7746 (mmtt) REVERT: U 474 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7386 (mt) REVERT: V 50 LYS cc_start: 0.7329 (mmtp) cc_final: 0.7085 (mmmm) REVERT: V 73 TRP cc_start: 0.7133 (m-10) cc_final: 0.6325 (m-10) REVERT: V 447 LYS cc_start: 0.7032 (tppt) cc_final: 0.6822 (tppt) REVERT: V 488 GLN cc_start: 0.8146 (pt0) cc_final: 0.7729 (pt0) REVERT: V 502 TYR cc_start: 0.7651 (t80) cc_final: 0.7414 (t80) REVERT: V 518 VAL cc_start: 0.7605 (OUTLIER) cc_final: 0.7351 (t) REVERT: V 547 ASP cc_start: 0.7246 (p0) cc_final: 0.6475 (t0) REVERT: X 226 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8030 (tp30) REVERT: X 366 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7525 (mtp180) REVERT: X 368 ILE cc_start: 0.8781 (mm) cc_final: 0.8455 (mp) REVERT: X 408 GLN cc_start: 0.7700 (tp40) cc_final: 0.7422 (tp40) REVERT: X 440 GLN cc_start: 0.8425 (mt0) cc_final: 0.8175 (mt0) REVERT: X 448 GLN cc_start: 0.8174 (tt0) cc_final: 0.7712 (mt0) REVERT: X 497 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7018 (mp0) REVERT: Y 359 ASP cc_start: 0.8403 (m-30) cc_final: 0.8096 (m-30) REVERT: Y 501 LYS cc_start: 0.7166 (tptt) cc_final: 0.6467 (mtpm) REVERT: Z 401 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6177 (mmp80) REVERT: Z 429 ASP cc_start: 0.6178 (OUTLIER) cc_final: 0.5932 (p0) REVERT: Z 502 MET cc_start: 0.6084 (mtm) cc_final: 0.5801 (mtm) outliers start: 101 outliers final: 53 residues processed: 463 average time/residue: 0.6245 time to fit residues: 351.7069 Evaluate side-chains 452 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 383 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 102 TYR Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 61 LYS Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 204 LYS Chi-restraints excluded: chain S residue 233 ILE Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 479 ARG Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 541 LYS Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 272 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 282 MET Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain X residue 226 GLU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 298 SER Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 366 ARG Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Z residue 198 ASN Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 325 ILE Chi-restraints excluded: chain Z residue 401 ARG Chi-restraints excluded: chain Z residue 429 ASP Chi-restraints excluded: chain Z residue 432 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: [148, 251, 82, 265, 106, 290, 425, 187, 308, 156, 339] chunk 148 optimal weight: 0.8980 chunk 251 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 265 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 290 optimal weight: 3.9990 chunk 425 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 308 optimal weight: 0.8980 chunk 156 optimal weight: 0.9980 chunk 339 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 87 ASN P 65 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN S 98 ASN ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN V 61 HIS ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 198 ASN Z 390 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.144425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.107252 restraints weight = 46265.394| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.68 r_work: 0.3113 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34418 Z= 0.125 Angle : 0.563 11.654 46642 Z= 0.284 Chirality : 0.043 0.275 5520 Planarity : 0.004 0.064 5995 Dihedral : 5.666 100.623 4825 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.70 % Favored : 96.19 % Rotamer: Outliers : 2.52 % Allowed : 18.51 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.13), residues: 4459 helix: 0.42 (0.12), residues: 2152 sheet: -0.88 (0.21), residues: 575 loop : -0.48 (0.16), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 435 TYR 0.035 0.001 TYR I 102 PHE 0.028 0.001 PHE U 508 TRP 0.018 0.001 TRP V 73 HIS 0.007 0.001 HIS V 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (34416) covalent geometry : angle 0.56325 / 0.28 (46642) hydrogen bonds : bond 0.03346 / 2.22 ( 1622) hydrogen bonds : angle 4.33754 / 3.06 ( 4674) Misc. bond : bond 0.00108 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 414 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.5862 (OUTLIER) cc_final: 0.5534 (ptp) REVERT: A 87 ASN cc_start: 0.7845 (OUTLIER) cc_final: 0.7440 (m-40) REVERT: B 81 MET cc_start: 0.7602 (tpp) cc_final: 0.7209 (tpp) REVERT: B 102 TYR cc_start: 0.7123 (m-10) cc_final: 0.6796 (m-80) REVERT: E 61 MET cc_start: 0.7990 (mtm) cc_final: 0.7741 (ttp) REVERT: E 78 LEU cc_start: 0.7201 (pp) cc_final: 0.6591 (mt) REVERT: E 95 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8114 (pp) REVERT: G 60 LYS cc_start: 0.7174 (ptpt) cc_final: 0.6774 (ptpt) REVERT: G 61 MET cc_start: 0.6733 (mmt) cc_final: 0.6508 (mmm) REVERT: J 119 LEU cc_start: 0.6962 (tt) cc_final: 0.6709 (tp) REVERT: J 126 PHE cc_start: 0.7234 (m-80) cc_final: 0.6877 (m-80) REVERT: P 64 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8128 (mp0) REVERT: P 106 SER cc_start: 0.8472 (m) cc_final: 0.8034 (p) REVERT: Q 42 ARG cc_start: 0.7587 (ptp-170) cc_final: 0.7125 (pmm-80) REVERT: Q 61 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7688 (tttm) REVERT: R 58 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7539 (mmtp) REVERT: S 48 ARG cc_start: 0.7948 (ttt180) cc_final: 0.7602 (ttp80) REVERT: S 68 MET cc_start: 0.7620 (ttt) cc_final: 0.7378 (ttp) REVERT: S 180 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7577 (mt-10) REVERT: S 204 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8100 (ptpp) REVERT: S 234 GLU cc_start: 0.8469 (tm-30) cc_final: 0.7967 (tm-30) REVERT: S 266 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8352 (tt0) REVERT: S 271 MET cc_start: 0.8230 (ttp) cc_final: 0.7811 (ttt) REVERT: S 275 GLU cc_start: 0.7881 (tp30) cc_final: 0.7617 (tp30) REVERT: T 300 PHE cc_start: 0.9376 (OUTLIER) cc_final: 0.8287 (t80) REVERT: T 407 PHE cc_start: 0.8249 (t80) cc_final: 0.7607 (m-80) REVERT: T 508 PHE cc_start: 0.8738 (m-80) cc_final: 0.8269 (m-80) REVERT: T 537 LYS cc_start: 0.8058 (tptt) cc_final: 0.7243 (ttpp) REVERT: T 541 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7854 (tttp) REVERT: U 447 LYS cc_start: 0.8057 (mmtt) cc_final: 0.7780 (mmtt) REVERT: U 474 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7352 (mt) REVERT: V 50 LYS cc_start: 0.7379 (mmtp) cc_final: 0.7112 (mmmm) REVERT: V 447 LYS cc_start: 0.6989 (tppt) cc_final: 0.6772 (tppt) REVERT: V 502 TYR cc_start: 0.7624 (t80) cc_final: 0.7408 (t80) REVERT: V 522 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7563 (mp0) REVERT: V 547 ASP cc_start: 0.7237 (p0) cc_final: 0.6465 (t0) REVERT: X 226 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8022 (tp30) REVERT: X 368 ILE cc_start: 0.8754 (mm) cc_final: 0.8426 (mp) REVERT: X 408 GLN cc_start: 0.7730 (tp40) cc_final: 0.7469 (tp40) REVERT: X 440 GLN cc_start: 0.8438 (mt0) cc_final: 0.8190 (mt0) REVERT: X 448 GLN cc_start: 0.8147 (tt0) cc_final: 0.7690 (mt0) REVERT: X 497 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7003 (mp0) REVERT: Y 66 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: Y 195 GLU cc_start: 0.8976 (tp30) cc_final: 0.8752 (tp30) REVERT: Y 359 ASP cc_start: 0.8299 (m-30) cc_final: 0.7987 (m-30) REVERT: Y 501 LYS cc_start: 0.7181 (tptt) cc_final: 0.6482 (mtpm) REVERT: Z 253 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8188 (mt-10) REVERT: Z 401 ARG cc_start: 0.7003 (mtp180) cc_final: 0.6142 (mmp80) REVERT: Z 429 ASP cc_start: 0.6186 (OUTLIER) cc_final: 0.5941 (p0) REVERT: Z 484 MET cc_start: 0.7534 (mmm) cc_final: 0.6117 (pmm) REVERT: Z 502 MET cc_start: 0.6146 (mtm) cc_final: 0.5845 (mtm) outliers start: 90 outliers final: 49 residues processed: 475 average time/residue: 0.6132 time to fit residues: 354.7455 Evaluate side-chains 449 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 385 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain G residue 102 TYR Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 66 CYS Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 61 LYS Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 204 LYS Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 479 ARG Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 541 LYS Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 272 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 282 MET Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain X residue 226 GLU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Z residue 198 ASN Chi-restraints excluded: chain Z residue 253 GLU Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 325 ILE Chi-restraints excluded: chain Z residue 429 ASP Chi-restraints excluded: chain Z residue 432 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: [203, 107, 84, 429, 135, 102, 19, 175, 253, 241, 341] chunk 203 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 429 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 175 optimal weight: 0.0170 chunk 253 optimal weight: 3.9990 chunk 241 optimal weight: 0.0980 chunk 341 optimal weight: 6.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 94 ASN J 87 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN S 98 ASN ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN U 149 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 198 ASN Z 390 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.145545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.108718 restraints weight = 46219.649| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.66 r_work: 0.3132 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 34418 Z= 0.113 Angle : 0.557 11.354 46642 Z= 0.281 Chirality : 0.043 0.267 5520 Planarity : 0.004 0.067 5995 Dihedral : 5.482 96.662 4825 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.36 % Favored : 96.52 % Rotamer: Outliers : 2.19 % Allowed : 19.47 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.13), residues: 4459 helix: 0.54 (0.12), residues: 2145 sheet: -0.77 (0.21), residues: 568 loop : -0.43 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 435 TYR 0.033 0.001 TYR I 102 PHE 0.034 0.001 PHE U 508 TRP 0.016 0.001 TRP V 73 HIS 0.003 0.001 HIS R 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (34416) covalent geometry : angle 0.55704 / 0.28 (46642) hydrogen bonds : bond 0.03210 / 2.13 ( 1622) hydrogen bonds : angle 4.26913 / 3.01 ( 4674) Misc. bond : bond 0.00082 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 410 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.5856 (OUTLIER) cc_final: 0.5602 (ptp) REVERT: A 87 ASN cc_start: 0.7909 (OUTLIER) cc_final: 0.7500 (m-40) REVERT: B 81 MET cc_start: 0.7619 (tpp) cc_final: 0.7345 (tpp) REVERT: B 102 TYR cc_start: 0.7087 (m-10) cc_final: 0.6588 (m-10) REVERT: E 61 MET cc_start: 0.7935 (mtm) cc_final: 0.7671 (ttm) REVERT: E 78 LEU cc_start: 0.7224 (pp) cc_final: 0.6617 (mt) REVERT: E 86 ILE cc_start: 0.7880 (mm) cc_final: 0.7614 (tt) REVERT: E 95 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8144 (pp) REVERT: G 60 LYS cc_start: 0.7237 (ptpt) cc_final: 0.6815 (ptpt) REVERT: H 120 VAL cc_start: 0.6639 (t) cc_final: 0.6397 (t) REVERT: J 119 LEU cc_start: 0.7023 (tt) cc_final: 0.6765 (tp) REVERT: J 126 PHE cc_start: 0.7173 (m-80) cc_final: 0.6853 (m-80) REVERT: P 64 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8137 (mp0) REVERT: P 106 SER cc_start: 0.8354 (m) cc_final: 0.7927 (p) REVERT: P 108 VAL cc_start: 0.8543 (t) cc_final: 0.8150 (p) REVERT: Q 42 ARG cc_start: 0.7619 (ptp-170) cc_final: 0.7218 (pmm-80) REVERT: R 58 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7493 (mmtp) REVERT: S 48 ARG cc_start: 0.7891 (ttt180) cc_final: 0.7596 (ttp80) REVERT: S 68 MET cc_start: 0.7648 (ttt) cc_final: 0.7418 (ttp) REVERT: S 180 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7540 (mt-10) REVERT: S 188 GLN cc_start: 0.7318 (mm110) cc_final: 0.6726 (mp-120) REVERT: S 234 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7923 (tm-30) REVERT: S 266 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8306 (tt0) REVERT: S 271 MET cc_start: 0.8230 (ttp) cc_final: 0.7816 (ttt) REVERT: S 275 GLU cc_start: 0.7887 (tp30) cc_final: 0.7638 (tp30) REVERT: T 300 PHE cc_start: 0.9338 (OUTLIER) cc_final: 0.8313 (t80) REVERT: T 407 PHE cc_start: 0.8229 (t80) cc_final: 0.7593 (m-80) REVERT: T 508 PHE cc_start: 0.8757 (m-80) cc_final: 0.8313 (m-80) REVERT: T 537 LYS cc_start: 0.8071 (tptt) cc_final: 0.7305 (ttpp) REVERT: T 541 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7818 (tttp) REVERT: U 76 SER cc_start: 0.8233 (OUTLIER) cc_final: 0.7808 (t) REVERT: U 447 LYS cc_start: 0.7965 (mmtt) cc_final: 0.7712 (mmtt) REVERT: U 474 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7412 (mt) REVERT: V 50 LYS cc_start: 0.7402 (mmtp) cc_final: 0.7115 (mmmm) REVERT: V 447 LYS cc_start: 0.7033 (tppt) cc_final: 0.6805 (tppt) REVERT: V 502 TYR cc_start: 0.7634 (t80) cc_final: 0.7415 (t80) REVERT: V 522 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7615 (mp0) REVERT: V 547 ASP cc_start: 0.7320 (p0) cc_final: 0.6580 (t0) REVERT: X 226 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7998 (tp30) REVERT: X 368 ILE cc_start: 0.8766 (mm) cc_final: 0.8412 (mp) REVERT: X 408 GLN cc_start: 0.7769 (tp40) cc_final: 0.7515 (tp40) REVERT: X 440 GLN cc_start: 0.8447 (mt0) cc_final: 0.8225 (mt0) REVERT: X 448 GLN cc_start: 0.8113 (tt0) cc_final: 0.7667 (mt0) REVERT: X 497 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7011 (mp0) REVERT: Y 66 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: Y 195 GLU cc_start: 0.8973 (tp30) cc_final: 0.8746 (tp30) REVERT: Y 359 ASP cc_start: 0.8200 (m-30) cc_final: 0.7936 (m-30) REVERT: Y 501 LYS cc_start: 0.7239 (tptt) cc_final: 0.6541 (mtpm) REVERT: Z 381 ASP cc_start: 0.8484 (t0) cc_final: 0.8272 (t0) REVERT: Z 401 ARG cc_start: 0.7036 (mtp180) cc_final: 0.6321 (mmp80) REVERT: Z 429 ASP cc_start: 0.6188 (OUTLIER) cc_final: 0.5958 (p0) REVERT: Z 484 MET cc_start: 0.7604 (mmm) cc_final: 0.6228 (pmm) REVERT: Z 502 MET cc_start: 0.6307 (mtm) cc_final: 0.5879 (mtm) outliers start: 78 outliers final: 44 residues processed: 466 average time/residue: 0.6143 time to fit residues: 349.6463 Evaluate side-chains 443 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 386 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain G residue 102 TYR Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 66 CYS Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 479 ARG Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 541 LYS Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 272 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 282 MET Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain X residue 226 GLU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Z residue 198 ASN Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 325 ILE Chi-restraints excluded: chain Z residue 429 ASP Chi-restraints excluded: chain Z residue 432 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: [389, 203, 15, 191, 377, 54, 257, 259, 192, 197, 138] chunk 389 optimal weight: 1.9990 chunk 203 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 191 optimal weight: 1.9990 chunk 377 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 257 optimal weight: 0.7980 chunk 259 optimal weight: 3.9990 chunk 192 optimal weight: 0.6980 chunk 197 optimal weight: 0.7980 chunk 138 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 87 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN S 98 ASN ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN U 149 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 68 HIS Z 198 ASN Z 390 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.145039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.108223 restraints weight = 46548.160| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.68 r_work: 0.3115 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 34418 Z= 0.124 Angle : 0.569 11.231 46642 Z= 0.287 Chirality : 0.043 0.258 5520 Planarity : 0.004 0.068 5995 Dihedral : 5.453 93.840 4825 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.54 % Favored : 96.34 % Rotamer: Outliers : 2.05 % Allowed : 19.80 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.13), residues: 4459 helix: 0.59 (0.12), residues: 2141 sheet: -0.74 (0.21), residues: 561 loop : -0.40 (0.15), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Y 435 TYR 0.033 0.001 TYR I 102 PHE 0.030 0.001 PHE A 107 TRP 0.025 0.002 TRP V 73 HIS 0.003 0.001 HIS R 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (34416) covalent geometry : angle 0.56905 / 0.29 (46642) hydrogen bonds : bond 0.03283 / 2.18 ( 1622) hydrogen bonds : angle 4.28548 / 3.02 ( 4674) Misc. bond : bond 0.00095 / 0.05 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 390 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.5803 (OUTLIER) cc_final: 0.5433 (ptp) REVERT: A 87 ASN cc_start: 0.7913 (OUTLIER) cc_final: 0.7507 (m-40) REVERT: B 102 TYR cc_start: 0.6949 (m-10) cc_final: 0.6383 (m-10) REVERT: E 61 MET cc_start: 0.7956 (mtm) cc_final: 0.7655 (ttm) REVERT: E 78 LEU cc_start: 0.7195 (pp) cc_final: 0.6541 (mt) REVERT: E 86 ILE cc_start: 0.7821 (mm) cc_final: 0.7515 (tt) REVERT: E 95 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8140 (pp) REVERT: G 60 LYS cc_start: 0.7244 (ptpt) cc_final: 0.6936 (ptpt) REVERT: J 119 LEU cc_start: 0.6946 (tt) cc_final: 0.6693 (tp) REVERT: J 126 PHE cc_start: 0.7084 (m-80) cc_final: 0.6729 (m-80) REVERT: P 64 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8127 (mp0) REVERT: P 106 SER cc_start: 0.8309 (m) cc_final: 0.7856 (p) REVERT: Q 42 ARG cc_start: 0.7613 (ptp-170) cc_final: 0.7160 (pmm-80) REVERT: R 30 PRO cc_start: 0.7068 (Cg_endo) cc_final: 0.6710 (Cg_exo) REVERT: R 58 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7500 (mmtp) REVERT: S 48 ARG cc_start: 0.7906 (ttt180) cc_final: 0.7600 (ttp80) REVERT: S 68 MET cc_start: 0.7611 (ttt) cc_final: 0.7363 (ttp) REVERT: S 188 GLN cc_start: 0.7221 (mm110) cc_final: 0.6654 (mp-120) REVERT: S 234 GLU cc_start: 0.8425 (tm-30) cc_final: 0.7956 (tm-30) REVERT: S 266 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8328 (tt0) REVERT: S 271 MET cc_start: 0.8268 (ttp) cc_final: 0.7839 (ttt) REVERT: S 275 GLU cc_start: 0.7911 (tp30) cc_final: 0.7654 (tp30) REVERT: T 199 ARG cc_start: 0.8105 (mtt90) cc_final: 0.7872 (mpt-90) REVERT: T 300 PHE cc_start: 0.9351 (OUTLIER) cc_final: 0.8291 (t80) REVERT: T 407 PHE cc_start: 0.8257 (t80) cc_final: 0.7600 (m-80) REVERT: T 508 PHE cc_start: 0.8759 (m-80) cc_final: 0.8305 (m-80) REVERT: T 537 LYS cc_start: 0.8059 (tptt) cc_final: 0.7219 (ttpp) REVERT: U 76 SER cc_start: 0.8234 (OUTLIER) cc_final: 0.7815 (t) REVERT: U 149 GLN cc_start: 0.8295 (mm-40) cc_final: 0.8075 (pt0) REVERT: U 152 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.7833 (m-40) REVERT: U 309 MET cc_start: 0.9228 (mtt) cc_final: 0.9021 (mtt) REVERT: U 447 LYS cc_start: 0.7925 (mmtt) cc_final: 0.7691 (mmtt) REVERT: U 474 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7368 (mt) REVERT: V 50 LYS cc_start: 0.7383 (mmtp) cc_final: 0.7102 (mmmm) REVERT: V 447 LYS cc_start: 0.7053 (tppt) cc_final: 0.6790 (tppt) REVERT: V 502 TYR cc_start: 0.7617 (t80) cc_final: 0.7383 (t80) REVERT: V 522 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7575 (mp0) REVERT: V 547 ASP cc_start: 0.7243 (p0) cc_final: 0.6509 (t0) REVERT: X 226 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8009 (tp30) REVERT: X 368 ILE cc_start: 0.8746 (mm) cc_final: 0.8391 (mp) REVERT: X 408 GLN cc_start: 0.7751 (tp40) cc_final: 0.7494 (tp40) REVERT: X 440 GLN cc_start: 0.8409 (mt0) cc_final: 0.8187 (mt0) REVERT: X 448 GLN cc_start: 0.8110 (tt0) cc_final: 0.7660 (mt0) REVERT: X 497 GLU cc_start: 0.7544 (mt-10) cc_final: 0.6958 (mp0) REVERT: Y 66 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: Y 195 GLU cc_start: 0.8997 (tp30) cc_final: 0.8734 (tp30) REVERT: Y 359 ASP cc_start: 0.8217 (m-30) cc_final: 0.7912 (m-30) REVERT: Y 501 LYS cc_start: 0.7204 (tptt) cc_final: 0.6504 (mtpm) REVERT: Z 253 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8088 (mt-10) REVERT: Z 401 ARG cc_start: 0.7020 (mtp180) cc_final: 0.6219 (mmp80) REVERT: Z 429 ASP cc_start: 0.6168 (OUTLIER) cc_final: 0.5939 (p0) REVERT: Z 484 MET cc_start: 0.7528 (mmm) cc_final: 0.6082 (pmm) REVERT: Z 502 MET cc_start: 0.6260 (mtm) cc_final: 0.5900 (mtm) outliers start: 73 outliers final: 45 residues processed: 444 average time/residue: 0.6271 time to fit residues: 338.7393 Evaluate side-chains 441 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 382 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain G residue 102 TYR Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 66 CYS Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 479 ARG Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 152 ASN Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 272 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 282 MET Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain X residue 226 GLU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 298 SER Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Z residue 198 ASN Chi-restraints excluded: chain Z residue 253 GLU Chi-restraints excluded: chain Z residue 325 ILE Chi-restraints excluded: chain Z residue 429 ASP Chi-restraints excluded: chain Z residue 432 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: [132, 354, 352, 222, 280, 432, 95, 381, 51, 126, 128] chunk 132 optimal weight: 2.9990 chunk 354 optimal weight: 0.8980 chunk 352 optimal weight: 0.0770 chunk 222 optimal weight: 7.9990 chunk 280 optimal weight: 10.0000 chunk 432 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 381 optimal weight: 0.0030 chunk 51 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 overall best weight: 0.5950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN C 94 ASN J 87 ASN Q 43 GLN ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN S 98 ASN ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 198 ASN Z 390 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.145713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.108600 restraints weight = 46085.918| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.70 r_work: 0.3125 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 34418 Z= 0.115 Angle : 0.561 12.244 46642 Z= 0.282 Chirality : 0.043 0.327 5520 Planarity : 0.004 0.068 5995 Dihedral : 5.362 90.008 4825 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.39 % Favored : 96.50 % Rotamer: Outliers : 1.80 % Allowed : 20.08 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.13), residues: 4459 helix: 0.64 (0.12), residues: 2142 sheet: -0.71 (0.21), residues: 566 loop : -0.38 (0.15), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Y 435 TYR 0.032 0.001 TYR I 102 PHE 0.030 0.001 PHE A 107 TRP 0.030 0.002 TRP V 73 HIS 0.003 0.001 HIS R 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (34416) covalent geometry : angle 0.56089 / 0.28 (46642) hydrogen bonds : bond 0.03205 / 2.13 ( 1622) hydrogen bonds : angle 4.26308 / 3.01 ( 4674) Misc. bond : bond 0.00069 / 0.04 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12816.84 seconds wall clock time: 218 minutes 23.02 seconds (13103.02 seconds total)