Starting phenix.real_space_refine on Fri Jun 20 00:29:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i5h_52629/06_2025/9i5h_52629.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i5h_52629/06_2025/9i5h_52629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9i5h_52629/06_2025/9i5h_52629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i5h_52629/06_2025/9i5h_52629.map" model { file = "/net/cci-nas-00/data/ceres_data/9i5h_52629/06_2025/9i5h_52629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i5h_52629/06_2025/9i5h_52629.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 3 Type Number sf(0) Gaussians C 14773 2.51 5 N 3706 2.21 5 O 4845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23324 Number of models: 1 Model: "" Number of chains: 17 Chain: "C" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1372 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 6, 'TRANS': 176} Chain: "D" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1372 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 6, 'TRANS': 176} Chain: "E" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1372 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 6, 'TRANS': 176} Chain: "F" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1372 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 6, 'TRANS': 176} Chain: "G" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1372 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 6, 'TRANS': 176} Chain: "H" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1372 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 6, 'TRANS': 176} Chain: "I" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1372 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 6, 'TRANS': 176} Chain: "J" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1372 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 6, 'TRANS': 176} Chain: "K" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1372 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 6, 'TRANS': 176} Chain: "L" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1372 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 6, 'TRANS': 176} Chain: "M" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1372 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 6, 'TRANS': 176} Chain: "N" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1372 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 6, 'TRANS': 176} Chain: "O" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1372 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 6, 'TRANS': 176} Chain: "P" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1372 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 6, 'TRANS': 176} Chain: "Q" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1372 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 6, 'TRANS': 176} Chain: "R" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1372 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 6, 'TRANS': 176} Chain: "S" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1372 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 6, 'TRANS': 176} Time building chain proxies: 14.78, per 1000 atoms: 0.63 Number of scatterers: 23324 At special positions: 0 Unit cell: (108.48, 110.4, 209.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 4845 8.00 N 3706 7.00 C 14773 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=0, symmetry=0 Time building additional restraints: 5.35 Conformation dependent library (CDL) restraints added in 2.9 seconds 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5780 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 50 sheets defined 25.7% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.63 Creating SS restraints... Processing helix chain 'C' and resid 3 through 46 removed outlier: 3.920A pdb=" N ILE C 7 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS C 34 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU C 35 " --> pdb=" O GLU C 31 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA C 36 " --> pdb=" O ARG C 32 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL C 37 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER C 42 " --> pdb=" O TYR C 38 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C 44 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG C 45 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 0 through 46 removed outlier: 3.817A pdb=" N ALA D 5 " --> pdb=" O ALA D 1 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE D 6 " --> pdb=" O LEU D 2 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D 7 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL D 37 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER D 42 " --> pdb=" O TYR D 38 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU D 43 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL D 44 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG D 45 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER D 46 " --> pdb=" O SER D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 removed outlier: 3.567A pdb=" N THR D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 0 through 45 removed outlier: 3.519A pdb=" N THR E 4 " --> pdb=" O THR E 0 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE E 6 " --> pdb=" O LEU E 2 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR E 27 " --> pdb=" O LEU E 23 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE E 28 " --> pdb=" O SER E 24 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL E 37 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL E 44 " --> pdb=" O GLY E 40 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG E 45 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 0 through 46 removed outlier: 3.988A pdb=" N ILE F 6 " --> pdb=" O LEU F 2 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL F 37 " --> pdb=" O GLY F 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 0 through 45 removed outlier: 3.777A pdb=" N ILE G 6 " --> pdb=" O LEU G 2 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL G 37 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER G 42 " --> pdb=" O TYR G 38 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL G 44 " --> pdb=" O GLY G 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 0 through 46 removed outlier: 3.834A pdb=" N ILE H 6 " --> pdb=" O LEU H 2 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL H 37 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR H 38 " --> pdb=" O LYS H 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 0 through 45 removed outlier: 4.306A pdb=" N ILE I 6 " --> pdb=" O LEU I 2 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE I 7 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU I 8 " --> pdb=" O THR I 4 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE I 9 " --> pdb=" O ALA I 5 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL I 44 " --> pdb=" O GLY I 40 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG I 45 " --> pdb=" O LEU I 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 0 through 45 removed outlier: 3.924A pdb=" N ILE J 6 " --> pdb=" O LEU J 2 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE J 7 " --> pdb=" O GLU J 3 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA J 36 " --> pdb=" O ARG J 32 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL J 37 " --> pdb=" O GLY J 33 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR J 38 " --> pdb=" O LYS J 34 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG J 45 " --> pdb=" O LEU J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 119 through 124 Processing helix chain 'K' and resid 0 through 46 removed outlier: 3.987A pdb=" N ILE K 6 " --> pdb=" O LEU K 2 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE K 7 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU K 35 " --> pdb=" O GLU K 31 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL K 37 " --> pdb=" O GLY K 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 46 removed outlier: 3.507A pdb=" N VAL L 37 " --> pdb=" O GLY L 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 0 through 45 removed outlier: 4.162A pdb=" N ILE M 6 " --> pdb=" O LEU M 2 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE M 7 " --> pdb=" O GLU M 3 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL M 37 " --> pdb=" O GLY M 33 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL M 44 " --> pdb=" O GLY M 40 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG M 45 " --> pdb=" O LEU M 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 0 through 46 removed outlier: 3.663A pdb=" N THR N 4 " --> pdb=" O THR N 0 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA N 5 " --> pdb=" O ALA N 1 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE N 6 " --> pdb=" O LEU N 2 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL N 12 " --> pdb=" O LEU N 8 " (cutoff:3.500A) Processing helix chain 'O' and resid 0 through 45 removed outlier: 3.843A pdb=" N THR O 4 " --> pdb=" O THR O 0 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE O 6 " --> pdb=" O LEU O 2 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE O 7 " --> pdb=" O GLU O 3 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL O 37 " --> pdb=" O GLY O 33 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL O 44 " --> pdb=" O GLY O 40 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG O 45 " --> pdb=" O LEU O 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 0 through 46 removed outlier: 3.689A pdb=" N ILE P 6 " --> pdb=" O LEU P 2 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL P 37 " --> pdb=" O GLY P 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 0 through 46 removed outlier: 3.780A pdb=" N THR Q 4 " --> pdb=" O THR Q 0 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA Q 5 " --> pdb=" O ALA Q 1 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE Q 6 " --> pdb=" O LEU Q 2 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE Q 7 " --> pdb=" O GLU Q 3 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL Q 37 " --> pdb=" O GLY Q 33 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL Q 44 " --> pdb=" O GLY Q 40 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG Q 45 " --> pdb=" O LEU Q 41 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER Q 46 " --> pdb=" O SER Q 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 0 through 45 removed outlier: 3.770A pdb=" N ILE R 6 " --> pdb=" O LEU R 2 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA R 36 " --> pdb=" O ARG R 32 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL R 37 " --> pdb=" O GLY R 33 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR R 38 " --> pdb=" O LYS R 34 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL R 44 " --> pdb=" O GLY R 40 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG R 45 " --> pdb=" O LEU R 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 0 through 45 removed outlier: 3.855A pdb=" N ILE S 6 " --> pdb=" O LEU S 2 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL S 37 " --> pdb=" O GLY S 33 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL S 44 " --> pdb=" O GLY S 40 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG S 45 " --> pdb=" O LEU S 41 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 48 through 50 Processing sheet with id=AA2, first strand: chain 'C' and resid 110 through 113 removed outlier: 6.847A pdb=" N THR C 66 " --> pdb=" O GLU C 59 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE C 57 " --> pdb=" O ASP C 68 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N VAL C 70 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL C 55 " --> pdb=" O VAL C 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 104 through 106 removed outlier: 3.665A pdb=" N VAL C 95 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE C 164 " --> pdb=" O VAL C 156 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 110 through 115 removed outlier: 3.734A pdb=" N LEU D 133 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N THR D 73 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N SER D 53 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA D 75 " --> pdb=" O LYS D 51 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS D 51 " --> pdb=" O ALA D 75 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL D 54 " --> pdb=" O LEU D 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 94 through 95 removed outlier: 3.657A pdb=" N VAL D 94 " --> pdb=" O LYS D 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 94 through 95 removed outlier: 3.657A pdb=" N VAL D 94 " --> pdb=" O LYS D 157 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE D 152 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG D 168 " --> pdb=" O PHE D 152 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE D 164 " --> pdb=" O VAL D 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 110 through 115 removed outlier: 4.018A pdb=" N LEU E 133 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR E 66 " --> pdb=" O GLU E 59 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE E 57 " --> pdb=" O ASP E 68 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL E 70 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL E 55 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N PHE E 72 " --> pdb=" O SER E 53 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N SER E 53 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL E 74 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LYS E 51 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N SER E 76 " --> pdb=" O GLU E 49 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLU E 49 " --> pdb=" O SER E 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 104 through 105 removed outlier: 3.550A pdb=" N VAL E 95 " --> pdb=" O LYS E 157 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE E 152 " --> pdb=" O ARG E 168 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG E 168 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE E 164 " --> pdb=" O VAL E 156 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 110 through 115 removed outlier: 3.944A pdb=" N LEU F 133 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N VAL F 67 " --> pdb=" O ILE F 57 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE F 57 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER F 69 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL F 55 " --> pdb=" O SER F 69 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ILE F 71 " --> pdb=" O SER F 53 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N SER F 53 " --> pdb=" O ILE F 71 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR F 73 " --> pdb=" O LYS F 51 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 83 through 84 removed outlier: 3.659A pdb=" N ILE F 83 " --> pdb=" O LEU F 128 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 104 through 106 removed outlier: 3.613A pdb=" N VAL F 95 " --> pdb=" O LYS F 157 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE F 152 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG F 168 " --> pdb=" O PHE F 152 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 48 through 50 removed outlier: 3.955A pdb=" N LEU G 133 " --> pdb=" O LEU G 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 48 through 50 removed outlier: 6.491A pdb=" N THR G 66 " --> pdb=" O GLU G 59 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE G 57 " --> pdb=" O ASP G 68 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL G 70 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL G 55 " --> pdb=" O VAL G 70 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 83 through 84 removed outlier: 3.564A pdb=" N ILE G 83 " --> pdb=" O LEU G 128 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 104 through 105 removed outlier: 3.598A pdb=" N VAL G 95 " --> pdb=" O LYS G 157 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE G 152 " --> pdb=" O ARG G 168 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG G 168 " --> pdb=" O PHE G 152 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE G 164 " --> pdb=" O VAL G 156 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 110 through 115 removed outlier: 4.097A pdb=" N LEU H 133 " --> pdb=" O LEU H 115 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR H 66 " --> pdb=" O GLU H 59 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE H 57 " --> pdb=" O ASP H 68 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL H 70 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL H 55 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N PHE H 72 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N SER H 53 " --> pdb=" O PHE H 72 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL H 74 " --> pdb=" O LYS H 51 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LYS H 51 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N SER H 76 " --> pdb=" O GLU H 49 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N GLU H 49 " --> pdb=" O SER H 76 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 83 through 84 removed outlier: 3.536A pdb=" N ILE H 83 " --> pdb=" O LEU H 128 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 104 through 105 removed outlier: 3.559A pdb=" N VAL H 95 " --> pdb=" O LYS H 157 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE H 152 " --> pdb=" O ARG H 168 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG H 168 " --> pdb=" O PHE H 152 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE H 164 " --> pdb=" O VAL H 156 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 48 through 50 removed outlier: 4.065A pdb=" N LEU I 133 " --> pdb=" O LEU I 115 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 48 through 50 removed outlier: 6.554A pdb=" N THR I 66 " --> pdb=" O GLU I 59 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE I 57 " --> pdb=" O ASP I 68 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL I 70 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL I 55 " --> pdb=" O VAL I 70 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 104 through 106 removed outlier: 3.598A pdb=" N VAL I 95 " --> pdb=" O LYS I 157 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE I 152 " --> pdb=" O ARG I 168 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG I 168 " --> pdb=" O PHE I 152 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE I 164 " --> pdb=" O VAL I 156 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 110 through 115 removed outlier: 4.036A pdb=" N LEU J 133 " --> pdb=" O LEU J 115 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR J 66 " --> pdb=" O GLU J 59 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE J 57 " --> pdb=" O ASP J 68 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N VAL J 70 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL J 55 " --> pdb=" O VAL J 70 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N PHE J 72 " --> pdb=" O SER J 53 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N SER J 53 " --> pdb=" O PHE J 72 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL J 74 " --> pdb=" O LYS J 51 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N LYS J 51 " --> pdb=" O VAL J 74 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N SER J 76 " --> pdb=" O GLU J 49 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLU J 49 " --> pdb=" O SER J 76 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 83 through 84 Processing sheet with id=AC6, first strand: chain 'J' and resid 104 through 105 removed outlier: 3.743A pdb=" N VAL J 95 " --> pdb=" O LYS J 157 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE J 152 " --> pdb=" O ARG J 168 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG J 168 " --> pdb=" O PHE J 152 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE J 164 " --> pdb=" O VAL J 156 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 48 through 50 removed outlier: 3.506A pdb=" N ALA K 75 " --> pdb=" O GLU K 49 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU K 133 " --> pdb=" O LEU K 115 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 48 through 50 removed outlier: 3.506A pdb=" N ALA K 75 " --> pdb=" O GLU K 49 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR K 66 " --> pdb=" O GLU K 59 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE K 57 " --> pdb=" O ASP K 68 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL K 70 " --> pdb=" O VAL K 55 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL K 55 " --> pdb=" O VAL K 70 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 83 through 84 removed outlier: 3.715A pdb=" N ILE K 83 " --> pdb=" O LEU K 128 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 104 through 106 removed outlier: 3.568A pdb=" N VAL K 95 " --> pdb=" O LYS K 157 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE K 152 " --> pdb=" O ARG K 168 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG K 168 " --> pdb=" O PHE K 152 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE K 164 " --> pdb=" O VAL K 156 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 110 through 115 removed outlier: 3.934A pdb=" N LEU L 133 " --> pdb=" O LEU L 115 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N THR L 73 " --> pdb=" O GLY L 52 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N GLY L 52 " --> pdb=" O THR L 73 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA L 75 " --> pdb=" O ILE L 50 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ILE L 50 " --> pdb=" O ALA L 75 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 104 through 105 removed outlier: 3.506A pdb=" N PHE L 152 " --> pdb=" O ARG L 168 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG L 168 " --> pdb=" O PHE L 152 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE L 164 " --> pdb=" O VAL L 156 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 110 through 115 removed outlier: 3.981A pdb=" N LEU M 133 " --> pdb=" O LEU M 115 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR M 66 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE M 57 " --> pdb=" O ASP M 68 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL M 70 " --> pdb=" O VAL M 55 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL M 55 " --> pdb=" O VAL M 70 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N PHE M 72 " --> pdb=" O SER M 53 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N SER M 53 " --> pdb=" O PHE M 72 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N VAL M 74 " --> pdb=" O LYS M 51 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LYS M 51 " --> pdb=" O VAL M 74 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N SER M 76 " --> pdb=" O GLU M 49 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N GLU M 49 " --> pdb=" O SER M 76 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL M 54 " --> pdb=" O LEU M 180 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 83 through 84 removed outlier: 3.657A pdb=" N ILE M 83 " --> pdb=" O LEU M 128 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 104 through 106 removed outlier: 3.604A pdb=" N VAL M 95 " --> pdb=" O LYS M 157 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE M 152 " --> pdb=" O ARG M 168 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG M 168 " --> pdb=" O PHE M 152 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE M 164 " --> pdb=" O VAL M 156 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 110 through 115 removed outlier: 3.846A pdb=" N LEU N 133 " --> pdb=" O LEU N 115 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR N 66 " --> pdb=" O GLU N 59 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE N 57 " --> pdb=" O ASP N 68 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL N 70 " --> pdb=" O VAL N 55 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL N 55 " --> pdb=" O VAL N 70 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N PHE N 72 " --> pdb=" O SER N 53 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N SER N 53 " --> pdb=" O PHE N 72 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL N 74 " --> pdb=" O LYS N 51 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LYS N 51 " --> pdb=" O VAL N 74 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N SER N 76 " --> pdb=" O GLU N 49 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N GLU N 49 " --> pdb=" O SER N 76 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL N 54 " --> pdb=" O LEU N 180 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 104 through 106 removed outlier: 3.543A pdb=" N VAL N 95 " --> pdb=" O LYS N 157 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 110 through 115 removed outlier: 4.057A pdb=" N LEU O 133 " --> pdb=" O LEU O 115 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VAL O 67 " --> pdb=" O ILE O 57 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE O 57 " --> pdb=" O VAL O 67 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N SER O 69 " --> pdb=" O VAL O 55 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL O 55 " --> pdb=" O SER O 69 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE O 71 " --> pdb=" O SER O 53 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N SER O 53 " --> pdb=" O ILE O 71 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR O 73 " --> pdb=" O LYS O 51 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA O 75 " --> pdb=" O GLU O 49 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 83 through 84 removed outlier: 3.734A pdb=" N ILE O 83 " --> pdb=" O LEU O 128 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 104 through 106 removed outlier: 3.575A pdb=" N VAL O 95 " --> pdb=" O LYS O 157 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE O 152 " --> pdb=" O ARG O 168 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG O 168 " --> pdb=" O PHE O 152 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE O 164 " --> pdb=" O VAL O 156 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 48 through 49 removed outlier: 3.584A pdb=" N ALA P 75 " --> pdb=" O GLU P 49 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU P 133 " --> pdb=" O LEU P 115 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 48 through 49 removed outlier: 3.584A pdb=" N ALA P 75 " --> pdb=" O GLU P 49 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR P 66 " --> pdb=" O GLU P 59 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE P 57 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL P 70 " --> pdb=" O VAL P 55 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL P 55 " --> pdb=" O VAL P 70 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 83 through 84 removed outlier: 3.583A pdb=" N ILE P 83 " --> pdb=" O LEU P 128 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P' and resid 104 through 106 removed outlier: 3.595A pdb=" N VAL P 95 " --> pdb=" O LYS P 157 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE P 152 " --> pdb=" O ARG P 168 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG P 168 " --> pdb=" O PHE P 152 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE P 164 " --> pdb=" O VAL P 156 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 110 through 115 removed outlier: 3.969A pdb=" N LEU Q 133 " --> pdb=" O LEU Q 115 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N THR Q 73 " --> pdb=" O SER Q 53 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N SER Q 53 " --> pdb=" O THR Q 73 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA Q 75 " --> pdb=" O LYS Q 51 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS Q 51 " --> pdb=" O ALA Q 75 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 104 through 105 removed outlier: 3.532A pdb=" N VAL Q 95 " --> pdb=" O LYS Q 157 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE Q 152 " --> pdb=" O ARG Q 168 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE Q 164 " --> pdb=" O VAL Q 156 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'R' and resid 48 through 50 removed outlier: 4.063A pdb=" N LEU R 133 " --> pdb=" O LEU R 115 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'R' and resid 48 through 50 removed outlier: 7.519A pdb=" N VAL R 67 " --> pdb=" O GLU R 59 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLU R 59 " --> pdb=" O VAL R 67 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 104 through 106 removed outlier: 3.562A pdb=" N VAL R 95 " --> pdb=" O LYS R 157 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE R 152 " --> pdb=" O ARG R 168 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG R 168 " --> pdb=" O PHE R 152 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE R 164 " --> pdb=" O VAL R 156 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'S' and resid 110 through 115 removed outlier: 3.950A pdb=" N LEU S 133 " --> pdb=" O LEU S 115 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL S 67 " --> pdb=" O GLU S 59 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N GLU S 59 " --> pdb=" O VAL S 67 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N THR S 73 " --> pdb=" O SER S 53 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N SER S 53 " --> pdb=" O THR S 73 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ALA S 75 " --> pdb=" O LYS S 51 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS S 51 " --> pdb=" O ALA S 75 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 83 through 84 Processing sheet with id=AF5, first strand: chain 'S' and resid 104 through 105 removed outlier: 3.609A pdb=" N VAL S 95 " --> pdb=" O LYS S 157 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE S 152 " --> pdb=" O ARG S 168 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG S 168 " --> pdb=" O PHE S 152 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE S 164 " --> pdb=" O VAL S 156 " (cutoff:3.500A) 1096 hydrogen bonds defined for protein. 3255 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.28 Time building geometry restraints manager: 6.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 4148 1.29 - 1.35: 3618 1.35 - 1.42: 1718 1.42 - 1.48: 3926 1.48 - 1.55: 10271 Bond restraints: 23681 Sorted by residual: bond pdb=" N GLY L 52 " pdb=" CA GLY L 52 " ideal model delta sigma weight residual 1.446 1.479 -0.033 9.70e-03 1.06e+04 1.17e+01 bond pdb=" N VAL L 54 " pdb=" CA VAL L 54 " ideal model delta sigma weight residual 1.458 1.497 -0.038 1.19e-02 7.06e+03 1.05e+01 bond pdb=" N GLU C 129 " pdb=" CA GLU C 129 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.26e+00 bond pdb=" N SER G 42 " pdb=" CA SER G 42 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.16e-02 7.43e+03 6.81e+00 bond pdb=" N GLU C 132 " pdb=" CA GLU C 132 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.20e-02 6.94e+03 6.37e+00 ... (remaining 23676 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 31886 2.10 - 4.21: 509 4.21 - 6.31: 64 6.31 - 8.41: 10 8.41 - 10.51: 1 Bond angle restraints: 32470 Sorted by residual: angle pdb=" N LEU C 146 " pdb=" CA LEU C 146 " pdb=" C LEU C 146 " ideal model delta sigma weight residual 111.24 100.73 10.51 1.38e+00 5.25e-01 5.81e+01 angle pdb=" CA GLY L 52 " pdb=" C GLY L 52 " pdb=" O GLY L 52 " ideal model delta sigma weight residual 122.22 118.10 4.12 6.50e-01 2.37e+00 4.02e+01 angle pdb=" N THR R 0 " pdb=" CA THR R 0 " pdb=" C THR R 0 " ideal model delta sigma weight residual 113.41 108.04 5.37 1.22e+00 6.72e-01 1.94e+01 angle pdb=" CA THR C 145 " pdb=" C THR C 145 " pdb=" O THR C 145 " ideal model delta sigma weight residual 120.10 115.55 4.55 1.13e+00 7.83e-01 1.62e+01 angle pdb=" CA GLN C 130 " pdb=" C GLN C 130 " pdb=" O GLN C 130 " ideal model delta sigma weight residual 122.44 117.54 4.90 1.34e+00 5.57e-01 1.34e+01 ... (remaining 32465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.47: 12935 16.47 - 32.94: 830 32.94 - 49.41: 140 49.41 - 65.88: 33 65.88 - 82.35: 19 Dihedral angle restraints: 13957 sinusoidal: 5015 harmonic: 8942 Sorted by residual: dihedral pdb=" CA ASP D 91 " pdb=" C ASP D 91 " pdb=" N ARG D 92 " pdb=" CA ARG D 92 " ideal model delta harmonic sigma weight residual -180.00 -150.49 -29.51 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA ARG D 92 " pdb=" C ARG D 92 " pdb=" N VAL D 93 " pdb=" CA VAL D 93 " ideal model delta harmonic sigma weight residual 180.00 150.93 29.07 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA TYR D 98 " pdb=" C TYR D 98 " pdb=" N ARG D 99 " pdb=" CA ARG D 99 " ideal model delta harmonic sigma weight residual 180.00 151.41 28.59 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 13954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3364 0.061 - 0.123: 747 0.123 - 0.184: 48 0.184 - 0.246: 4 0.246 - 0.307: 2 Chirality restraints: 4165 Sorted by residual: chirality pdb=" CB ILE D -1 " pdb=" CA ILE D -1 " pdb=" CG1 ILE D -1 " pdb=" CG2 ILE D -1 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA LEU C 146 " pdb=" N LEU C 146 " pdb=" C LEU C 146 " pdb=" CB LEU C 146 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CG LEU F 140 " pdb=" CB LEU F 140 " pdb=" CD1 LEU F 140 " pdb=" CD2 LEU F 140 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 4162 not shown) Planarity restraints: 4131 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 88 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO D 89 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 89 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 89 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU L 81 " 0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO L 82 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO L 82 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO L 82 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS L 157 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO L 158 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO L 158 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO L 158 " -0.021 5.00e-02 4.00e+02 ... (remaining 4128 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2788 2.74 - 3.28: 22461 3.28 - 3.82: 35938 3.82 - 4.36: 39391 4.36 - 4.90: 74013 Nonbonded interactions: 174591 Sorted by model distance: nonbonded pdb=" NH2 ARG E 92 " pdb=" OD1 ASP E 109 " model vdw 2.199 3.120 nonbonded pdb=" O THR S 0 " pdb=" OG1 THR S 4 " model vdw 2.208 3.040 nonbonded pdb=" NH2 ARG O 92 " pdb=" OD1 ASP O 109 " model vdw 2.212 3.120 nonbonded pdb=" N GLU D 59 " pdb=" OE1 GLU D 59 " model vdw 2.241 3.120 nonbonded pdb=" NH2 ARG D 32 " pdb=" OE2 GLU D 35 " model vdw 2.256 3.120 ... (remaining 174586 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: 0.01 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.980 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 55.270 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.320 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 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 : 0.008 0.051 23681 Z= 0.329 Angle : 0.682 10.515 32470 Z= 0.396 Chirality : 0.050 0.307 4165 Planarity : 0.003 0.050 4131 Dihedral : 12.014 82.347 8177 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.91 % Favored : 95.03 % Rotamer: Outliers : 0.27 % Allowed : 0.35 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.15), residues: 3077 helix: 3.93 (0.16), residues: 650 sheet: 1.42 (0.17), residues: 864 loop : -2.16 (0.14), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 114 HIS 0.009 0.001 HIS D 105 PHE 0.018 0.002 PHE C 20 TYR 0.021 0.001 TYR D 98 ARG 0.016 0.001 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.26917 ( 1087) hydrogen bonds : angle 6.94598 ( 3255) covalent geometry : bond 0.00759 (23681) covalent geometry : angle 0.68242 (32470) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 395 time to evaluate : 2.524 Fit side-chains REVERT: C 11 PHE cc_start: 0.9217 (m-80) cc_final: 0.8795 (m-80) REVERT: C 31 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8102 (tm-30) REVERT: C 32 ARG cc_start: 0.8610 (mmp80) cc_final: 0.8230 (mmp80) REVERT: C 43 GLU cc_start: 0.8378 (mp0) cc_final: 0.8073 (mp0) REVERT: D 35 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8239 (mt-10) REVERT: D 43 GLU cc_start: 0.8957 (pm20) cc_final: 0.8711 (pm20) REVERT: D 81 GLU cc_start: 0.8398 (tp30) cc_final: 0.7868 (tp30) REVERT: D 155 GLU cc_start: 0.8304 (tt0) cc_final: 0.8064 (tt0) REVERT: D 157 LYS cc_start: 0.9205 (mttp) cc_final: 0.8993 (mttp) REVERT: D 179 ASP cc_start: 0.8980 (p0) cc_final: 0.8741 (p0) REVERT: E 31 GLU cc_start: 0.9287 (mm-30) cc_final: 0.9067 (mm-30) REVERT: F 35 GLU cc_start: 0.9049 (tt0) cc_final: 0.8829 (tt0) REVERT: G 43 GLU cc_start: 0.8627 (mp0) cc_final: 0.8402 (mp0) REVERT: G 49 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8102 (mt-10) REVERT: H 31 GLU cc_start: 0.9304 (tp30) cc_final: 0.8676 (tp30) REVERT: I 32 ARG cc_start: 0.9359 (mmp80) cc_final: 0.9124 (mmp80) REVERT: K 35 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7655 (mt-10) REVERT: L 32 ARG cc_start: 0.9208 (mmp80) cc_final: 0.8979 (mmp80) REVERT: L 43 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8577 (mm-30) REVERT: N 175 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8482 (mm-30) REVERT: O 35 GLU cc_start: 0.9068 (tt0) cc_final: 0.8795 (tt0) REVERT: O 117 LYS cc_start: 0.8826 (ttpt) cc_final: 0.8594 (ttmm) REVERT: Q 31 GLU cc_start: 0.8434 (tm-30) cc_final: 0.7902 (tm-30) REVERT: Q 35 GLU cc_start: 0.8533 (pt0) cc_final: 0.8226 (pt0) REVERT: Q 129 GLU cc_start: 0.7975 (pm20) cc_final: 0.7770 (pm20) REVERT: Q 178 ASN cc_start: 0.8093 (m110) cc_final: 0.7509 (m110) REVERT: Q 179 ASP cc_start: 0.8954 (p0) cc_final: 0.8684 (p0) REVERT: R 31 GLU cc_start: 0.7721 (pp20) cc_final: 0.7390 (pp20) REVERT: R 32 ARG cc_start: 0.7307 (tpt170) cc_final: 0.7060 (mmm160) REVERT: R 35 GLU cc_start: 0.8497 (mt-10) cc_final: 0.7907 (mt-10) REVERT: R 43 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8342 (mm-30) REVERT: S 130 GLN cc_start: 0.8891 (mm110) cc_final: 0.8566 (mp10) outliers start: 7 outliers final: 2 residues processed: 400 average time/residue: 2.0540 time to fit residues: 905.1812 Evaluate side-chains 330 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 328 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain P residue 117 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 7.9990 chunk 231 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 239 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 145 optimal weight: 7.9990 chunk 178 optimal weight: 8.9990 chunk 277 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 ASN C 178 ASN D 118 ASN E 181 GLN J 167 GLN ** L 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 167 GLN S 167 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.070834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.056344 restraints weight = 52155.001| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 3.72 r_work: 0.2580 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 23681 Z= 0.255 Angle : 0.635 10.215 32470 Z= 0.348 Chirality : 0.049 0.162 4165 Planarity : 0.004 0.053 4131 Dihedral : 5.003 58.164 3270 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.93 % Allowed : 9.75 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.15), residues: 3077 helix: 4.56 (0.16), residues: 654 sheet: 1.71 (0.17), residues: 804 loop : -2.22 (0.13), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 114 HIS 0.006 0.001 HIS D 105 PHE 0.012 0.002 PHE M 28 TYR 0.024 0.001 TYR D 98 ARG 0.008 0.001 ARG L 45 Details of bonding type rmsd hydrogen bonds : bond 0.10297 ( 1087) hydrogen bonds : angle 5.09243 ( 3255) covalent geometry : bond 0.00589 (23681) covalent geometry : angle 0.63479 (32470) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 395 time to evaluate : 2.675 Fit side-chains revert: symmetry clash REVERT: C 11 PHE cc_start: 0.9237 (m-80) cc_final: 0.9017 (m-80) REVERT: C 31 GLU cc_start: 0.9170 (tm-30) cc_final: 0.8568 (tm-30) REVERT: C 32 ARG cc_start: 0.9101 (mmp80) cc_final: 0.8669 (mmp80) REVERT: C 35 GLU cc_start: 0.8487 (pm20) cc_final: 0.8138 (pm20) REVERT: C 43 GLU cc_start: 0.8738 (mp0) cc_final: 0.8433 (mp0) REVERT: C 59 GLU cc_start: 0.9116 (pp20) cc_final: 0.8912 (pp20) REVERT: D 31 GLU cc_start: 0.9488 (tp30) cc_final: 0.9097 (mm-30) REVERT: D 43 GLU cc_start: 0.9100 (pm20) cc_final: 0.8817 (pm20) REVERT: D 99 ARG cc_start: 0.8204 (mtm110) cc_final: 0.8000 (mtm110) REVERT: D 155 GLU cc_start: 0.8764 (tt0) cc_final: 0.8533 (tt0) REVERT: F 129 GLU cc_start: 0.8235 (pm20) cc_final: 0.7970 (pm20) REVERT: G 3 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8352 (mp0) REVERT: G 31 GLU cc_start: 0.9534 (tp30) cc_final: 0.9262 (mm-30) REVERT: G 49 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8112 (mt-10) REVERT: G 130 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8630 (mp10) REVERT: H 3 GLU cc_start: 0.8856 (pm20) cc_final: 0.8599 (pm20) REVERT: H 31 GLU cc_start: 0.9446 (tp30) cc_final: 0.8899 (tp30) REVERT: H 45 ARG cc_start: 0.8962 (mtm110) cc_final: 0.8756 (mtm-85) REVERT: H 130 GLN cc_start: 0.9307 (OUTLIER) cc_final: 0.9029 (mp10) REVERT: I 32 ARG cc_start: 0.9450 (mmp80) cc_final: 0.9236 (mmp80) REVERT: J 47 SER cc_start: 0.9803 (m) cc_final: 0.9495 (t) REVERT: J 129 GLU cc_start: 0.7745 (pm20) cc_final: 0.7218 (pm20) REVERT: K 35 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8358 (mt-10) REVERT: K 43 GLU cc_start: 0.9396 (tt0) cc_final: 0.8996 (tm-30) REVERT: K 45 ARG cc_start: 0.9002 (mtm110) cc_final: 0.8779 (mtm-85) REVERT: K 81 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8454 (tm-30) REVERT: K 130 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8484 (mp10) REVERT: L 32 ARG cc_start: 0.9373 (mmp80) cc_final: 0.9170 (mmp80) REVERT: L 34 LYS cc_start: 0.9319 (ptmm) cc_final: 0.8985 (ptmm) REVERT: L 68 ASP cc_start: 0.7594 (m-30) cc_final: 0.7299 (t0) REVERT: M 49 GLU cc_start: 0.9011 (pt0) cc_final: 0.8810 (pt0) REVERT: M 129 GLU cc_start: 0.8027 (pm20) cc_final: 0.7390 (pm20) REVERT: M 130 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8613 (mp10) REVERT: N 175 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8711 (mm-30) REVERT: P 129 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7132 (pm20) REVERT: P 130 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8566 (mp10) REVERT: Q 31 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8302 (tm-30) REVERT: Q 32 ARG cc_start: 0.9204 (mmp80) cc_final: 0.8710 (mmp80) REVERT: Q 49 GLU cc_start: 0.8893 (pp20) cc_final: 0.8546 (pp20) REVERT: Q 84 ASP cc_start: 0.9160 (m-30) cc_final: 0.8751 (t0) REVERT: Q 129 GLU cc_start: 0.8199 (pm20) cc_final: 0.7964 (pm20) REVERT: Q 179 ASP cc_start: 0.9154 (p0) cc_final: 0.8853 (p0) REVERT: R 35 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8726 (mt-10) REVERT: R 129 GLU cc_start: 0.7991 (pm20) cc_final: 0.7567 (pm20) REVERT: S 31 GLU cc_start: 0.9512 (mm-30) cc_final: 0.9232 (mm-30) REVERT: S 35 GLU cc_start: 0.9035 (pt0) cc_final: 0.8739 (pt0) outliers start: 50 outliers final: 14 residues processed: 417 average time/residue: 2.3317 time to fit residues: 1075.1865 Evaluate side-chains 371 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 351 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain H residue 130 GLN Chi-restraints excluded: chain I residue 135 GLU Chi-restraints excluded: chain K residue 130 GLN Chi-restraints excluded: chain K residue 135 GLU Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain N residue 135 GLU Chi-restraints excluded: chain N residue 168 ARG Chi-restraints excluded: chain O residue 135 GLU Chi-restraints excluded: chain P residue 129 GLU Chi-restraints excluded: chain P residue 130 GLN Chi-restraints excluded: chain Q residue 127 LEU Chi-restraints excluded: chain R residue 167 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 65 optimal weight: 5.9990 chunk 292 optimal weight: 5.9990 chunk 305 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 214 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 249 optimal weight: 4.9990 chunk 295 optimal weight: 5.9990 chunk 302 optimal weight: 0.6980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 118 ASN J 167 GLN L 181 GLN ** N 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.072232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.057690 restraints weight = 51552.409| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 3.73 r_work: 0.2610 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23681 Z= 0.180 Angle : 0.566 10.490 32470 Z= 0.306 Chirality : 0.047 0.156 4165 Planarity : 0.003 0.052 4131 Dihedral : 4.553 32.417 3266 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.40 % Allowed : 12.54 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.15), residues: 3077 helix: 4.70 (0.16), residues: 654 sheet: 1.71 (0.17), residues: 803 loop : -2.11 (0.13), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 114 HIS 0.004 0.001 HIS D 105 PHE 0.027 0.001 PHE L 20 TYR 0.018 0.001 TYR D 98 ARG 0.004 0.000 ARG N 45 Details of bonding type rmsd hydrogen bonds : bond 0.09010 ( 1087) hydrogen bonds : angle 4.65810 ( 3255) covalent geometry : bond 0.00392 (23681) covalent geometry : angle 0.56592 (32470) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 415 time to evaluate : 3.428 Fit side-chains revert: symmetry clash REVERT: C 11 PHE cc_start: 0.9279 (m-80) cc_final: 0.9038 (m-80) REVERT: C 31 GLU cc_start: 0.9131 (tm-30) cc_final: 0.8662 (tm-30) REVERT: C 32 ARG cc_start: 0.9069 (mmp80) cc_final: 0.8788 (tpp-160) REVERT: C 34 LYS cc_start: 0.9508 (ptmm) cc_final: 0.9271 (ptmm) REVERT: C 35 GLU cc_start: 0.8441 (pm20) cc_final: 0.8189 (pm20) REVERT: C 43 GLU cc_start: 0.8676 (mp0) cc_final: 0.8237 (mp0) REVERT: C 59 GLU cc_start: 0.9114 (pp20) cc_final: 0.8546 (pp20) REVERT: D 43 GLU cc_start: 0.9097 (pm20) cc_final: 0.8814 (pm20) REVERT: F 31 GLU cc_start: 0.9538 (mm-30) cc_final: 0.9317 (mm-30) REVERT: G -1 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7459 (pt) REVERT: G 3 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8238 (mp0) REVERT: G 129 GLU cc_start: 0.8029 (pm20) cc_final: 0.7480 (pm20) REVERT: G 130 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8615 (mp10) REVERT: H 31 GLU cc_start: 0.9474 (tp30) cc_final: 0.8937 (tp30) REVERT: H 130 GLN cc_start: 0.9297 (OUTLIER) cc_final: 0.8970 (mp10) REVERT: I 32 ARG cc_start: 0.9459 (mmp80) cc_final: 0.9249 (mmp80) REVERT: J 31 GLU cc_start: 0.9468 (tp30) cc_final: 0.9075 (tp30) REVERT: J 47 SER cc_start: 0.9807 (m) cc_final: 0.9517 (t) REVERT: K 43 GLU cc_start: 0.9383 (tt0) cc_final: 0.9014 (tm-30) REVERT: K 81 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8436 (tm-30) REVERT: K 129 GLU cc_start: 0.8082 (pm20) cc_final: 0.7484 (pm20) REVERT: K 130 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8522 (mp10) REVERT: L 32 ARG cc_start: 0.9379 (mmp80) cc_final: 0.9163 (mmp80) REVERT: L 34 LYS cc_start: 0.9295 (ptmm) cc_final: 0.8990 (ptmm) REVERT: L 68 ASP cc_start: 0.7560 (m-30) cc_final: 0.7269 (t0) REVERT: M 49 GLU cc_start: 0.8997 (pt0) cc_final: 0.8767 (pt0) REVERT: M 129 GLU cc_start: 0.7952 (pm20) cc_final: 0.7390 (pm20) REVERT: M 130 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8596 (mp10) REVERT: O 34 LYS cc_start: 0.9620 (ttpp) cc_final: 0.9408 (ttpp) REVERT: P 129 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7167 (pm20) REVERT: P 130 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8530 (mp10) REVERT: Q 31 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8376 (tm-30) REVERT: Q 32 ARG cc_start: 0.9251 (mmp80) cc_final: 0.8914 (mmp80) REVERT: Q 35 GLU cc_start: 0.9097 (pt0) cc_final: 0.8725 (pt0) REVERT: Q 49 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8677 (pp20) REVERT: Q 84 ASP cc_start: 0.9171 (m-30) cc_final: 0.8772 (t0) REVERT: Q 129 GLU cc_start: 0.8131 (pm20) cc_final: 0.7628 (pm20) REVERT: Q 179 ASP cc_start: 0.9158 (p0) cc_final: 0.8881 (p0) REVERT: R 31 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7833 (pp20) REVERT: R 32 ARG cc_start: 0.7611 (tpt170) cc_final: 0.7367 (mmm160) REVERT: R 35 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8667 (mt-10) REVERT: R 129 GLU cc_start: 0.8029 (pm20) cc_final: 0.7512 (pm20) REVERT: S 31 GLU cc_start: 0.9510 (mm-30) cc_final: 0.9190 (mm-30) REVERT: S 35 GLU cc_start: 0.9123 (pt0) cc_final: 0.8832 (pt0) outliers start: 62 outliers final: 18 residues processed: 444 average time/residue: 2.0076 time to fit residues: 988.2808 Evaluate side-chains 395 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 369 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain F residue 0 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain G residue -1 ILE Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain H residue 130 GLN Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain K residue 130 GLN Chi-restraints excluded: chain K residue 167 GLN Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 168 ARG Chi-restraints excluded: chain P residue 129 GLU Chi-restraints excluded: chain P residue 130 GLN Chi-restraints excluded: chain Q residue 49 GLU Chi-restraints excluded: chain Q residue 127 LEU Chi-restraints excluded: chain S residue 3 GLU Chi-restraints excluded: chain S residue 41 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 49 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 chunk 164 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 187 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 126 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 291 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 178 ASN O 167 GLN Q 105 HIS S 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.072469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.058253 restraints weight = 51511.489| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 3.67 r_work: 0.2618 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23681 Z= 0.180 Angle : 0.558 11.236 32470 Z= 0.299 Chirality : 0.047 0.171 4165 Planarity : 0.003 0.051 4131 Dihedral : 4.424 35.772 3266 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.02 % Allowed : 14.20 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.15), residues: 3077 helix: 4.77 (0.16), residues: 654 sheet: 1.70 (0.17), residues: 803 loop : -2.03 (0.13), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 114 HIS 0.004 0.001 HIS D 105 PHE 0.023 0.001 PHE L 20 TYR 0.018 0.001 TYR D 98 ARG 0.006 0.000 ARG M 32 Details of bonding type rmsd hydrogen bonds : bond 0.08249 ( 1087) hydrogen bonds : angle 4.44778 ( 3255) covalent geometry : bond 0.00402 (23681) covalent geometry : angle 0.55756 (32470) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 401 time to evaluate : 2.432 Fit side-chains REVERT: C 11 PHE cc_start: 0.9305 (m-80) cc_final: 0.9043 (m-80) REVERT: C 31 GLU cc_start: 0.9127 (tm-30) cc_final: 0.8359 (tm-30) REVERT: C 32 ARG cc_start: 0.9041 (mmp80) cc_final: 0.8602 (tpp-160) REVERT: C 34 LYS cc_start: 0.9513 (ptmm) cc_final: 0.9233 (ptmm) REVERT: C 35 GLU cc_start: 0.8429 (pm20) cc_final: 0.8000 (pm20) REVERT: C 43 GLU cc_start: 0.8635 (mp0) cc_final: 0.8192 (mp0) REVERT: D 31 GLU cc_start: 0.9449 (tp30) cc_final: 0.8988 (tp30) REVERT: D 35 GLU cc_start: 0.8702 (pt0) cc_final: 0.8401 (pt0) REVERT: F 31 GLU cc_start: 0.9552 (mm-30) cc_final: 0.9293 (mm-30) REVERT: F 129 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7399 (pm20) REVERT: G -1 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7294 (pt) REVERT: G 3 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8282 (mp0) REVERT: G 129 GLU cc_start: 0.7977 (pm20) cc_final: 0.7495 (pm20) REVERT: G 130 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8607 (mp10) REVERT: H 31 GLU cc_start: 0.9463 (tp30) cc_final: 0.8892 (tp30) REVERT: H 45 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8317 (mtp85) REVERT: H 130 GLN cc_start: 0.9268 (OUTLIER) cc_final: 0.8909 (mp10) REVERT: I 32 ARG cc_start: 0.9450 (mmp80) cc_final: 0.9104 (mmp80) REVERT: J 47 SER cc_start: 0.9786 (m) cc_final: 0.9487 (t) REVERT: J 129 GLU cc_start: 0.7651 (pm20) cc_final: 0.7209 (pm20) REVERT: K 43 GLU cc_start: 0.9320 (tt0) cc_final: 0.9008 (tm-30) REVERT: K 81 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8466 (tm-30) REVERT: K 130 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8511 (mp10) REVERT: L 32 ARG cc_start: 0.9364 (mmp80) cc_final: 0.9104 (mmp80) REVERT: L 34 LYS cc_start: 0.9313 (ptmm) cc_final: 0.9085 (ptmm) REVERT: L 38 TYR cc_start: 0.9365 (m-80) cc_final: 0.9165 (m-80) REVERT: L 59 GLU cc_start: -0.0141 (OUTLIER) cc_final: -0.0950 (pm20) REVERT: L 68 ASP cc_start: 0.7487 (m-30) cc_final: 0.7203 (t0) REVERT: M 31 GLU cc_start: 0.9460 (mm-30) cc_final: 0.9001 (mm-30) REVERT: M 49 GLU cc_start: 0.8998 (pt0) cc_final: 0.8781 (pt0) REVERT: N 3 GLU cc_start: 0.8892 (pm20) cc_final: 0.8633 (mp0) REVERT: O 129 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7004 (pm20) REVERT: O 130 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8455 (mp10) REVERT: P 130 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8509 (mp10) REVERT: Q 31 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8454 (tm-30) REVERT: Q 35 GLU cc_start: 0.9037 (pt0) cc_final: 0.8632 (pt0) REVERT: Q 49 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8480 (pp20) REVERT: Q 59 GLU cc_start: 0.8867 (tp30) cc_final: 0.8547 (mm-30) REVERT: Q 84 ASP cc_start: 0.9197 (m-30) cc_final: 0.8742 (t0) REVERT: Q 129 GLU cc_start: 0.8054 (pm20) cc_final: 0.7797 (pm20) REVERT: Q 179 ASP cc_start: 0.9184 (p0) cc_final: 0.8889 (p0) REVERT: R 129 GLU cc_start: 0.8001 (pm20) cc_final: 0.7545 (pm20) REVERT: S 31 GLU cc_start: 0.9514 (mm-30) cc_final: 0.9165 (mm-30) REVERT: S 35 GLU cc_start: 0.9075 (pt0) cc_final: 0.8758 (pt0) outliers start: 78 outliers final: 32 residues processed: 434 average time/residue: 1.7247 time to fit residues: 830.2828 Evaluate side-chains 424 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 381 time to evaluate : 2.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 167 GLN Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain F residue 0 THR Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain G residue -1 ILE Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain H residue 130 GLN Chi-restraints excluded: chain K residue 130 GLN Chi-restraints excluded: chain K residue 167 GLN Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 43 GLU Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 167 GLN Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 135 GLU Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 129 GLU Chi-restraints excluded: chain O residue 130 GLN Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 130 GLN Chi-restraints excluded: chain Q residue 49 GLU Chi-restraints excluded: chain Q residue 127 LEU Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 167 GLN Chi-restraints excluded: chain S residue 3 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 85 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 221 optimal weight: 1.9990 chunk 102 optimal weight: 0.0030 chunk 7 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 228 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 167 GLN M 167 GLN O 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.074964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.060603 restraints weight = 51004.385| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 3.68 r_work: 0.2664 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23681 Z= 0.135 Angle : 0.527 12.020 32470 Z= 0.279 Chirality : 0.046 0.148 4165 Planarity : 0.003 0.050 4131 Dihedral : 4.054 24.765 3264 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.67 % Allowed : 15.52 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.15), residues: 3077 helix: 4.87 (0.16), residues: 655 sheet: 1.68 (0.17), residues: 805 loop : -1.89 (0.13), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP L 114 HIS 0.004 0.000 HIS D 105 PHE 0.031 0.001 PHE C 20 TYR 0.013 0.001 TYR D 98 ARG 0.007 0.000 ARG J 32 Details of bonding type rmsd hydrogen bonds : bond 0.07128 ( 1087) hydrogen bonds : angle 4.14938 ( 3255) covalent geometry : bond 0.00273 (23681) covalent geometry : angle 0.52715 (32470) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 440 time to evaluate : 2.600 Fit side-chains revert: symmetry clash REVERT: C 11 PHE cc_start: 0.9288 (m-80) cc_final: 0.9051 (m-80) REVERT: C 31 GLU cc_start: 0.9136 (tm-30) cc_final: 0.8478 (tm-30) REVERT: C 32 ARG cc_start: 0.9030 (mmp80) cc_final: 0.8716 (tpp80) REVERT: C 34 LYS cc_start: 0.9519 (ptmm) cc_final: 0.9205 (ptmm) REVERT: C 35 GLU cc_start: 0.8390 (pm20) cc_final: 0.7777 (pm20) REVERT: C 43 GLU cc_start: 0.8604 (mp0) cc_final: 0.8132 (mp0) REVERT: C 175 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8730 (mm-30) REVERT: D 31 GLU cc_start: 0.9440 (tp30) cc_final: 0.9193 (mm-30) REVERT: D 35 GLU cc_start: 0.8667 (pt0) cc_final: 0.8392 (pt0) REVERT: D 86 ASN cc_start: 0.8989 (t0) cc_final: 0.8769 (t0) REVERT: D 155 GLU cc_start: 0.8693 (tt0) cc_final: 0.8484 (tt0) REVERT: G -1 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7009 (mt) REVERT: G 31 GLU cc_start: 0.9524 (tp30) cc_final: 0.9065 (tp30) REVERT: G 49 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8129 (mt-10) REVERT: G 130 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8618 (mp10) REVERT: H 31 GLU cc_start: 0.9464 (tp30) cc_final: 0.8907 (tp30) REVERT: H 130 GLN cc_start: 0.9289 (OUTLIER) cc_final: 0.8897 (mp10) REVERT: I 32 ARG cc_start: 0.9415 (mmp80) cc_final: 0.9067 (mmp80) REVERT: J 47 SER cc_start: 0.9763 (m) cc_final: 0.9478 (t) REVERT: J 129 GLU cc_start: 0.7623 (pm20) cc_final: 0.7018 (pm20) REVERT: J 175 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8281 (mt-10) REVERT: K 43 GLU cc_start: 0.9295 (tt0) cc_final: 0.8992 (tm-30) REVERT: K 81 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8519 (tm-30) REVERT: K 129 GLU cc_start: 0.7951 (pm20) cc_final: 0.7272 (pm20) REVERT: L 32 ARG cc_start: 0.9353 (mmp80) cc_final: 0.9135 (mmp80) REVERT: L 38 TYR cc_start: 0.9349 (m-80) cc_final: 0.9103 (m-80) REVERT: L 68 ASP cc_start: 0.7565 (m-30) cc_final: 0.7253 (t0) REVERT: M 0 THR cc_start: 0.4978 (p) cc_final: 0.4205 (m) REVERT: M 31 GLU cc_start: 0.9460 (mm-30) cc_final: 0.9114 (mm-30) REVERT: M 35 GLU cc_start: 0.8722 (pt0) cc_final: 0.8472 (pt0) REVERT: M 49 GLU cc_start: 0.9025 (pt0) cc_final: 0.8776 (pt0) REVERT: P 130 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8415 (mp10) REVERT: Q 31 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8561 (tm-30) REVERT: Q 35 GLU cc_start: 0.8990 (pt0) cc_final: 0.8771 (pt0) REVERT: Q 49 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8392 (pp20) REVERT: Q 84 ASP cc_start: 0.9226 (m-30) cc_final: 0.8768 (t0) REVERT: Q 129 GLU cc_start: 0.7973 (pm20) cc_final: 0.7658 (pm20) REVERT: Q 179 ASP cc_start: 0.9155 (p0) cc_final: 0.8849 (p0) REVERT: R 35 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8514 (mt-10) REVERT: R 129 GLU cc_start: 0.8058 (pm20) cc_final: 0.7584 (pm20) REVERT: S 31 GLU cc_start: 0.9520 (mm-30) cc_final: 0.8790 (tp30) REVERT: S 35 GLU cc_start: 0.9003 (pt0) cc_final: 0.8631 (pt0) REVERT: S 81 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8556 (tm-30) outliers start: 69 outliers final: 22 residues processed: 471 average time/residue: 1.5855 time to fit residues: 834.9003 Evaluate side-chains 421 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 393 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain F residue 0 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue -1 ILE Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain H residue 130 GLN Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain P residue 130 GLN Chi-restraints excluded: chain Q residue 3 GLU Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 49 GLU Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 127 LEU Chi-restraints excluded: chain R residue 3 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 235 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 212 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 227 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 195 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 167 GLN M 167 GLN O 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.075555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.061120 restraints weight = 50839.215| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 3.69 r_work: 0.2677 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 23681 Z= 0.125 Angle : 0.532 12.505 32470 Z= 0.279 Chirality : 0.046 0.152 4165 Planarity : 0.003 0.048 4131 Dihedral : 3.946 23.348 3264 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.40 % Allowed : 17.34 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.15), residues: 3077 helix: 4.86 (0.17), residues: 656 sheet: 1.69 (0.17), residues: 802 loop : -1.78 (0.14), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP L 114 HIS 0.003 0.000 HIS D 105 PHE 0.029 0.001 PHE L 20 TYR 0.013 0.001 TYR D 98 ARG 0.004 0.000 ARG J 32 Details of bonding type rmsd hydrogen bonds : bond 0.06760 ( 1087) hydrogen bonds : angle 4.04409 ( 3255) covalent geometry : bond 0.00250 (23681) covalent geometry : angle 0.53243 (32470) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 430 time to evaluate : 2.482 Fit side-chains REVERT: C 11 PHE cc_start: 0.9290 (m-80) cc_final: 0.9050 (m-80) REVERT: C 31 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8431 (tm-30) REVERT: C 32 ARG cc_start: 0.8997 (mmp80) cc_final: 0.8705 (tpp80) REVERT: C 34 LYS cc_start: 0.9515 (ptmm) cc_final: 0.9188 (ptmm) REVERT: C 35 GLU cc_start: 0.8393 (pm20) cc_final: 0.7815 (pm20) REVERT: C 43 GLU cc_start: 0.8573 (mp0) cc_final: 0.8103 (mp0) REVERT: C 175 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8530 (mm-30) REVERT: D 31 GLU cc_start: 0.9435 (tp30) cc_final: 0.9221 (mm-30) REVERT: D 86 ASN cc_start: 0.9005 (t0) cc_final: 0.8795 (t0) REVERT: D 155 GLU cc_start: 0.8649 (tt0) cc_final: 0.8422 (tt0) REVERT: F 31 GLU cc_start: 0.9400 (mm-30) cc_final: 0.9193 (mm-30) REVERT: F 129 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7180 (pm20) REVERT: F 140 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8194 (pp) REVERT: G 31 GLU cc_start: 0.9527 (tp30) cc_final: 0.9258 (tp30) REVERT: G 35 GLU cc_start: 0.9350 (tp30) cc_final: 0.8922 (tt0) REVERT: G 129 GLU cc_start: 0.7920 (pm20) cc_final: 0.7454 (pm20) REVERT: G 130 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8629 (mp10) REVERT: H 31 GLU cc_start: 0.9457 (tp30) cc_final: 0.8937 (tp30) REVERT: H 129 GLU cc_start: 0.7969 (pm20) cc_final: 0.7717 (pm20) REVERT: H 130 GLN cc_start: 0.9283 (OUTLIER) cc_final: 0.8889 (mp10) REVERT: I 32 ARG cc_start: 0.9399 (mmp80) cc_final: 0.9054 (mmp80) REVERT: J 31 GLU cc_start: 0.9431 (tp30) cc_final: 0.9159 (tp30) REVERT: J 34 LYS cc_start: 0.9383 (OUTLIER) cc_final: 0.8638 (tmmm) REVERT: J 47 SER cc_start: 0.9751 (m) cc_final: 0.9477 (t) REVERT: J 175 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8295 (mt-10) REVERT: K 43 GLU cc_start: 0.9270 (tt0) cc_final: 0.8993 (tm-30) REVERT: K 81 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8490 (tm-30) REVERT: K 129 GLU cc_start: 0.7930 (pm20) cc_final: 0.7248 (pm20) REVERT: L 32 ARG cc_start: 0.9363 (mmp80) cc_final: 0.9147 (mmp80) REVERT: L 48 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.8955 (tt) REVERT: L 68 ASP cc_start: 0.7646 (m-30) cc_final: 0.7351 (t0) REVERT: M 31 GLU cc_start: 0.9437 (mm-30) cc_final: 0.9037 (mm-30) REVERT: M 32 ARG cc_start: 0.9208 (mmp80) cc_final: 0.8942 (mmp80) REVERT: M 35 GLU cc_start: 0.8649 (pt0) cc_final: 0.8220 (pt0) REVERT: M 49 GLU cc_start: 0.9044 (pt0) cc_final: 0.8801 (pt0) REVERT: Q 31 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8421 (tm-30) REVERT: Q 32 ARG cc_start: 0.9267 (mmp80) cc_final: 0.8922 (mmp80) REVERT: Q 59 GLU cc_start: 0.8760 (tp30) cc_final: 0.8315 (mm-30) REVERT: Q 84 ASP cc_start: 0.9233 (m-30) cc_final: 0.8812 (t0) REVERT: Q 129 GLU cc_start: 0.7931 (pm20) cc_final: 0.7615 (pm20) REVERT: Q 179 ASP cc_start: 0.9131 (p0) cc_final: 0.8837 (p0) REVERT: R 129 GLU cc_start: 0.8069 (pm20) cc_final: 0.7487 (pm20) REVERT: S 31 GLU cc_start: 0.9527 (mm-30) cc_final: 0.8781 (tp30) REVERT: S 35 GLU cc_start: 0.8917 (pt0) cc_final: 0.8458 (pt0) REVERT: S 81 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8502 (tm-30) REVERT: S 175 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8645 (mt-10) outliers start: 62 outliers final: 31 residues processed: 459 average time/residue: 1.6492 time to fit residues: 845.0217 Evaluate side-chains 431 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 393 time to evaluate : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 167 GLN Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain F residue 0 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain G residue 0 THR Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain H residue 130 GLN Chi-restraints excluded: chain J residue 34 LYS Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 167 GLN Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 43 GLU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 137 THR Chi-restraints excluded: chain N residue 180 LEU Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain S residue 41 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 75 optimal weight: 6.9990 chunk 202 optimal weight: 9.9990 chunk 158 optimal weight: 0.4980 chunk 203 optimal weight: 4.9990 chunk 78 optimal weight: 0.0970 chunk 37 optimal weight: 7.9990 chunk 297 optimal weight: 0.3980 chunk 212 optimal weight: 1.9990 chunk 284 optimal weight: 1.9990 chunk 250 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 178 ASN M 167 GLN O 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.076940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.062518 restraints weight = 50882.813| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.72 r_work: 0.2704 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 23681 Z= 0.119 Angle : 0.538 17.010 32470 Z= 0.279 Chirality : 0.046 0.187 4165 Planarity : 0.003 0.046 4131 Dihedral : 3.772 22.068 3264 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.32 % Allowed : 18.07 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.15), residues: 3077 helix: 4.79 (0.17), residues: 656 sheet: 1.70 (0.17), residues: 804 loop : -1.66 (0.14), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP D 110 HIS 0.003 0.000 HIS D 105 PHE 0.031 0.001 PHE C 20 TYR 0.012 0.001 TYR L 38 ARG 0.003 0.000 ARG J 32 Details of bonding type rmsd hydrogen bonds : bond 0.06202 ( 1087) hydrogen bonds : angle 3.92309 ( 3255) covalent geometry : bond 0.00238 (23681) covalent geometry : angle 0.53791 (32470) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 441 time to evaluate : 2.224 Fit side-chains REVERT: C 11 PHE cc_start: 0.9258 (m-80) cc_final: 0.9049 (m-80) REVERT: C 31 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8321 (tm-30) REVERT: C 32 ARG cc_start: 0.8968 (mmp80) cc_final: 0.8624 (tpp80) REVERT: C 34 LYS cc_start: 0.9491 (ptmm) cc_final: 0.9168 (ptmm) REVERT: C 35 GLU cc_start: 0.8423 (pm20) cc_final: 0.7900 (pm20) REVERT: C 43 GLU cc_start: 0.8541 (mp0) cc_final: 0.8062 (mp0) REVERT: C 175 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8559 (mm-30) REVERT: F 31 GLU cc_start: 0.9412 (mm-30) cc_final: 0.9207 (mm-30) REVERT: F 129 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7142 (pm20) REVERT: F 140 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8108 (pp) REVERT: G 31 GLU cc_start: 0.9536 (tp30) cc_final: 0.9296 (tp30) REVERT: G 129 GLU cc_start: 0.7885 (pm20) cc_final: 0.7429 (pm20) REVERT: G 130 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8591 (mp10) REVERT: H 3 GLU cc_start: 0.8959 (pm20) cc_final: 0.8652 (mp0) REVERT: H 31 GLU cc_start: 0.9461 (tp30) cc_final: 0.8889 (tp30) REVERT: H 129 GLU cc_start: 0.7938 (pm20) cc_final: 0.7413 (pm20) REVERT: H 130 GLN cc_start: 0.9239 (OUTLIER) cc_final: 0.8694 (mp10) REVERT: I 32 ARG cc_start: 0.9371 (mmp80) cc_final: 0.9050 (mmp80) REVERT: J 31 GLU cc_start: 0.9392 (tp30) cc_final: 0.9099 (tm-30) REVERT: J 47 SER cc_start: 0.9735 (m) cc_final: 0.9490 (t) REVERT: J 175 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8320 (mt-10) REVERT: K 81 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8502 (tm-30) REVERT: K 129 GLU cc_start: 0.7931 (pm20) cc_final: 0.7274 (pm20) REVERT: L 48 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.8945 (tt) REVERT: L 59 GLU cc_start: -0.0240 (OUTLIER) cc_final: -0.0921 (pm20) REVERT: L 68 ASP cc_start: 0.7703 (m-30) cc_final: 0.7295 (t0) REVERT: M 31 GLU cc_start: 0.9415 (mm-30) cc_final: 0.9012 (mm-30) REVERT: M 35 GLU cc_start: 0.8611 (pt0) cc_final: 0.8403 (pt0) REVERT: M 49 GLU cc_start: 0.9046 (pt0) cc_final: 0.8791 (pt0) REVERT: O 129 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.6772 (pm20) REVERT: Q 31 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8447 (tm-30) REVERT: Q 35 GLU cc_start: 0.9333 (tp30) cc_final: 0.9069 (tt0) REVERT: Q 84 ASP cc_start: 0.9219 (m-30) cc_final: 0.8750 (t0) REVERT: Q 129 GLU cc_start: 0.7918 (pm20) cc_final: 0.7677 (pm20) REVERT: Q 179 ASP cc_start: 0.9113 (p0) cc_final: 0.8805 (p0) REVERT: S 31 GLU cc_start: 0.9534 (mm-30) cc_final: 0.8879 (tp30) REVERT: S 32 ARG cc_start: 0.9137 (mmp80) cc_final: 0.8858 (mmp80) REVERT: S 59 GLU cc_start: 0.9286 (pt0) cc_final: 0.8890 (pp20) REVERT: S 81 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8572 (tm-30) outliers start: 60 outliers final: 25 residues processed: 470 average time/residue: 2.2806 time to fit residues: 1194.3248 Evaluate side-chains 431 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 398 time to evaluate : 2.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 167 GLN Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain H residue 130 GLN Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain L residue 43 GLU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain N residue 41 LEU Chi-restraints excluded: chain N residue 137 THR Chi-restraints excluded: chain N residue 180 LEU Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 129 GLU Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain R residue 3 GLU Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 167 GLN Chi-restraints excluded: chain S residue 41 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 196 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 chunk 211 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 202 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 235 optimal weight: 8.9990 chunk 304 optimal weight: 0.0050 chunk 85 optimal weight: 9.9990 overall best weight: 2.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 167 GLN N 178 ASN O 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.075917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.061233 restraints weight = 51134.551| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 3.76 r_work: 0.2679 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23681 Z= 0.135 Angle : 0.571 15.741 32470 Z= 0.292 Chirality : 0.046 0.196 4165 Planarity : 0.003 0.045 4131 Dihedral : 3.810 22.255 3264 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.44 % Allowed : 18.77 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.15), residues: 3077 helix: 4.73 (0.17), residues: 657 sheet: 1.70 (0.17), residues: 807 loop : -1.63 (0.14), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 114 HIS 0.003 0.000 HIS D 105 PHE 0.027 0.001 PHE R 20 TYR 0.014 0.001 TYR D 98 ARG 0.006 0.000 ARG M 32 Details of bonding type rmsd hydrogen bonds : bond 0.06261 ( 1087) hydrogen bonds : angle 3.97109 ( 3255) covalent geometry : bond 0.00297 (23681) covalent geometry : angle 0.57139 (32470) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 403 time to evaluate : 2.657 Fit side-chains REVERT: C 11 PHE cc_start: 0.9199 (m-80) cc_final: 0.8970 (m-80) REVERT: C 31 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8342 (tm-30) REVERT: C 32 ARG cc_start: 0.8952 (mmp80) cc_final: 0.8617 (tpp80) REVERT: C 34 LYS cc_start: 0.9501 (ptmm) cc_final: 0.9172 (ptmm) REVERT: C 35 GLU cc_start: 0.8398 (pm20) cc_final: 0.7880 (pm20) REVERT: C 43 GLU cc_start: 0.8556 (mp0) cc_final: 0.8082 (mp0) REVERT: C 175 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8564 (mm-30) REVERT: D 31 GLU cc_start: 0.9417 (mm-30) cc_final: 0.8927 (tp30) REVERT: D 35 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8271 (pt0) REVERT: F 31 GLU cc_start: 0.9419 (mm-30) cc_final: 0.9200 (mm-30) REVERT: F 129 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7285 (pm20) REVERT: G 3 GLU cc_start: 0.9163 (mp0) cc_final: 0.8947 (pm20) REVERT: G 31 GLU cc_start: 0.9569 (tp30) cc_final: 0.9197 (tp30) REVERT: G 49 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7835 (mt-10) REVERT: H 31 GLU cc_start: 0.9447 (tp30) cc_final: 0.8969 (tp30) REVERT: H 49 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8390 (mt-10) REVERT: H 130 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8827 (mp10) REVERT: I 32 ARG cc_start: 0.9373 (mmp80) cc_final: 0.9041 (mmp80) REVERT: J 31 GLU cc_start: 0.9393 (tp30) cc_final: 0.8986 (tp30) REVERT: J 47 SER cc_start: 0.9733 (m) cc_final: 0.9475 (t) REVERT: J 175 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8348 (mt-10) REVERT: K 43 GLU cc_start: 0.9213 (tt0) cc_final: 0.9000 (tm-30) REVERT: K 81 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8502 (tm-30) REVERT: K 129 GLU cc_start: 0.7859 (pm20) cc_final: 0.7314 (pm20) REVERT: L 32 ARG cc_start: 0.9331 (mmp80) cc_final: 0.8990 (mmp80) REVERT: L 48 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.8995 (tt) REVERT: L 59 GLU cc_start: 0.0076 (OUTLIER) cc_final: -0.0673 (pm20) REVERT: L 68 ASP cc_start: 0.7633 (m-30) cc_final: 0.7308 (t0) REVERT: M 31 GLU cc_start: 0.9461 (mm-30) cc_final: 0.9111 (mm-30) REVERT: M 49 GLU cc_start: 0.9029 (pt0) cc_final: 0.8776 (pt0) REVERT: O 129 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6858 (pm20) REVERT: Q 31 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8542 (tm-30) REVERT: Q 59 GLU cc_start: 0.9019 (tp30) cc_final: 0.8772 (mm-30) REVERT: Q 84 ASP cc_start: 0.9166 (m-30) cc_final: 0.8743 (t0) REVERT: Q 129 GLU cc_start: 0.8035 (pm20) cc_final: 0.7660 (pm20) REVERT: Q 179 ASP cc_start: 0.9138 (p0) cc_final: 0.8827 (p0) REVERT: R 34 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8724 (tptm) REVERT: S 31 GLU cc_start: 0.9517 (mm-30) cc_final: 0.9229 (mm-30) REVERT: S 35 GLU cc_start: 0.9364 (tp30) cc_final: 0.9116 (pt0) REVERT: S 81 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8034 (tm-30) outliers start: 63 outliers final: 26 residues processed: 438 average time/residue: 1.6826 time to fit residues: 820.7179 Evaluate side-chains 429 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 395 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 167 GLN Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 167 GLN Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain H residue 130 GLN Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain L residue 43 GLU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 137 THR Chi-restraints excluded: chain N residue 180 LEU Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 129 GLU Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain R residue 34 LYS Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain S residue 41 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 186 optimal weight: 3.9990 chunk 303 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 246 optimal weight: 0.8980 chunk 154 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 226 optimal weight: 0.5980 chunk 194 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.077562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.063108 restraints weight = 50667.993| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.71 r_work: 0.2716 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 23681 Z= 0.119 Angle : 0.570 20.444 32470 Z= 0.290 Chirality : 0.046 0.163 4165 Planarity : 0.003 0.047 4131 Dihedral : 3.692 20.964 3264 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.66 % Allowed : 20.01 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.15), residues: 3077 helix: 4.65 (0.17), residues: 657 sheet: 1.73 (0.17), residues: 807 loop : -1.57 (0.14), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP D 110 HIS 0.003 0.000 HIS D 105 PHE 0.028 0.001 PHE R 20 TYR 0.010 0.001 TYR D 98 ARG 0.005 0.000 ARG M 32 Details of bonding type rmsd hydrogen bonds : bond 0.05835 ( 1087) hydrogen bonds : angle 3.87239 ( 3255) covalent geometry : bond 0.00248 (23681) covalent geometry : angle 0.56982 (32470) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 431 time to evaluate : 2.473 Fit side-chains REVERT: C 11 PHE cc_start: 0.9219 (m-80) cc_final: 0.8997 (m-80) REVERT: C 31 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8325 (tm-30) REVERT: C 32 ARG cc_start: 0.8984 (mmp80) cc_final: 0.8690 (tpp80) REVERT: C 34 LYS cc_start: 0.9500 (ptmm) cc_final: 0.9169 (ptmm) REVERT: C 35 GLU cc_start: 0.8407 (pm20) cc_final: 0.7874 (pm20) REVERT: C 43 GLU cc_start: 0.8523 (mp0) cc_final: 0.8037 (mp0) REVERT: C 175 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8571 (mm-30) REVERT: D 31 GLU cc_start: 0.9400 (mm-30) cc_final: 0.8914 (tp30) REVERT: D 35 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8269 (pt0) REVERT: E 181 GLN cc_start: 0.7012 (pt0) cc_final: 0.6545 (pt0) REVERT: F 31 GLU cc_start: 0.9425 (mm-30) cc_final: 0.9224 (mm-30) REVERT: F 129 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7093 (pm20) REVERT: G 35 GLU cc_start: 0.9358 (tp30) cc_final: 0.8913 (tt0) REVERT: G 129 GLU cc_start: 0.7871 (pm20) cc_final: 0.7379 (pm20) REVERT: H 31 GLU cc_start: 0.9439 (tp30) cc_final: 0.8931 (tp30) REVERT: H 129 GLU cc_start: 0.7777 (pm20) cc_final: 0.7554 (pm20) REVERT: H 130 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8786 (mp10) REVERT: I 32 ARG cc_start: 0.9355 (mmp80) cc_final: 0.9026 (mmp80) REVERT: J 31 GLU cc_start: 0.9368 (tp30) cc_final: 0.9002 (tp30) REVERT: J 35 GLU cc_start: 0.8373 (pt0) cc_final: 0.7699 (pt0) REVERT: J 47 SER cc_start: 0.9707 (m) cc_final: 0.9460 (t) REVERT: J 175 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8347 (mt-10) REVERT: K 43 GLU cc_start: 0.9202 (tt0) cc_final: 0.8992 (tm-30) REVERT: K 81 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8515 (tm-30) REVERT: K 129 GLU cc_start: 0.7950 (pm20) cc_final: 0.7312 (pm20) REVERT: L 18 PHE cc_start: 0.9334 (t80) cc_final: 0.9108 (t80) REVERT: L 32 ARG cc_start: 0.9329 (mmp80) cc_final: 0.9020 (mmp80) REVERT: L 35 GLU cc_start: 0.9452 (tt0) cc_final: 0.9232 (tt0) REVERT: L 48 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8966 (tt) REVERT: L 59 GLU cc_start: -0.0213 (OUTLIER) cc_final: -0.0922 (pm20) REVERT: L 68 ASP cc_start: 0.7688 (m-30) cc_final: 0.7351 (t0) REVERT: M 31 GLU cc_start: 0.9438 (mm-30) cc_final: 0.9039 (mm-30) REVERT: M 49 GLU cc_start: 0.9027 (pt0) cc_final: 0.8752 (pt0) REVERT: O 129 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6811 (pm20) REVERT: Q 31 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8499 (tm-30) REVERT: Q 35 GLU cc_start: 0.9279 (tp30) cc_final: 0.8923 (tt0) REVERT: Q 84 ASP cc_start: 0.9147 (m-30) cc_final: 0.8756 (t0) REVERT: Q 129 GLU cc_start: 0.8022 (pm20) cc_final: 0.7656 (pm20) REVERT: Q 179 ASP cc_start: 0.9114 (p0) cc_final: 0.8799 (p0) REVERT: S 31 GLU cc_start: 0.9535 (mm-30) cc_final: 0.9320 (mm-30) REVERT: S 81 GLU cc_start: 0.8934 (tm-30) cc_final: 0.7997 (tm-30) outliers start: 43 outliers final: 27 residues processed: 456 average time/residue: 1.6669 time to fit residues: 851.1466 Evaluate side-chains 437 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 403 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 167 GLN Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain H residue 130 GLN Chi-restraints excluded: chain J residue 3 GLU Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain L residue 43 GLU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 137 THR Chi-restraints excluded: chain N residue 180 LEU Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 129 GLU Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain S residue 41 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 235 optimal weight: 0.9990 chunk 256 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 193 optimal weight: 3.9990 chunk 253 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 238 optimal weight: 10.0000 chunk 258 optimal weight: 20.0000 chunk 160 optimal weight: 0.1980 chunk 282 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 ASN G 130 GLN J 167 GLN M 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.075616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.061249 restraints weight = 51066.028| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 3.70 r_work: 0.2674 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23681 Z= 0.150 Angle : 0.609 22.046 32470 Z= 0.308 Chirality : 0.046 0.195 4165 Planarity : 0.003 0.046 4131 Dihedral : 3.826 22.083 3264 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.63 % Allowed : 20.59 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.15), residues: 3077 helix: 4.57 (0.17), residues: 657 sheet: 1.74 (0.17), residues: 807 loop : -1.59 (0.14), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 114 HIS 0.003 0.000 HIS D 105 PHE 0.029 0.001 PHE R 20 TYR 0.013 0.001 TYR D 98 ARG 0.003 0.000 ARG E 168 Details of bonding type rmsd hydrogen bonds : bond 0.06177 ( 1087) hydrogen bonds : angle 4.02038 ( 3255) covalent geometry : bond 0.00345 (23681) covalent geometry : angle 0.60891 (32470) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 402 time to evaluate : 2.759 Fit side-chains REVERT: C 11 PHE cc_start: 0.9206 (m-80) cc_final: 0.8996 (m-80) REVERT: C 31 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8430 (tm-30) REVERT: C 32 ARG cc_start: 0.8919 (mmp80) cc_final: 0.8623 (tpp80) REVERT: C 35 GLU cc_start: 0.8413 (pm20) cc_final: 0.7717 (pm20) REVERT: C 43 GLU cc_start: 0.8552 (mp0) cc_final: 0.8071 (mp0) REVERT: D 31 GLU cc_start: 0.9389 (mm-30) cc_final: 0.8899 (tp30) REVERT: D 35 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8342 (pt0) REVERT: D 179 ASP cc_start: 0.8916 (p0) cc_final: 0.8606 (p0) REVERT: F 31 GLU cc_start: 0.9443 (mm-30) cc_final: 0.9230 (mm-30) REVERT: F 129 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7272 (pm20) REVERT: G 31 GLU cc_start: 0.9382 (tp30) cc_final: 0.9083 (tp30) REVERT: G 35 GLU cc_start: 0.9398 (tp30) cc_final: 0.8904 (tt0) REVERT: G 129 GLU cc_start: 0.7878 (pm20) cc_final: 0.7228 (pm20) REVERT: H 31 GLU cc_start: 0.9452 (tp30) cc_final: 0.8990 (tp30) REVERT: H 49 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8393 (mt-10) REVERT: H 130 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8803 (mp10) REVERT: I 32 ARG cc_start: 0.9369 (mmp80) cc_final: 0.9037 (mmp80) REVERT: J 31 GLU cc_start: 0.9372 (tp30) cc_final: 0.8932 (tp30) REVERT: J 35 GLU cc_start: 0.8451 (pt0) cc_final: 0.7741 (pt0) REVERT: J 47 SER cc_start: 0.9733 (m) cc_final: 0.9466 (t) REVERT: J 175 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8352 (mt-10) REVERT: K 43 GLU cc_start: 0.9237 (tt0) cc_final: 0.9024 (tm-30) REVERT: K 81 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8471 (tm-30) REVERT: K 129 GLU cc_start: 0.7750 (pm20) cc_final: 0.7233 (pm20) REVERT: L 32 ARG cc_start: 0.9320 (mmp80) cc_final: 0.9022 (mmp80) REVERT: L 35 GLU cc_start: 0.9467 (tt0) cc_final: 0.9245 (tt0) REVERT: L 48 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.9044 (tt) REVERT: L 59 GLU cc_start: 0.0117 (OUTLIER) cc_final: -0.0705 (pm20) REVERT: L 68 ASP cc_start: 0.7640 (m-30) cc_final: 0.7342 (t0) REVERT: M 31 GLU cc_start: 0.9460 (mm-30) cc_final: 0.9081 (mm-30) REVERT: M 49 GLU cc_start: 0.9029 (pt0) cc_final: 0.8776 (pt0) REVERT: O 129 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6725 (pm20) REVERT: Q 31 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8522 (tm-30) REVERT: Q 35 GLU cc_start: 0.9332 (tp30) cc_final: 0.8973 (tt0) REVERT: Q 84 ASP cc_start: 0.9199 (m-30) cc_final: 0.8789 (t0) REVERT: Q 129 GLU cc_start: 0.8052 (pm20) cc_final: 0.7631 (pm20) REVERT: Q 179 ASP cc_start: 0.9135 (p0) cc_final: 0.8826 (p0) REVERT: R 43 GLU cc_start: 0.9113 (tm-30) cc_final: 0.8849 (tm-30) REVERT: S 31 GLU cc_start: 0.9546 (mm-30) cc_final: 0.9007 (tp30) REVERT: S 81 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8640 (tm-30) outliers start: 42 outliers final: 27 residues processed: 427 average time/residue: 1.6940 time to fit residues: 805.1495 Evaluate side-chains 424 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 390 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 167 GLN Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain H residue 130 GLN Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain L residue 43 GLU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 137 THR Chi-restraints excluded: chain N residue 180 LEU Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 129 GLU Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 167 GLN Chi-restraints excluded: chain S residue 41 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 152 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 298 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 252 optimal weight: 5.9990 chunk 287 optimal weight: 0.0570 chunk 247 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 219 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 167 GLN G 130 GLN J 167 GLN M 167 GLN O 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.076696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.062279 restraints weight = 50824.498| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.71 r_work: 0.2699 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23681 Z= 0.127 Angle : 0.595 21.866 32470 Z= 0.302 Chirality : 0.046 0.181 4165 Planarity : 0.003 0.046 4131 Dihedral : 3.747 21.337 3264 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.59 % Allowed : 20.82 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.15), residues: 3077 helix: 4.57 (0.17), residues: 657 sheet: 1.73 (0.17), residues: 808 loop : -1.56 (0.14), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP L 114 HIS 0.003 0.000 HIS D 105 PHE 0.029 0.001 PHE C 20 TYR 0.009 0.001 TYR Q 38 ARG 0.003 0.000 ARG E 168 Details of bonding type rmsd hydrogen bonds : bond 0.05907 ( 1087) hydrogen bonds : angle 3.93534 ( 3255) covalent geometry : bond 0.00278 (23681) covalent geometry : angle 0.59507 (32470) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18287.77 seconds wall clock time: 318 minutes 32.97 seconds (19112.97 seconds total)