Starting phenix.real_space_refine on Fri Sep 19 04:28:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i5h_52629/09_2025/9i5h_52629.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i5h_52629/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9i5h_52629/09_2025/9i5h_52629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i5h_52629/09_2025/9i5h_52629.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i5h_52629/09_2025/9i5h_52629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i5h_52629/09_2025/9i5h_52629.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 5.58, per 1000 atoms: 0.24 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: 1.89 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.91 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: 4.35 Time building geometry restraints manager: 2.53 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: 0.00 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 21.560 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.750 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.016 0.001 ARG D 99 TYR 0.021 0.001 TYR D 98 PHE 0.018 0.002 PHE C 20 TRP 0.018 0.001 TRP L 114 HIS 0.009 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00759 (23681) covalent geometry : angle 0.68242 (32470) hydrogen bonds : bond 0.26917 ( 1087) hydrogen bonds : angle 6.94598 ( 3255) *********************** 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 : 0.925 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: 0.8673 time to fit residues: 381.7343 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 : 0.624 ------------------------------------------------------------------------------- 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 197 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.0870 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 1.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 ASN E 181 GLN J 167 GLN L 181 GLN ** N 178 ASN ** 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 = 0.3041 r_free = 0.3041 target = 0.073250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.058549 restraints weight = 51462.155| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 3.75 r_work: 0.2626 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 23681 Z= 0.168 Angle : 0.584 10.520 32470 Z= 0.319 Chirality : 0.048 0.161 4165 Planarity : 0.004 0.051 4131 Dihedral : 4.680 56.629 3270 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.66 % Allowed : 9.06 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.15), residues: 3077 helix: 4.63 (0.16), residues: 654 sheet: 1.73 (0.17), residues: 810 loop : -2.09 (0.13), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 45 TYR 0.016 0.001 TYR D 98 PHE 0.011 0.001 PHE R 72 TRP 0.008 0.001 TRP D 114 HIS 0.005 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00328 (23681) covalent geometry : angle 0.58384 (32470) hydrogen bonds : bond 0.09871 ( 1087) hydrogen bonds : angle 4.93625 ( 3255) *********************** 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 477 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 434 time to evaluate : 0.835 Fit side-chains REVERT: C 11 PHE cc_start: 0.9235 (m-80) cc_final: 0.8992 (m-80) REVERT: C 31 GLU cc_start: 0.9190 (tm-30) cc_final: 0.8371 (tm-30) REVERT: C 32 ARG cc_start: 0.9090 (mmp80) cc_final: 0.8359 (mmp80) REVERT: C 35 GLU cc_start: 0.8515 (pm20) cc_final: 0.7884 (pm20) REVERT: C 59 GLU cc_start: 0.9040 (pp20) cc_final: 0.8483 (pp20) REVERT: D 31 GLU cc_start: 0.9464 (tp30) cc_final: 0.9227 (mm-30) REVERT: D 43 GLU cc_start: 0.9087 (pm20) cc_final: 0.8830 (pm20) REVERT: D 155 GLU cc_start: 0.8736 (tt0) cc_final: 0.8427 (tt0) REVERT: F 129 GLU cc_start: 0.8460 (pm20) cc_final: 0.8133 (pm20) REVERT: G 3 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8333 (mp0) REVERT: G 31 GLU cc_start: 0.9522 (tp30) cc_final: 0.9257 (mm-30) REVERT: G 49 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8004 (mt-10) REVERT: G 130 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8580 (mp10) REVERT: H 3 GLU cc_start: 0.8854 (pm20) cc_final: 0.8592 (pm20) REVERT: H 31 GLU cc_start: 0.9456 (tp30) cc_final: 0.8862 (tp30) REVERT: H 130 GLN cc_start: 0.9307 (OUTLIER) cc_final: 0.9028 (mp10) REVERT: I 32 ARG cc_start: 0.9453 (mmp80) cc_final: 0.9228 (mmp80) REVERT: J 47 SER cc_start: 0.9791 (m) cc_final: 0.9505 (t) REVERT: J 129 GLU cc_start: 0.7896 (pm20) cc_final: 0.7549 (pm20) REVERT: K 81 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8481 (tm-30) REVERT: K 129 GLU cc_start: 0.8274 (pm20) cc_final: 0.7596 (pm20) REVERT: K 130 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8466 (mp10) REVERT: L 32 ARG cc_start: 0.9372 (mmp80) cc_final: 0.9168 (mmp80) REVERT: L 34 LYS cc_start: 0.9277 (ptmm) cc_final: 0.9003 (ptmm) REVERT: L 68 ASP cc_start: 0.7686 (m-30) cc_final: 0.7362 (t0) REVERT: M 49 GLU cc_start: 0.9022 (pt0) cc_final: 0.8805 (pt0) REVERT: M 129 GLU cc_start: 0.8152 (pm20) cc_final: 0.7620 (pm20) REVERT: M 130 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8591 (mp10) REVERT: N 35 GLU cc_start: 0.9301 (tt0) cc_final: 0.8921 (pt0) REVERT: N 175 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8640 (mm-30) REVERT: O 35 GLU cc_start: 0.9371 (tt0) cc_final: 0.8779 (pt0) REVERT: P 129 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7173 (pm20) REVERT: P 130 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8516 (mp10) REVERT: Q 31 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8274 (tm-30) REVERT: Q 32 ARG cc_start: 0.9180 (mmp80) cc_final: 0.8727 (mmp80) REVERT: Q 59 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8515 (pp20) REVERT: Q 84 ASP cc_start: 0.9147 (m-30) cc_final: 0.8726 (t0) REVERT: Q 129 GLU cc_start: 0.8168 (pm20) cc_final: 0.7955 (pm20) REVERT: Q 178 ASN cc_start: 0.8709 (m110) cc_final: 0.8192 (m110) REVERT: Q 179 ASP cc_start: 0.9135 (p0) cc_final: 0.8812 (p0) REVERT: R 35 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8704 (mt-10) REVERT: R 129 GLU cc_start: 0.8205 (pm20) cc_final: 0.7585 (pm20) REVERT: S 31 GLU cc_start: 0.9508 (mm-30) cc_final: 0.9220 (mm-30) REVERT: S 35 GLU cc_start: 0.9044 (pt0) cc_final: 0.8710 (pt0) outliers start: 43 outliers final: 9 residues processed: 451 average time/residue: 0.8137 time to fit residues: 405.8772 Evaluate side-chains 380 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 365 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 136 ILE 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 K residue 130 GLN Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain M residue 130 GLN 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 57 optimal weight: 3.9990 chunk 99 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 270 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 292 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 178 ASN D 118 ASN N 178 ASN O 167 GLN S 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.072290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.057715 restraints weight = 52069.440| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 3.74 r_work: 0.2608 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23681 Z= 0.192 Angle : 0.567 10.052 32470 Z= 0.306 Chirality : 0.047 0.154 4165 Planarity : 0.004 0.050 4131 Dihedral : 4.464 32.599 3266 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.59 % Allowed : 12.46 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.15), residues: 3077 helix: 4.78 (0.16), residues: 655 sheet: 1.73 (0.17), residues: 811 loop : -2.02 (0.13), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 99 TYR 0.012 0.001 TYR D 98 PHE 0.028 0.001 PHE L 20 TRP 0.010 0.001 TRP L 114 HIS 0.005 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00429 (23681) covalent geometry : angle 0.56692 (32470) hydrogen bonds : bond 0.08867 ( 1087) hydrogen bonds : angle 4.59610 ( 3255) *********************** 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 481 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 414 time to evaluate : 0.960 Fit side-chains REVERT: C 11 PHE cc_start: 0.9271 (m-80) cc_final: 0.9039 (m-80) REVERT: C 31 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8517 (tm-30) REVERT: C 32 ARG cc_start: 0.9061 (mmp80) cc_final: 0.8649 (tpp-160) REVERT: C 35 GLU cc_start: 0.8423 (pm20) cc_final: 0.8170 (pm20) REVERT: C 43 GLU cc_start: 0.8654 (mp0) cc_final: 0.8200 (mp0) REVERT: C 59 GLU cc_start: 0.9102 (pp20) cc_final: 0.8856 (pp20) REVERT: D 35 GLU cc_start: 0.9339 (tp30) cc_final: 0.9104 (tt0) REVERT: D 43 GLU cc_start: 0.9063 (pm20) cc_final: 0.8786 (pm20) REVERT: F 31 GLU cc_start: 0.9537 (mm-30) cc_final: 0.9320 (mm-30) REVERT: G -1 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7341 (pt) REVERT: G 3 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8287 (mp0) REVERT: G 130 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8626 (mp10) REVERT: H 31 GLU cc_start: 0.9460 (tp30) cc_final: 0.8928 (tp30) REVERT: H 130 GLN cc_start: 0.9303 (OUTLIER) cc_final: 0.8905 (mp10) REVERT: I 32 ARG cc_start: 0.9452 (mmp80) cc_final: 0.9120 (mmp80) REVERT: J 31 GLU cc_start: 0.9461 (tp30) cc_final: 0.9076 (tp30) REVERT: J 47 SER cc_start: 0.9800 (m) cc_final: 0.9495 (t) REVERT: K 81 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8468 (tm-30) REVERT: K 129 GLU cc_start: 0.7891 (pm20) cc_final: 0.7228 (pm20) REVERT: L 32 ARG cc_start: 0.9358 (mmp80) cc_final: 0.9111 (mmp80) REVERT: L 34 LYS cc_start: 0.9287 (ptmm) cc_final: 0.8992 (ptmm) REVERT: L 68 ASP cc_start: 0.7576 (m-30) cc_final: 0.7284 (t0) REVERT: M 49 GLU cc_start: 0.8994 (pt0) cc_final: 0.8771 (pt0) REVERT: M 129 GLU cc_start: 0.8061 (pm20) cc_final: 0.7453 (pm20) REVERT: N 3 GLU cc_start: 0.8997 (pm20) cc_final: 0.8740 (mp0) REVERT: O 34 LYS cc_start: 0.9615 (ttpp) cc_final: 0.9391 (ttpp) REVERT: O 35 GLU cc_start: 0.9378 (tt0) cc_final: 0.9146 (tt0) REVERT: P 129 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7146 (pm20) REVERT: P 130 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8577 (mp10) REVERT: Q 31 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8378 (tm-30) REVERT: Q 32 ARG cc_start: 0.9243 (mmp80) cc_final: 0.8945 (mmp80) REVERT: Q 35 GLU cc_start: 0.9116 (pt0) cc_final: 0.8786 (pt0) REVERT: Q 59 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8755 (mm-30) REVERT: Q 84 ASP cc_start: 0.9175 (m-30) cc_final: 0.8752 (t0) REVERT: Q 129 GLU cc_start: 0.8141 (pm20) cc_final: 0.7885 (pm20) REVERT: Q 179 ASP cc_start: 0.9070 (p0) cc_final: 0.8859 (p0) REVERT: R 31 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7756 (pp20) REVERT: R 35 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8670 (mt-10) REVERT: R 129 GLU cc_start: 0.7975 (pm20) cc_final: 0.7556 (pm20) REVERT: S 31 GLU cc_start: 0.9511 (mm-30) cc_final: 0.9173 (mm-30) REVERT: S 35 GLU cc_start: 0.9121 (pt0) cc_final: 0.8824 (pt0) outliers start: 67 outliers final: 24 residues processed: 442 average time/residue: 0.7920 time to fit residues: 388.7782 Evaluate side-chains 406 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 376 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C 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 130 GLN 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 117 LYS Chi-restraints excluded: chain H residue 130 GLN Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 135 GLU 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 41 LEU Chi-restraints excluded: chain Q residue 127 LEU Chi-restraints excluded: chain R residue 3 GLU Chi-restraints excluded: chain R residue 31 GLU 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 55 optimal weight: 4.9990 chunk 247 optimal weight: 3.9990 chunk 263 optimal weight: 10.0000 chunk 246 optimal weight: 10.0000 chunk 277 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 283 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 173 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 167 GLN 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 = 0.3022 r_free = 0.3022 target = 0.072160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.057623 restraints weight = 51941.389| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 3.74 r_work: 0.2606 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 23681 Z= 0.197 Angle : 0.570 11.487 32470 Z= 0.304 Chirality : 0.047 0.152 4165 Planarity : 0.003 0.051 4131 Dihedral : 4.387 26.533 3264 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.90 % Allowed : 14.40 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.15), residues: 3077 helix: 4.76 (0.16), residues: 656 sheet: 1.72 (0.17), residues: 805 loop : -1.99 (0.13), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 168 TYR 0.023 0.001 TYR D 98 PHE 0.027 0.001 PHE R 20 TRP 0.007 0.001 TRP L 114 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00452 (23681) covalent geometry : angle 0.57007 (32470) hydrogen bonds : bond 0.08256 ( 1087) hydrogen bonds : angle 4.47816 ( 3255) *********************** 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 467 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 392 time to evaluate : 0.732 Fit side-chains REVERT: C 11 PHE cc_start: 0.9282 (m-80) cc_final: 0.9067 (m-80) REVERT: C 31 GLU cc_start: 0.9129 (tm-30) cc_final: 0.8465 (tm-30) REVERT: C 32 ARG cc_start: 0.9030 (mmp80) cc_final: 0.8677 (tpp80) REVERT: C 35 GLU cc_start: 0.8421 (pm20) cc_final: 0.7824 (pm20) REVERT: C 43 GLU cc_start: 0.8629 (mp0) cc_final: 0.8195 (mp0) REVERT: D 31 GLU cc_start: 0.9473 (tp30) cc_final: 0.9110 (tp30) REVERT: D 155 GLU cc_start: 0.8604 (tt0) cc_final: 0.8272 (tt0) REVERT: F 31 GLU cc_start: 0.9561 (mm-30) cc_final: 0.9337 (mm-30) REVERT: F 129 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7416 (pm20) REVERT: G -1 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7310 (pt) REVERT: G 3 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8324 (mp0) REVERT: G 31 GLU cc_start: 0.9527 (tp30) cc_final: 0.8990 (tp30) REVERT: G 35 GLU cc_start: 0.9362 (tp30) cc_final: 0.9076 (tt0) REVERT: G 49 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8167 (mt-10) REVERT: G 129 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7074 (pm20) REVERT: H 31 GLU cc_start: 0.9452 (tp30) cc_final: 0.8879 (tp30) REVERT: H 130 GLN cc_start: 0.9272 (OUTLIER) cc_final: 0.8916 (mp10) REVERT: I 32 ARG cc_start: 0.9437 (mmp80) cc_final: 0.9094 (mmp80) REVERT: J 47 SER cc_start: 0.9782 (m) cc_final: 0.9478 (t) REVERT: J 129 GLU cc_start: 0.7622 (pm20) cc_final: 0.7174 (pm20) REVERT: K 43 GLU cc_start: 0.9349 (tt0) cc_final: 0.9025 (tm-30) REVERT: K 81 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8447 (tm-30) REVERT: L 32 ARG cc_start: 0.9357 (mmp80) cc_final: 0.9085 (mmp80) REVERT: L 68 ASP cc_start: 0.7489 (m-30) cc_final: 0.7231 (t0) REVERT: M 49 GLU cc_start: 0.8995 (pt0) cc_final: 0.8759 (pt0) REVERT: M 129 GLU cc_start: 0.8035 (pm20) cc_final: 0.7518 (pm20) REVERT: N 3 GLU cc_start: 0.8902 (pm20) cc_final: 0.8642 (mp0) REVERT: N 130 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8640 (mp10) REVERT: P 129 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7116 (pm20) REVERT: P 130 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8519 (mp10) REVERT: Q 31 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8623 (tm-30) REVERT: Q 59 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8715 (mm-30) REVERT: Q 84 ASP cc_start: 0.9191 (m-30) cc_final: 0.8735 (t0) REVERT: Q 129 GLU cc_start: 0.8158 (pm20) cc_final: 0.7830 (pm20) REVERT: Q 179 ASP cc_start: 0.9182 (p0) cc_final: 0.8885 (p0) REVERT: R 35 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8645 (mt-10) REVERT: R 129 GLU cc_start: 0.8002 (pm20) cc_final: 0.7509 (pm20) REVERT: S 31 GLU cc_start: 0.9513 (mm-30) cc_final: 0.9113 (mm-30) REVERT: S 35 GLU cc_start: 0.9081 (pt0) cc_final: 0.8771 (pt0) REVERT: S 81 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8601 (tm-30) outliers start: 75 outliers final: 35 residues processed: 430 average time/residue: 0.7739 time to fit residues: 368.7793 Evaluate side-chains 419 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 377 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 153 ILE Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 167 GLN 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 129 GLU Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 130 GLN Chi-restraints excluded: chain H residue 167 GLN Chi-restraints excluded: chain I residue 135 GLU Chi-restraints excluded: chain J residue 103 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 137 THR Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 167 GLN Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 130 GLN Chi-restraints excluded: chain O residue 135 GLU Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 129 GLU Chi-restraints excluded: chain P residue 130 GLN Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 127 LEU Chi-restraints excluded: chain R residue 51 LYS 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 117 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 225 optimal weight: 2.9990 chunk 214 optimal weight: 0.6980 chunk 250 optimal weight: 8.9990 chunk 267 optimal weight: 4.9990 chunk 228 optimal weight: 6.9990 chunk 84 optimal weight: 0.1980 chunk 299 optimal weight: 0.9990 chunk 305 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 167 GLN O 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.074127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.059453 restraints weight = 51032.589| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 3.74 r_work: 0.2643 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23681 Z= 0.136 Angle : 0.531 12.033 32470 Z= 0.282 Chirality : 0.046 0.149 4165 Planarity : 0.003 0.050 4131 Dihedral : 4.145 25.117 3264 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.98 % Allowed : 15.25 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.15), residues: 3077 helix: 4.85 (0.16), residues: 657 sheet: 1.70 (0.17), residues: 807 loop : -1.87 (0.13), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 32 TYR 0.016 0.001 TYR D 98 PHE 0.025 0.001 PHE C 20 TRP 0.006 0.000 TRP L 114 HIS 0.003 0.000 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00275 (23681) covalent geometry : angle 0.53107 (32470) hydrogen bonds : bond 0.07505 ( 1087) hydrogen bonds : angle 4.23577 ( 3255) *********************** 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 498 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 421 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: C 11 PHE cc_start: 0.9264 (m-80) cc_final: 0.9043 (m-80) REVERT: C 31 GLU cc_start: 0.9133 (tm-30) cc_final: 0.8439 (tm-30) REVERT: C 32 ARG cc_start: 0.9038 (mmp80) cc_final: 0.8703 (tpp80) REVERT: C 35 GLU cc_start: 0.8407 (pm20) cc_final: 0.7825 (pm20) REVERT: C 43 GLU cc_start: 0.8619 (mp0) cc_final: 0.8151 (mp0) REVERT: C 175 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8741 (mm-30) REVERT: D 31 GLU cc_start: 0.9482 (tp30) cc_final: 0.9256 (mm-30) REVERT: D 86 ASN cc_start: 0.9021 (t0) cc_final: 0.8780 (t0) REVERT: D 155 GLU cc_start: 0.8565 (tt0) cc_final: 0.8228 (tt0) REVERT: F 31 GLU cc_start: 0.9554 (mm-30) cc_final: 0.9354 (mm-30) REVERT: F 129 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7296 (pm20) REVERT: G 31 GLU cc_start: 0.9506 (tp30) cc_final: 0.9024 (tp30) REVERT: G 49 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8083 (mt-10) REVERT: G 129 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7060 (pm20) REVERT: G 130 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8611 (mp10) REVERT: H 31 GLU cc_start: 0.9454 (tp30) cc_final: 0.8891 (tp30) REVERT: H 130 GLN cc_start: 0.9269 (OUTLIER) cc_final: 0.8873 (mp10) REVERT: I 32 ARG cc_start: 0.9418 (mmp80) cc_final: 0.9075 (mmp80) REVERT: J 47 SER cc_start: 0.9772 (m) cc_final: 0.9483 (t) REVERT: J 129 GLU cc_start: 0.7573 (pm20) cc_final: 0.6942 (pm20) REVERT: J 175 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8255 (mt-10) REVERT: K 43 GLU cc_start: 0.9289 (tt0) cc_final: 0.9003 (tm-30) REVERT: K 81 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8512 (tm-30) REVERT: L 32 ARG cc_start: 0.9344 (mmp80) cc_final: 0.9135 (mmp80) REVERT: L 59 GLU cc_start: -0.0298 (OUTLIER) cc_final: -0.0985 (pm20) REVERT: L 68 ASP cc_start: 0.7497 (m-30) cc_final: 0.7167 (t0) REVERT: M 49 GLU cc_start: 0.9015 (pt0) cc_final: 0.8790 (pt0) REVERT: M 129 GLU cc_start: 0.8026 (pm20) cc_final: 0.7544 (pm20) REVERT: O 35 GLU cc_start: 0.9359 (tt0) cc_final: 0.9131 (tp30) REVERT: P 130 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8476 (mp10) REVERT: Q 31 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8307 (tm-30) REVERT: Q 32 ARG cc_start: 0.9238 (mmp80) cc_final: 0.8723 (mmp80) REVERT: Q 59 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8679 (mm-30) REVERT: Q 84 ASP cc_start: 0.9208 (m-30) cc_final: 0.8786 (t0) REVERT: Q 129 GLU cc_start: 0.8099 (pm20) cc_final: 0.7789 (pm20) REVERT: Q 179 ASP cc_start: 0.9162 (p0) cc_final: 0.8841 (p0) REVERT: R 32 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.5900 (mmt180) REVERT: R 35 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8398 (mt-10) REVERT: R 129 GLU cc_start: 0.8057 (pm20) cc_final: 0.7589 (pm20) REVERT: S 31 GLU cc_start: 0.9492 (mm-30) cc_final: 0.9145 (mm-30) REVERT: S 35 GLU cc_start: 0.9045 (pt0) cc_final: 0.8730 (pt0) REVERT: S 81 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8033 (tm-30) outliers start: 77 outliers final: 25 residues processed: 457 average time/residue: 0.7705 time to fit residues: 391.6515 Evaluate side-chains 422 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 389 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 167 GLN 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 G residue 48 ILE Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain H residue 130 GLN Chi-restraints excluded: chain J residue 103 GLN 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 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 130 GLN Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 168 ARG Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain P residue 130 GLN Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 127 LEU Chi-restraints excluded: chain R residue 3 GLU Chi-restraints excluded: chain R residue 32 ARG Chi-restraints excluded: chain R residue 167 GLN Chi-restraints excluded: chain S residue 3 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 72 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 295 optimal weight: 10.0000 chunk 238 optimal weight: 4.9990 chunk 222 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 167 GLN ** O 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.071292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.056763 restraints weight = 52061.395| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 3.73 r_work: 0.2588 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 23681 Z= 0.267 Angle : 0.615 13.426 32470 Z= 0.327 Chirality : 0.048 0.157 4165 Planarity : 0.004 0.049 4131 Dihedral : 4.480 26.545 3264 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.44 % Allowed : 15.87 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.15), residues: 3077 helix: 4.64 (0.16), residues: 657 sheet: 1.66 (0.17), residues: 808 loop : -1.96 (0.13), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 168 TYR 0.024 0.001 TYR D 98 PHE 0.028 0.002 PHE K 20 TRP 0.006 0.001 TRP L 114 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00637 (23681) covalent geometry : angle 0.61524 (32470) hydrogen bonds : bond 0.08049 ( 1087) hydrogen bonds : angle 4.49950 ( 3255) *********************** 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 474 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 385 time to evaluate : 0.694 Fit side-chains REVERT: C 31 GLU cc_start: 0.9127 (tm-30) cc_final: 0.8364 (tm-30) REVERT: C 32 ARG cc_start: 0.9000 (mmp80) cc_final: 0.8636 (tpp-160) REVERT: C 35 GLU cc_start: 0.8390 (pm20) cc_final: 0.7864 (pm20) REVERT: C 43 GLU cc_start: 0.8629 (mp0) cc_final: 0.8200 (mp0) REVERT: D 31 GLU cc_start: 0.9499 (tp30) cc_final: 0.9152 (tp30) REVERT: D 155 GLU cc_start: 0.8629 (tt0) cc_final: 0.8266 (tt0) REVERT: F 129 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7157 (pm20) REVERT: G 129 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6903 (pm20) REVERT: G 130 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8642 (mp10) REVERT: H 3 GLU cc_start: 0.9090 (pm20) cc_final: 0.8663 (mp0) REVERT: H 31 GLU cc_start: 0.9462 (tp30) cc_final: 0.8893 (tp30) REVERT: H 130 GLN cc_start: 0.9281 (OUTLIER) cc_final: 0.8909 (mp10) REVERT: I 32 ARG cc_start: 0.9395 (mmp80) cc_final: 0.9045 (mmp80) REVERT: J 47 SER cc_start: 0.9795 (m) cc_final: 0.9486 (t) REVERT: J 129 GLU cc_start: 0.7556 (pm20) cc_final: 0.7247 (pm20) REVERT: J 130 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8185 (mp10) REVERT: K 43 GLU cc_start: 0.9325 (tt0) cc_final: 0.9026 (tm-30) REVERT: K 81 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8506 (tm-30) REVERT: L 59 GLU cc_start: 0.0157 (OUTLIER) cc_final: -0.0716 (pm20) REVERT: L 68 ASP cc_start: 0.7576 (m-30) cc_final: 0.7364 (t0) REVERT: M 129 GLU cc_start: 0.7743 (pm20) cc_final: 0.7118 (pm20) REVERT: N 130 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8660 (mp10) REVERT: O 35 GLU cc_start: 0.9338 (tt0) cc_final: 0.9111 (tt0) REVERT: P 35 GLU cc_start: 0.9294 (tt0) cc_final: 0.9067 (tp30) REVERT: Q 31 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8716 (tm-30) REVERT: Q 84 ASP cc_start: 0.9220 (m-30) cc_final: 0.8710 (t0) REVERT: Q 129 GLU cc_start: 0.8147 (pm20) cc_final: 0.7794 (pm20) REVERT: Q 179 ASP cc_start: 0.9162 (p0) cc_final: 0.8875 (p0) REVERT: R 32 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.5987 (mmt180) REVERT: R 35 GLU cc_start: 0.8891 (mt-10) cc_final: 0.7981 (mt-10) REVERT: R 129 GLU cc_start: 0.7982 (pm20) cc_final: 0.7550 (pm20) REVERT: S 31 GLU cc_start: 0.9499 (mm-30) cc_final: 0.9173 (mm-30) REVERT: S 35 GLU cc_start: 0.9071 (pt0) cc_final: 0.8813 (pt0) REVERT: S 81 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8646 (tm-30) REVERT: S 175 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8683 (mt-10) outliers start: 89 outliers final: 45 residues processed: 429 average time/residue: 0.8007 time to fit residues: 381.5751 Evaluate side-chains 423 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 369 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 137 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain D residue 167 GLN Chi-restraints excluded: chain F residue 0 THR Chi-restraints excluded: chain F residue 59 GLU 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 3 GLU Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 130 GLN Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 130 GLN Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 135 GLU Chi-restraints excluded: chain K residue 167 GLN Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 51 LYS 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 L residue 140 LEU Chi-restraints excluded: chain M residue 0 THR Chi-restraints excluded: chain M residue 41 LEU 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 50 ILE Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 130 GLN Chi-restraints excluded: chain N residue 137 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 127 LEU Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain R residue 3 GLU Chi-restraints excluded: chain R residue 32 ARG Chi-restraints excluded: chain S residue 3 GLU Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 130 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 224 optimal weight: 7.9990 chunk 298 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 289 optimal weight: 4.9990 chunk 292 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 249 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 264 optimal weight: 20.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.3045 r_free = 0.3045 target = 0.073386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.058678 restraints weight = 51547.026| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 3.75 r_work: 0.2628 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23681 Z= 0.157 Angle : 0.561 15.886 32470 Z= 0.296 Chirality : 0.047 0.172 4165 Planarity : 0.003 0.050 4131 Dihedral : 4.244 26.042 3264 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.83 % Allowed : 16.80 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.15), residues: 3077 helix: 4.74 (0.17), residues: 657 sheet: 1.66 (0.17), residues: 807 loop : -1.88 (0.14), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 168 TYR 0.018 0.001 TYR D 98 PHE 0.028 0.001 PHE R 20 TRP 0.006 0.001 TRP L 114 HIS 0.003 0.000 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00347 (23681) covalent geometry : angle 0.56067 (32470) hydrogen bonds : bond 0.07379 ( 1087) hydrogen bonds : angle 4.27462 ( 3255) *********************** 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 464 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 391 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: C 11 PHE cc_start: 0.9235 (m-80) cc_final: 0.9026 (m-80) REVERT: C 31 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8498 (tm-30) REVERT: C 32 ARG cc_start: 0.9033 (mmp80) cc_final: 0.8696 (tpp80) REVERT: C 35 GLU cc_start: 0.8367 (pm20) cc_final: 0.7586 (pm20) REVERT: C 43 GLU cc_start: 0.8604 (mp0) cc_final: 0.8156 (mp0) REVERT: C 148 THR cc_start: 0.9415 (OUTLIER) cc_final: 0.9208 (m) REVERT: D 31 GLU cc_start: 0.9494 (tp30) cc_final: 0.9265 (mm-30) REVERT: D 35 GLU cc_start: 0.9388 (tp30) cc_final: 0.8968 (tt0) REVERT: D 155 GLU cc_start: 0.8612 (tt0) cc_final: 0.8278 (tt0) REVERT: F 31 GLU cc_start: 0.9408 (mm-30) cc_final: 0.9184 (mm-30) REVERT: F 129 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7230 (pm20) REVERT: G 35 GLU cc_start: 0.9377 (tp30) cc_final: 0.9091 (tt0) REVERT: G 129 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7084 (pm20) REVERT: G 130 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8606 (mp10) REVERT: H 3 GLU cc_start: 0.9046 (pm20) cc_final: 0.8616 (mp0) REVERT: H 31 GLU cc_start: 0.9455 (tp30) cc_final: 0.8952 (tp30) REVERT: H 130 GLN cc_start: 0.9265 (OUTLIER) cc_final: 0.8870 (mp10) REVERT: I 32 ARG cc_start: 0.9391 (mmp80) cc_final: 0.9045 (mmp80) REVERT: J 47 SER cc_start: 0.9770 (m) cc_final: 0.9480 (t) REVERT: J 130 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8082 (mp10) REVERT: J 175 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8297 (mt-10) REVERT: K 81 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8503 (tm-30) REVERT: K 129 GLU cc_start: 0.7734 (pm20) cc_final: 0.7206 (pm20) REVERT: L 59 GLU cc_start: 0.0111 (OUTLIER) cc_final: -0.0737 (pm20) REVERT: M 49 GLU cc_start: 0.9011 (pt0) cc_final: 0.8791 (pt0) REVERT: M 129 GLU cc_start: 0.7831 (pm20) cc_final: 0.7242 (pm20) REVERT: N 135 GLU cc_start: 0.8875 (tt0) cc_final: 0.8532 (tt0) REVERT: O 35 GLU cc_start: 0.9331 (tt0) cc_final: 0.9085 (tp30) REVERT: Q 31 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8723 (tm-30) REVERT: Q 32 ARG cc_start: 0.9217 (mmp80) cc_final: 0.8989 (mmp80) REVERT: Q 84 ASP cc_start: 0.9189 (m-30) cc_final: 0.8721 (t0) REVERT: Q 129 GLU cc_start: 0.8071 (pm20) cc_final: 0.7710 (pm20) REVERT: Q 179 ASP cc_start: 0.9137 (p0) cc_final: 0.8838 (p0) REVERT: S 31 GLU cc_start: 0.9514 (mm-30) cc_final: 0.9192 (mm-30) REVERT: S 35 GLU cc_start: 0.9043 (pt0) cc_final: 0.8775 (pt0) REVERT: S 81 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8710 (tm-30) REVERT: S 175 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8710 (mt-10) outliers start: 73 outliers final: 35 residues processed: 430 average time/residue: 0.7675 time to fit residues: 365.8714 Evaluate side-chains 418 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 375 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 148 THR Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain D residue 41 LEU 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 140 LEU Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 129 GLU 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 29 SER Chi-restraints excluded: chain J residue 103 GLN Chi-restraints excluded: chain J residue 130 GLN 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 56 ILE Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain M residue 0 THR Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain N residue 137 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 117 LYS Chi-restraints excluded: chain Q residue 3 GLU Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 127 LEU Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain R residue 3 GLU Chi-restraints excluded: chain R residue 32 ARG Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain S residue 3 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 6 optimal weight: 6.9990 chunk 252 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 295 optimal weight: 6.9990 chunk 190 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 167 optimal weight: 0.0870 chunk 35 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 overall best weight: 3.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 167 GLN O 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.073240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.058482 restraints weight = 51357.959| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 3.76 r_work: 0.2624 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23681 Z= 0.175 Angle : 0.571 14.050 32470 Z= 0.301 Chirality : 0.047 0.164 4165 Planarity : 0.003 0.050 4131 Dihedral : 4.222 25.701 3264 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.71 % Allowed : 17.26 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.15), residues: 3077 helix: 4.72 (0.17), residues: 657 sheet: 1.65 (0.17), residues: 805 loop : -1.87 (0.14), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 32 TYR 0.015 0.001 TYR D 98 PHE 0.029 0.001 PHE R 20 TRP 0.005 0.001 TRP L 114 HIS 0.003 0.000 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00400 (23681) covalent geometry : angle 0.57107 (32470) hydrogen bonds : bond 0.07283 ( 1087) hydrogen bonds : angle 4.27556 ( 3255) *********************** 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 455 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 385 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: C 31 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8610 (tm-30) REVERT: C 35 GLU cc_start: 0.8366 (pm20) cc_final: 0.7605 (pm20) REVERT: C 43 GLU cc_start: 0.8630 (mp0) cc_final: 0.8168 (mp0) REVERT: C 148 THR cc_start: 0.9406 (OUTLIER) cc_final: 0.9191 (m) REVERT: D 31 GLU cc_start: 0.9478 (tp30) cc_final: 0.9173 (tp30) REVERT: D 155 GLU cc_start: 0.8663 (tt0) cc_final: 0.8301 (tt0) REVERT: F 31 GLU cc_start: 0.9415 (mm-30) cc_final: 0.9190 (mm-30) REVERT: F 129 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7183 (pm20) REVERT: G 35 GLU cc_start: 0.9401 (tp30) cc_final: 0.9114 (tt0) REVERT: G 129 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7059 (pm20) REVERT: G 130 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8613 (mp10) REVERT: H 31 GLU cc_start: 0.9466 (tp30) cc_final: 0.8979 (tp30) REVERT: H 49 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8672 (mt-10) REVERT: H 130 GLN cc_start: 0.9260 (OUTLIER) cc_final: 0.8869 (mp10) REVERT: I 32 ARG cc_start: 0.9387 (mmp80) cc_final: 0.9041 (mmp80) REVERT: J 31 GLU cc_start: 0.9447 (tp30) cc_final: 0.9205 (tp30) REVERT: J 47 SER cc_start: 0.9780 (m) cc_final: 0.9488 (t) REVERT: J 130 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8071 (mp10) REVERT: J 175 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8299 (mt-10) REVERT: K 81 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8477 (tm-30) REVERT: K 129 GLU cc_start: 0.7533 (pm20) cc_final: 0.7034 (pm20) REVERT: M 31 GLU cc_start: 0.9498 (mm-30) cc_final: 0.9057 (mm-30) REVERT: M 49 GLU cc_start: 0.9012 (pt0) cc_final: 0.8772 (pt0) REVERT: M 129 GLU cc_start: 0.7852 (pm20) cc_final: 0.7228 (pm20) REVERT: N 135 GLU cc_start: 0.8893 (tt0) cc_final: 0.8616 (tt0) REVERT: O 35 GLU cc_start: 0.9328 (tt0) cc_final: 0.9096 (tt0) REVERT: Q 31 GLU cc_start: 0.9083 (tm-30) cc_final: 0.8700 (tm-30) REVERT: Q 35 GLU cc_start: 0.9403 (tp30) cc_final: 0.9179 (tt0) REVERT: Q 84 ASP cc_start: 0.9198 (m-30) cc_final: 0.8715 (t0) REVERT: Q 129 GLU cc_start: 0.8119 (pm20) cc_final: 0.7775 (pm20) REVERT: Q 179 ASP cc_start: 0.9148 (p0) cc_final: 0.8850 (p0) REVERT: R 32 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.5807 (mmt180) REVERT: S 31 GLU cc_start: 0.9520 (mm-30) cc_final: 0.9203 (mm-30) REVERT: S 35 GLU cc_start: 0.9034 (pt0) cc_final: 0.8767 (pt0) REVERT: S 81 GLU cc_start: 0.9004 (tm-30) cc_final: 0.8699 (tm-30) REVERT: S 175 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8719 (mt-10) outliers start: 70 outliers final: 38 residues processed: 424 average time/residue: 0.7941 time to fit residues: 373.8220 Evaluate side-chains 417 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 371 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 83 ILE 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 148 THR 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 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 130 GLN Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 129 GLU 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 29 SER Chi-restraints excluded: chain J residue 103 GLN Chi-restraints excluded: chain J residue 130 GLN 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 56 ILE Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 137 THR 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 O residue 41 LEU Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain Q residue 3 GLU Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 127 LEU Chi-restraints excluded: chain R residue 3 GLU Chi-restraints excluded: chain R residue 32 ARG Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain S residue 3 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 259 optimal weight: 8.9990 chunk 261 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 293 optimal weight: 9.9990 chunk 209 optimal weight: 1.9990 chunk 262 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 288 optimal weight: 3.9990 chunk 236 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3065 r_free = 0.3065 target = 0.074540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.060019 restraints weight = 50790.050| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 3.69 r_work: 0.2654 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23681 Z= 0.141 Angle : 0.559 13.536 32470 Z= 0.293 Chirality : 0.046 0.151 4165 Planarity : 0.003 0.050 4131 Dihedral : 4.068 24.939 3264 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.01 % Allowed : 18.30 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.15), residues: 3077 helix: 4.74 (0.17), residues: 657 sheet: 1.67 (0.17), residues: 800 loop : -1.79 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 32 TYR 0.012 0.001 TYR C 38 PHE 0.030 0.001 PHE C 20 TRP 0.005 0.001 TRP L 114 HIS 0.003 0.000 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00307 (23681) covalent geometry : angle 0.55897 (32470) hydrogen bonds : bond 0.06846 ( 1087) hydrogen bonds : angle 4.14161 ( 3255) *********************** 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 456 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 404 time to evaluate : 0.857 Fit side-chains REVERT: C 31 GLU cc_start: 0.9286 (tm-30) cc_final: 0.8510 (tm-30) REVERT: C 32 ARG cc_start: 0.9004 (tpp80) cc_final: 0.8573 (mmp80) REVERT: C 35 GLU cc_start: 0.8668 (pm20) cc_final: 0.8067 (pm20) REVERT: C 43 GLU cc_start: 0.8606 (mp0) cc_final: 0.8134 (mp0) REVERT: D 31 GLU cc_start: 0.9457 (tp30) cc_final: 0.9152 (tp30) REVERT: D 35 GLU cc_start: 0.9402 (tp30) cc_final: 0.8934 (tt0) REVERT: D 155 GLU cc_start: 0.8641 (tt0) cc_final: 0.8286 (tt0) REVERT: F 31 GLU cc_start: 0.9424 (mm-30) cc_final: 0.9199 (mm-30) REVERT: F 129 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7216 (pm20) REVERT: G 31 GLU cc_start: 0.9527 (tp30) cc_final: 0.9245 (tp30) REVERT: G 35 GLU cc_start: 0.9363 (tp30) cc_final: 0.9029 (tt0) REVERT: G 129 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7027 (pm20) REVERT: H 31 GLU cc_start: 0.9462 (tp30) cc_final: 0.8949 (tp30) REVERT: H 35 GLU cc_start: 0.9387 (tp30) cc_final: 0.8989 (tt0) REVERT: H 130 GLN cc_start: 0.9234 (OUTLIER) cc_final: 0.8818 (mp10) REVERT: I 32 ARG cc_start: 0.9375 (mmp80) cc_final: 0.9032 (mmp80) REVERT: J 31 GLU cc_start: 0.9446 (tp30) cc_final: 0.9202 (tp30) REVERT: J 47 SER cc_start: 0.9760 (m) cc_final: 0.9491 (t) REVERT: J 175 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8364 (mt-10) REVERT: K 43 GLU cc_start: 0.9287 (tt0) cc_final: 0.9042 (tm-30) REVERT: K 81 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8485 (tm-30) REVERT: L 48 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.9001 (tt) REVERT: M 31 GLU cc_start: 0.9495 (mm-30) cc_final: 0.9078 (mm-30) REVERT: M 49 GLU cc_start: 0.9038 (pt0) cc_final: 0.8804 (pt0) REVERT: N 135 GLU cc_start: 0.8856 (tt0) cc_final: 0.8590 (tt0) REVERT: O 35 GLU cc_start: 0.9316 (tt0) cc_final: 0.9068 (tt0) REVERT: Q 31 GLU cc_start: 0.9063 (tm-30) cc_final: 0.8602 (tm-30) REVERT: Q 35 GLU cc_start: 0.9390 (tp30) cc_final: 0.9104 (tt0) REVERT: Q 59 GLU cc_start: 0.8847 (tp30) cc_final: 0.8397 (mm-30) REVERT: Q 84 ASP cc_start: 0.9204 (m-30) cc_final: 0.8712 (t0) REVERT: Q 179 ASP cc_start: 0.9137 (p0) cc_final: 0.8830 (p0) REVERT: S 31 GLU cc_start: 0.9514 (mm-30) cc_final: 0.9208 (mm-30) REVERT: S 35 GLU cc_start: 0.8963 (pt0) cc_final: 0.8682 (pt0) REVERT: S 175 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8702 (mt-10) outliers start: 52 outliers final: 34 residues processed: 433 average time/residue: 0.8374 time to fit residues: 402.5687 Evaluate side-chains 419 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 380 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 83 ILE 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 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 140 LEU Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 130 GLN Chi-restraints excluded: chain J residue 103 GLN Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 167 GLN Chi-restraints excluded: chain L residue 43 GLU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 137 THR 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 O residue 48 ILE Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain Q residue 3 GLU Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 127 LEU Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain S residue 3 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 146 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 42 optimal weight: 0.0170 chunk 22 optimal weight: 7.9990 chunk 198 optimal weight: 9.9990 chunk 277 optimal weight: 7.9990 chunk 169 optimal weight: 10.0000 chunk 259 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 242 optimal weight: 0.0020 chunk 197 optimal weight: 3.9990 overall best weight: 2.0032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 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 = 0.3076 r_free = 0.3076 target = 0.075179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.060340 restraints weight = 51304.222| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 3.76 r_work: 0.2662 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 23681 Z= 0.136 Angle : 0.570 13.015 32470 Z= 0.296 Chirality : 0.046 0.150 4165 Planarity : 0.003 0.050 4131 Dihedral : 3.980 23.638 3264 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.93 % Allowed : 19.12 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.15), residues: 3077 helix: 4.74 (0.17), residues: 655 sheet: 1.69 (0.17), residues: 805 loop : -1.73 (0.14), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 32 TYR 0.011 0.001 TYR D 38 PHE 0.034 0.001 PHE L 20 TRP 0.006 0.001 TRP L 114 HIS 0.002 0.000 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00298 (23681) covalent geometry : angle 0.57027 (32470) hydrogen bonds : bond 0.06572 ( 1087) hydrogen bonds : angle 4.10896 ( 3255) ********************** 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 460 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 410 time to evaluate : 0.962 Fit side-chains REVERT: C 31 GLU cc_start: 0.9212 (tm-30) cc_final: 0.8018 (tm-30) REVERT: C 32 ARG cc_start: 0.9028 (tpp80) cc_final: 0.8294 (mmp80) REVERT: C 35 GLU cc_start: 0.8627 (pm20) cc_final: 0.7830 (pm20) REVERT: C 43 GLU cc_start: 0.8608 (mp0) cc_final: 0.8141 (mp0) REVERT: D 31 GLU cc_start: 0.9476 (tp30) cc_final: 0.9252 (tp30) REVERT: D 35 GLU cc_start: 0.9411 (tp30) cc_final: 0.8940 (tt0) REVERT: D 155 GLU cc_start: 0.8634 (tt0) cc_final: 0.8282 (tt0) REVERT: F 31 GLU cc_start: 0.9423 (mm-30) cc_final: 0.9201 (mm-30) REVERT: F 129 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7246 (pm20) REVERT: G 31 GLU cc_start: 0.9532 (tp30) cc_final: 0.9255 (tp30) REVERT: G 35 GLU cc_start: 0.9375 (tp30) cc_final: 0.9075 (tt0) REVERT: G 129 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6982 (pm20) REVERT: H 31 GLU cc_start: 0.9469 (tp30) cc_final: 0.8907 (tp30) REVERT: H 35 GLU cc_start: 0.9386 (tp30) cc_final: 0.8960 (tt0) REVERT: H 130 GLN cc_start: 0.9232 (OUTLIER) cc_final: 0.8831 (mp10) REVERT: I 32 ARG cc_start: 0.9369 (mmp80) cc_final: 0.9035 (mmp80) REVERT: J 31 GLU cc_start: 0.9420 (tp30) cc_final: 0.9185 (tp30) REVERT: J 32 ARG cc_start: 0.9126 (mmp80) cc_final: 0.8780 (mmp80) REVERT: J 47 SER cc_start: 0.9764 (m) cc_final: 0.9504 (t) REVERT: J 81 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8725 (tp30) REVERT: J 175 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8399 (mt-10) REVERT: K 43 GLU cc_start: 0.9266 (tt0) cc_final: 0.9053 (tm-30) REVERT: K 81 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8495 (tm-30) REVERT: L 48 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.8994 (tt) REVERT: M 31 GLU cc_start: 0.9507 (mm-30) cc_final: 0.9113 (mm-30) REVERT: M 49 GLU cc_start: 0.9043 (pt0) cc_final: 0.8813 (pt0) REVERT: N 135 GLU cc_start: 0.8883 (tt0) cc_final: 0.8630 (tt0) REVERT: O 35 GLU cc_start: 0.9304 (tt0) cc_final: 0.9047 (tt0) REVERT: Q 31 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8549 (tm-30) REVERT: Q 35 GLU cc_start: 0.9413 (tp30) cc_final: 0.9082 (tt0) REVERT: Q 59 GLU cc_start: 0.8838 (tp30) cc_final: 0.8476 (mm-30) REVERT: Q 84 ASP cc_start: 0.9199 (m-30) cc_final: 0.8707 (t0) REVERT: Q 179 ASP cc_start: 0.9147 (p0) cc_final: 0.8844 (p0) REVERT: S 31 GLU cc_start: 0.9523 (mm-30) cc_final: 0.9222 (mm-30) REVERT: S 35 GLU cc_start: 0.8947 (pt0) cc_final: 0.8652 (pt0) REVERT: S 81 GLU cc_start: 0.9094 (tm-30) cc_final: 0.8705 (tm-30) REVERT: S 175 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8707 (mt-10) outliers start: 50 outliers final: 30 residues processed: 434 average time/residue: 0.8585 time to fit residues: 413.6606 Evaluate side-chains 420 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 385 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 83 ILE 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 E residue 48 ILE Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 130 GLN Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 103 GLN Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 167 GLN 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 127 LEU Chi-restraints excluded: chain L residue 137 THR 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 O residue 48 ILE Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain Q residue 3 GLU Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 127 LEU Chi-restraints excluded: chain S residue 3 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 225 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 ASN E 167 GLN M 167 GLN O 118 ASN O 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.074643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.060143 restraints weight = 50880.777| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 3.69 r_work: 0.2658 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 23681 Z= 0.154 Angle : 0.588 17.294 32470 Z= 0.306 Chirality : 0.047 0.152 4165 Planarity : 0.003 0.049 4131 Dihedral : 3.997 23.582 3264 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.15), residues: 3077 helix: 4.59 (0.17), residues: 669 sheet: 1.70 (0.17), residues: 805 loop : -1.75 (0.14), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 99 TYR 0.018 0.001 TYR C 38 PHE 0.029 0.001 PHE R 20 TRP 0.006 0.001 TRP L 114 HIS 0.002 0.000 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00351 (23681) covalent geometry : angle 0.58811 (32470) hydrogen bonds : bond 0.06626 ( 1087) hydrogen bonds : angle 4.13293 ( 3255) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8206.56 seconds wall clock time: 140 minutes 2.97 seconds (8402.97 seconds total)