Starting phenix.real_space_refine on Fri Mar 6 13:17:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xfv_66838/03_2026/9xfv_66838.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xfv_66838/03_2026/9xfv_66838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xfv_66838/03_2026/9xfv_66838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xfv_66838/03_2026/9xfv_66838.map" model { file = "/net/cci-nas-00/data/ceres_data/9xfv_66838/03_2026/9xfv_66838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xfv_66838/03_2026/9xfv_66838.cif" } resolution = 3.07 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= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 19425 2.51 5 N 5075 2.21 5 O 6225 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30825 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1233 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 4, 'TRANS': 168} Chain: "B" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1233 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 4, 'TRANS': 168} Chain: "C" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1233 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 4, 'TRANS': 168} Chain: "D" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1233 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 4, 'TRANS': 168} Chain: "E" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1233 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 4, 'TRANS': 168} Chain: "F" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1233 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 4, 'TRANS': 168} Chain: "G" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1233 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 4, 'TRANS': 168} Chain: "H" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1233 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 4, 'TRANS': 168} Chain: "I" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1233 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 4, 'TRANS': 168} Chain: "J" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1233 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 4, 'TRANS': 168} Chain: "K" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1233 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 4, 'TRANS': 168} Chain: "L" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1233 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 4, 'TRANS': 168} Chain: "M" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1233 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 4, 'TRANS': 168} Chain: "N" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1233 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 4, 'TRANS': 168} Chain: "O" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1233 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 4, 'TRANS': 168} Chain: "P" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1233 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 4, 'TRANS': 168} Chain: "Q" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1233 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 4, 'TRANS': 168} Chain: "R" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1233 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 4, 'TRANS': 168} Chain: "S" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1233 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 4, 'TRANS': 168} Chain: "T" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1233 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 4, 'TRANS': 168} Chain: "U" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1233 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 4, 'TRANS': 168} Chain: "V" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1233 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 4, 'TRANS': 168} Chain: "W" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1233 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 4, 'TRANS': 168} Chain: "X" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1233 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 4, 'TRANS': 168} Chain: "Z" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1233 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 4, 'TRANS': 168} Time building chain proxies: 6.23, per 1000 atoms: 0.20 Number of scatterers: 30825 At special positions: 0 Unit cell: (102.897, 102.897, 328.158, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 6225 8.00 N 5075 7.00 C 19425 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: 2.42 Conformation dependent library (CDL) restraints added in 1.8 seconds 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7650 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 2 sheets defined 30.4% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 84 through 100 Processing helix chain 'A' and resid 103 through 116 Processing helix chain 'A' and resid 122 through 137 Processing helix chain 'A' and resid 141 through 145 removed outlier: 3.543A pdb=" N GLY A 144 " --> pdb=" O ASP A 141 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 145 " --> pdb=" O VAL A 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 141 through 145' Processing helix chain 'B' and resid 84 through 100 Processing helix chain 'B' and resid 103 through 116 Processing helix chain 'B' and resid 122 through 137 removed outlier: 3.555A pdb=" N LEU B 135 " --> pdb=" O GLU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 145 removed outlier: 3.753A pdb=" N ALA B 145 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 100 Processing helix chain 'C' and resid 103 through 116 Processing helix chain 'C' and resid 122 through 137 removed outlier: 3.503A pdb=" N LEU C 135 " --> pdb=" O GLU C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 145 removed outlier: 3.800A pdb=" N ALA C 145 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 101 Processing helix chain 'D' and resid 103 through 116 Processing helix chain 'D' and resid 122 through 137 removed outlier: 3.567A pdb=" N LEU D 135 " --> pdb=" O GLU D 131 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 145 removed outlier: 3.793A pdb=" N ALA D 145 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 101 Processing helix chain 'E' and resid 103 through 116 Processing helix chain 'E' and resid 122 through 137 removed outlier: 3.508A pdb=" N LEU E 135 " --> pdb=" O GLU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 145 removed outlier: 3.775A pdb=" N ALA E 145 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 100 Processing helix chain 'F' and resid 103 through 116 Processing helix chain 'F' and resid 122 through 137 removed outlier: 3.552A pdb=" N LEU F 135 " --> pdb=" O GLU F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 145 removed outlier: 3.561A pdb=" N ALA F 145 " --> pdb=" O VAL F 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 100 Processing helix chain 'G' and resid 103 through 116 Processing helix chain 'G' and resid 122 through 137 removed outlier: 3.666A pdb=" N LEU G 135 " --> pdb=" O GLU G 131 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR G 136 " --> pdb=" O LEU G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 145 removed outlier: 3.837A pdb=" N ALA G 145 " --> pdb=" O VAL G 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 100 Processing helix chain 'H' and resid 103 through 116 Processing helix chain 'H' and resid 122 through 137 removed outlier: 3.529A pdb=" N LEU H 135 " --> pdb=" O GLU H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 145 removed outlier: 3.505A pdb=" N GLY H 144 " --> pdb=" O ASP H 141 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA H 145 " --> pdb=" O VAL H 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 141 through 145' Processing helix chain 'I' and resid 84 through 101 Processing helix chain 'I' and resid 103 through 116 Processing helix chain 'I' and resid 122 through 137 Processing helix chain 'I' and resid 141 through 145 removed outlier: 3.679A pdb=" N ALA I 145 " --> pdb=" O VAL I 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 101 Processing helix chain 'J' and resid 103 through 116 Processing helix chain 'J' and resid 122 through 137 removed outlier: 3.727A pdb=" N LEU J 135 " --> pdb=" O GLU J 131 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR J 136 " --> pdb=" O LEU J 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 145 removed outlier: 3.544A pdb=" N GLY J 144 " --> pdb=" O ASP J 141 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 100 Processing helix chain 'K' and resid 103 through 116 Processing helix chain 'K' and resid 122 through 137 Processing helix chain 'K' and resid 141 through 145 removed outlier: 3.925A pdb=" N ALA K 145 " --> pdb=" O VAL K 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 101 Processing helix chain 'L' and resid 103 through 116 Processing helix chain 'L' and resid 122 through 137 removed outlier: 3.537A pdb=" N LEU L 135 " --> pdb=" O GLU L 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 145 removed outlier: 3.925A pdb=" N ALA L 145 " --> pdb=" O VAL L 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 101 Processing helix chain 'M' and resid 103 through 116 Processing helix chain 'M' and resid 122 through 137 Processing helix chain 'M' and resid 141 through 145 removed outlier: 3.916A pdb=" N ALA M 145 " --> pdb=" O VAL M 142 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 101 Processing helix chain 'N' and resid 103 through 116 Processing helix chain 'N' and resid 122 through 137 Processing helix chain 'N' and resid 141 through 145 removed outlier: 3.898A pdb=" N ALA N 145 " --> pdb=" O VAL N 142 " (cutoff:3.500A) Processing helix chain 'O' and resid 84 through 101 Processing helix chain 'O' and resid 103 through 116 Processing helix chain 'O' and resid 122 through 137 removed outlier: 3.583A pdb=" N LYS O 134 " --> pdb=" O THR O 130 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU O 135 " --> pdb=" O GLU O 131 " (cutoff:3.500A) Processing helix chain 'O' and resid 141 through 145 removed outlier: 3.952A pdb=" N ALA O 145 " --> pdb=" O VAL O 142 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 101 Processing helix chain 'P' and resid 103 through 116 Processing helix chain 'P' and resid 122 through 137 removed outlier: 3.597A pdb=" N LYS P 134 " --> pdb=" O THR P 130 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU P 135 " --> pdb=" O GLU P 131 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR P 136 " --> pdb=" O LEU P 132 " (cutoff:3.500A) Processing helix chain 'P' and resid 141 through 145 removed outlier: 3.982A pdb=" N ALA P 145 " --> pdb=" O VAL P 142 " (cutoff:3.500A) Processing helix chain 'Q' and resid 84 through 100 Processing helix chain 'Q' and resid 103 through 116 Processing helix chain 'Q' and resid 122 through 137 removed outlier: 3.574A pdb=" N LEU Q 135 " --> pdb=" O GLU Q 131 " (cutoff:3.500A) Processing helix chain 'Q' and resid 141 through 145 removed outlier: 4.122A pdb=" N ALA Q 145 " --> pdb=" O VAL Q 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 100 Processing helix chain 'R' and resid 103 through 116 Processing helix chain 'R' and resid 122 through 137 Processing helix chain 'R' and resid 141 through 145 removed outlier: 3.766A pdb=" N ALA R 145 " --> pdb=" O VAL R 142 " (cutoff:3.500A) Processing helix chain 'S' and resid 84 through 101 Processing helix chain 'S' and resid 103 through 116 Processing helix chain 'S' and resid 122 through 137 Processing helix chain 'S' and resid 141 through 145 removed outlier: 3.900A pdb=" N ALA S 145 " --> pdb=" O VAL S 142 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 100 Processing helix chain 'T' and resid 103 through 116 Processing helix chain 'T' and resid 122 through 137 Processing helix chain 'T' and resid 141 through 145 removed outlier: 3.930A pdb=" N ALA T 145 " --> pdb=" O VAL T 142 " (cutoff:3.500A) Processing helix chain 'U' and resid 84 through 101 Processing helix chain 'U' and resid 103 through 116 Processing helix chain 'U' and resid 122 through 137 Processing helix chain 'U' and resid 141 through 145 removed outlier: 3.910A pdb=" N ALA U 145 " --> pdb=" O VAL U 142 " (cutoff:3.500A) Processing helix chain 'V' and resid 84 through 101 Processing helix chain 'V' and resid 103 through 116 Processing helix chain 'V' and resid 122 through 137 removed outlier: 3.559A pdb=" N LEU V 135 " --> pdb=" O GLU V 131 " (cutoff:3.500A) Processing helix chain 'V' and resid 141 through 145 removed outlier: 3.506A pdb=" N ALA V 145 " --> pdb=" O VAL V 142 " (cutoff:3.500A) Processing helix chain 'W' and resid 84 through 101 Processing helix chain 'W' and resid 103 through 116 removed outlier: 3.511A pdb=" N GLY W 116 " --> pdb=" O ALA W 112 " (cutoff:3.500A) Processing helix chain 'W' and resid 122 through 137 Processing helix chain 'W' and resid 141 through 145 removed outlier: 3.743A pdb=" N ALA W 145 " --> pdb=" O VAL W 142 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 101 Processing helix chain 'X' and resid 103 through 116 Processing helix chain 'X' and resid 122 through 137 Processing helix chain 'X' and resid 141 through 145 removed outlier: 3.823A pdb=" N ALA X 145 " --> pdb=" O VAL X 142 " (cutoff:3.500A) Processing helix chain 'Z' and resid 84 through 101 Processing helix chain 'Z' and resid 103 through 116 Processing helix chain 'Z' and resid 122 through 137 removed outlier: 3.692A pdb=" N LYS Z 134 " --> pdb=" O THR Z 130 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU Z 135 " --> pdb=" O GLU Z 131 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR Z 136 " --> pdb=" O LEU Z 132 " (cutoff:3.500A) Processing helix chain 'Z' and resid 141 through 145 removed outlier: 3.987A pdb=" N ALA Z 145 " --> pdb=" O VAL Z 142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 48 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 40 through 48 current: chain 'A' and resid 63 through 68 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 63 through 68 current: chain 'A' and resid 159 through 162 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 159 through 162 current: chain 'B' and resid 63 through 68 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 63 through 68 current: chain 'B' and resid 158 through 162 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 158 through 162 current: chain 'C' and resid 63 through 68 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 63 through 68 current: chain 'C' and resid 158 through 162 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 158 through 162 current: chain 'D' and resid 63 through 68 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 63 through 68 current: chain 'D' and resid 158 through 162 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 158 through 162 current: chain 'E' and resid 63 through 83 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 158 through 162 current: chain 'E' and resid 192 through 196 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 192 through 196 current: chain 'F' and resid 63 through 68 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 63 through 68 current: chain 'F' and resid 159 through 162 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 159 through 162 current: chain 'G' and resid 63 through 68 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 63 through 68 current: chain 'G' and resid 158 through 162 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 158 through 162 current: chain 'H' and resid 63 through 68 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 63 through 68 current: chain 'H' and resid 159 through 162 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 159 through 162 current: chain 'I' and resid 63 through 83 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 158 through 162 current: chain 'I' and resid 192 through 196 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 192 through 196 current: chain 'J' and resid 63 through 70 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 63 through 70 current: chain 'J' and resid 158 through 162 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 158 through 162 current: chain 'J' and resid 192 through 196 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 192 through 196 current: chain 'K' and resid 63 through 82 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 159 through 162 current: chain 'K' and resid 192 through 196 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 192 through 196 current: chain 'L' and resid 63 through 83 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 158 through 162 current: chain 'L' and resid 192 through 196 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 192 through 196 current: chain 'M' and resid 63 through 70 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 63 through 70 current: chain 'M' and resid 158 through 162 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 158 through 162 current: chain 'M' and resid 192 through 196 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 192 through 196 current: chain 'N' and resid 63 through 83 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 158 through 162 current: chain 'N' and resid 192 through 196 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 192 through 196 current: chain 'O' and resid 63 through 82 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 159 through 162 current: chain 'O' and resid 192 through 196 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 192 through 196 current: chain 'P' and resid 63 through 68 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 63 through 68 current: chain 'P' and resid 158 through 162 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 158 through 162 current: chain 'Q' and resid 72 through 83 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 158 through 162 current: chain 'Q' and resid 192 through 196 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 192 through 196 current: chain 'R' and resid 63 through 66 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 63 through 66 current: chain 'R' and resid 158 through 162 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 158 through 162 current: chain 'R' and resid 192 through 196 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 192 through 196 current: chain 'S' and resid 40 through 48 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 40 through 48 current: chain 'S' and resid 63 through 66 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 63 through 66 current: chain 'S' and resid 158 through 162 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 158 through 162 current: chain 'S' and resid 192 through 196 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 192 through 196 current: chain 'T' and resid 40 through 48 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 40 through 48 current: chain 'T' and resid 63 through 82 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 159 through 162 current: chain 'T' and resid 192 through 196 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 192 through 196 current: chain 'U' and resid 40 through 48 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 40 through 48 current: chain 'U' and resid 63 through 68 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 63 through 68 current: chain 'U' and resid 158 through 162 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 158 through 162 current: chain 'V' and resid 40 through 48 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 40 through 48 current: chain 'V' and resid 63 through 70 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 63 through 70 current: chain 'V' and resid 158 through 162 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 158 through 162 current: chain 'V' and resid 192 through 196 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 192 through 196 current: chain 'W' and resid 40 through 48 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 40 through 48 current: chain 'W' and resid 63 through 83 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 158 through 162 current: chain 'W' and resid 192 through 196 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 192 through 196 current: chain 'X' and resid 40 through 42 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 40 through 42 current: chain 'X' and resid 64 through 75 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 64 through 75 current: chain 'X' and resid 158 through 162 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 158 through 162 current: chain 'X' and resid 193 through 195 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 193 through 195 current: chain 'Z' and resid 72 through 83 Processing sheet with id=AA2, first strand: chain 'Q' and resid 180 through 183 removed outlier: 6.674A pdb=" N VAL Z 178 " --> pdb=" O ILE Z 70 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE Z 70 " --> pdb=" O VAL Z 178 " (cutoff:3.500A) 976 hydrogen bonds defined for protein. 2823 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: 5.57 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9992 1.34 - 1.45: 4291 1.45 - 1.57: 16867 1.57 - 1.69: 0 1.69 - 1.80: 200 Bond restraints: 31350 Sorted by residual: bond pdb=" CG MET G 183 " pdb=" SD MET G 183 " ideal model delta sigma weight residual 1.803 1.766 0.037 2.50e-02 1.60e+03 2.19e+00 bond pdb=" CB VAL H 92 " pdb=" CG2 VAL H 92 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.10e+00 bond pdb=" CB ILE C 42 " pdb=" CG2 ILE C 42 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.95e+00 bond pdb=" CB VAL B 92 " pdb=" CG2 VAL B 92 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.87e+00 bond pdb=" CB VAL R 159 " pdb=" CG2 VAL R 159 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.81e+00 ... (remaining 31345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 40722 1.42 - 2.84: 1593 2.84 - 4.26: 197 4.26 - 5.68: 30 5.68 - 7.10: 8 Bond angle restraints: 42550 Sorted by residual: angle pdb=" C ASP M 59 " pdb=" CA ASP M 59 " pdb=" CB ASP M 59 " ideal model delta sigma weight residual 115.79 109.94 5.85 1.19e+00 7.06e-01 2.42e+01 angle pdb=" C ASP H 59 " pdb=" CA ASP H 59 " pdb=" CB ASP H 59 " ideal model delta sigma weight residual 115.79 109.94 5.85 1.19e+00 7.06e-01 2.41e+01 angle pdb=" C ASP W 59 " pdb=" CA ASP W 59 " pdb=" CB ASP W 59 " ideal model delta sigma weight residual 115.79 110.03 5.76 1.19e+00 7.06e-01 2.34e+01 angle pdb=" C ASP V 59 " pdb=" CA ASP V 59 " pdb=" CB ASP V 59 " ideal model delta sigma weight residual 115.79 110.07 5.72 1.19e+00 7.06e-01 2.31e+01 angle pdb=" C ASP L 59 " pdb=" CA ASP L 59 " pdb=" CB ASP L 59 " ideal model delta sigma weight residual 115.79 110.10 5.69 1.19e+00 7.06e-01 2.29e+01 ... (remaining 42545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 15452 16.25 - 32.51: 1824 32.51 - 48.76: 655 48.76 - 65.01: 167 65.01 - 81.27: 52 Dihedral angle restraints: 18150 sinusoidal: 6125 harmonic: 12025 Sorted by residual: dihedral pdb=" CA SER E 156 " pdb=" C SER E 156 " pdb=" N ASP E 157 " pdb=" CA ASP E 157 " ideal model delta harmonic sigma weight residual 180.00 158.58 21.42 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA SER D 156 " pdb=" C SER D 156 " pdb=" N ASP D 157 " pdb=" CA ASP D 157 " ideal model delta harmonic sigma weight residual 180.00 159.94 20.06 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA SER G 156 " pdb=" C SER G 156 " pdb=" N ASP G 157 " pdb=" CA ASP G 157 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 18147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3205 0.039 - 0.078: 1233 0.078 - 0.117: 451 0.117 - 0.156: 81 0.156 - 0.195: 5 Chirality restraints: 4975 Sorted by residual: chirality pdb=" CB ILE K 198 " pdb=" CA ILE K 198 " pdb=" CG1 ILE K 198 " pdb=" CG2 ILE K 198 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.48e-01 chirality pdb=" CA ILE J 42 " pdb=" N ILE J 42 " pdb=" C ILE J 42 " pdb=" CB ILE J 42 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.68e-01 chirality pdb=" CB ILE S 181 " pdb=" CA ILE S 181 " pdb=" CG1 ILE S 181 " pdb=" CG2 ILE S 181 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.43e-01 ... (remaining 4972 not shown) Planarity restraints: 5525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 181 " 0.006 2.00e-02 2.50e+03 1.25e-02 1.56e+00 pdb=" C ILE R 181 " -0.022 2.00e-02 2.50e+03 pdb=" O ILE R 181 " 0.008 2.00e-02 2.50e+03 pdb=" N LYS R 182 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE Z 205 " 0.013 2.00e-02 2.50e+03 8.96e-03 1.40e+00 pdb=" CG PHE Z 205 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE Z 205 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE Z 205 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE Z 205 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE Z 205 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE Z 205 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE S 181 " 0.006 2.00e-02 2.50e+03 1.14e-02 1.30e+00 pdb=" C ILE S 181 " -0.020 2.00e-02 2.50e+03 pdb=" O ILE S 181 " 0.007 2.00e-02 2.50e+03 pdb=" N LYS S 182 " 0.007 2.00e-02 2.50e+03 ... (remaining 5522 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3747 2.75 - 3.28: 31328 3.28 - 3.82: 52997 3.82 - 4.36: 64256 4.36 - 4.90: 117420 Nonbonded interactions: 269748 Sorted by model distance: nonbonded pdb=" O SER A 155 " pdb=" OG SER A 155 " model vdw 2.207 3.040 nonbonded pdb=" O GLN F 104 " pdb=" ND2 ASN F 108 " model vdw 2.217 3.120 nonbonded pdb=" OD2 ASP Q 81 " pdb=" NE2 HIS Z 210 " model vdw 2.223 3.120 nonbonded pdb=" O SER F 155 " pdb=" OG SER F 155 " model vdw 2.228 3.040 nonbonded pdb=" OD2 ASP I 81 " pdb=" NE2 HIS J 210 " model vdw 2.266 3.120 ... (remaining 269743 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' 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' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' } 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: 0.010 Normalize map: mean=0, sd=1: 4.320 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: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 25.850 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 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 : 0.006 0.048 31350 Z= 0.272 Angle : 0.638 7.097 42550 Z= 0.391 Chirality : 0.047 0.195 4975 Planarity : 0.003 0.026 5525 Dihedral : 17.377 81.267 10500 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 0.44 % Allowed : 33.66 % Favored : 65.91 % 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 are not related in a simple way. whole: -1.80 (0.13), residues: 4275 helix: 1.51 (0.15), residues: 1175 sheet: -2.57 (0.14), residues: 1150 loop : -2.00 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 99 TYR 0.009 0.001 TYR V 102 PHE 0.018 0.002 PHE Z 205 TRP 0.010 0.001 TRP U 208 HIS 0.002 0.001 HIS T 210 Details of bonding type rmsd covalent geometry : bond 0.00621 (31350) covalent geometry : angle 0.63843 (42550) hydrogen bonds : bond 0.14944 ( 976) hydrogen bonds : angle 5.08412 ( 2823) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 403 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: B 47 ASN cc_start: 0.9324 (t0) cc_final: 0.9010 (t0) REVERT: D 157 ASP cc_start: 0.8575 (m-30) cc_final: 0.8368 (m-30) REVERT: J 71 LYS cc_start: 0.8469 (mttt) cc_final: 0.8169 (mttt) REVERT: M 47 ASN cc_start: 0.8892 (t0) cc_final: 0.8404 (t0) REVERT: M 135 LEU cc_start: 0.7900 (mp) cc_final: 0.7672 (mt) REVERT: N 134 LYS cc_start: 0.7909 (mttt) cc_final: 0.7682 (mttt) REVERT: O 47 ASN cc_start: 0.8542 (t0) cc_final: 0.8188 (t0) REVERT: P 130 THR cc_start: 0.7472 (t) cc_final: 0.6767 (p) REVERT: Q 47 ASN cc_start: 0.7660 (t0) cc_final: 0.7327 (t0) REVERT: Q 77 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.6860 (tm130) REVERT: Q 78 MET cc_start: 0.7866 (ttp) cc_final: 0.7460 (ttp) REVERT: Q 183 MET cc_start: 0.8385 (mtm) cc_final: 0.8167 (mtp) REVERT: R 47 ASN cc_start: 0.9091 (t0) cc_final: 0.8728 (t0) REVERT: U 182 LYS cc_start: 0.7890 (mmtt) cc_final: 0.7675 (mmtm) REVERT: V 71 LYS cc_start: 0.7828 (mttt) cc_final: 0.6986 (mtmt) REVERT: W 64 SER cc_start: 0.8437 (p) cc_final: 0.8155 (t) REVERT: W 75 MET cc_start: 0.8233 (mtp) cc_final: 0.7939 (mtp) REVERT: W 81 ASP cc_start: 0.7420 (m-30) cc_final: 0.7018 (m-30) REVERT: W 169 ASP cc_start: 0.7792 (t0) cc_final: 0.7578 (t0) REVERT: W 201 GLN cc_start: 0.8534 (mt0) cc_final: 0.8231 (mt0) REVERT: W 204 LYS cc_start: 0.8285 (mttp) cc_final: 0.8083 (mtmt) REVERT: X 64 SER cc_start: 0.8168 (p) cc_final: 0.7890 (p) REVERT: X 71 LYS cc_start: 0.6798 (mttt) cc_final: 0.6572 (mttt) REVERT: X 183 MET cc_start: 0.7678 (mtm) cc_final: 0.7356 (mtm) REVERT: Z 47 ASN cc_start: 0.7087 (t0) cc_final: 0.6703 (t0) outliers start: 14 outliers final: 6 residues processed: 411 average time/residue: 0.1621 time to fit residues: 112.1360 Evaluate side-chains 380 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 373 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain Q residue 77 GLN Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 86 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 0.0020 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 overall best weight: 1.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 ASN P 108 ASN Q 77 GLN U 201 GLN V 201 GLN W 49 ASN X 197 ASN X 201 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.115613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.095191 restraints weight = 37263.188| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.60 r_work: 0.3247 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 31350 Z= 0.226 Angle : 0.536 6.844 42550 Z= 0.300 Chirality : 0.045 0.173 4975 Planarity : 0.003 0.026 5525 Dihedral : 5.704 43.201 4411 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 3.81 % Allowed : 29.75 % Favored : 66.44 % 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 are not related in a simple way. whole: -1.66 (0.13), residues: 4275 helix: 1.84 (0.15), residues: 1175 sheet: -2.57 (0.14), residues: 1150 loop : -2.00 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 99 TYR 0.008 0.001 TYR D 152 PHE 0.018 0.002 PHE Z 205 TRP 0.012 0.002 TRP K 208 HIS 0.002 0.001 HIS F 210 Details of bonding type rmsd covalent geometry : bond 0.00538 (31350) covalent geometry : angle 0.53586 (42550) hydrogen bonds : bond 0.03752 ( 976) hydrogen bonds : angle 3.97343 ( 2823) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 353 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: C 99 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7302 (mmm160) REVERT: D 99 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.6144 (mmm160) REVERT: E 99 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7076 (mmm160) REVERT: F 135 LEU cc_start: 0.6501 (OUTLIER) cc_final: 0.6196 (mp) REVERT: H 99 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.6671 (mmm160) REVERT: H 172 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7925 (mt) REVERT: J 71 LYS cc_start: 0.8389 (mttt) cc_final: 0.8081 (mttt) REVERT: M 135 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7167 (mp) REVERT: M 182 LYS cc_start: 0.8624 (mttp) cc_final: 0.8286 (mttp) REVERT: O 204 LYS cc_start: 0.8765 (mtmm) cc_final: 0.8526 (mtmt) REVERT: Q 47 ASN cc_start: 0.8893 (OUTLIER) cc_final: 0.8622 (t0) REVERT: R 99 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.6119 (mmm160) REVERT: R 152 TYR cc_start: 0.8978 (t80) cc_final: 0.8707 (t80) REVERT: U 57 ASP cc_start: 0.8269 (t70) cc_final: 0.8065 (t70) REVERT: U 169 ASP cc_start: 0.8651 (t0) cc_final: 0.8397 (t0) REVERT: X 38 ASP cc_start: 0.7257 (t70) cc_final: 0.6912 (m-30) REVERT: X 102 TYR cc_start: 0.7904 (m-10) cc_final: 0.7624 (m-80) REVERT: X 183 MET cc_start: 0.8341 (mtm) cc_final: 0.8043 (mtm) REVERT: X 207 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8578 (ttm) outliers start: 122 outliers final: 68 residues processed: 444 average time/residue: 0.1671 time to fit residues: 122.9524 Evaluate side-chains 410 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 332 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 198 ILE Chi-restraints excluded: chain L residue 47 ASN Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain M residue 64 SER Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain M residue 156 SER Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 170 SER Chi-restraints excluded: chain N residue 47 ASN Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 86 SER Chi-restraints excluded: chain O residue 151 VAL Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain Q residue 47 ASN Chi-restraints excluded: chain Q residue 207 MET Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 99 ARG Chi-restraints excluded: chain R residue 192 SER Chi-restraints excluded: chain S residue 47 ASN Chi-restraints excluded: chain S residue 59 ASP Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 120 THR Chi-restraints excluded: chain T residue 47 ASN Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 86 SER Chi-restraints excluded: chain U residue 192 SER Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 183 MET Chi-restraints excluded: chain W residue 66 SER Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 207 MET Chi-restraints excluded: chain X residue 66 SER Chi-restraints excluded: chain X residue 86 SER Chi-restraints excluded: chain X residue 207 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 320 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 343 optimal weight: 0.8980 chunk 396 optimal weight: 1.9990 chunk 161 optimal weight: 9.9990 chunk 192 optimal weight: 1.9990 chunk 333 optimal weight: 5.9990 chunk 242 optimal weight: 2.9990 chunk 250 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 276 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 104 GLN K 108 ASN P 108 ASN S 201 GLN W 49 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.116462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.095993 restraints weight = 36972.951| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.57 r_work: 0.3228 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 31350 Z= 0.176 Angle : 0.489 6.217 42550 Z= 0.275 Chirality : 0.045 0.184 4975 Planarity : 0.003 0.025 5525 Dihedral : 5.400 21.923 4402 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 4.34 % Allowed : 28.88 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.13), residues: 4275 helix: 2.01 (0.15), residues: 1175 sheet: -2.52 (0.14), residues: 1150 loop : -1.97 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG T 99 TYR 0.006 0.001 TYR R 102 PHE 0.016 0.002 PHE Z 205 TRP 0.011 0.001 TRP K 208 HIS 0.001 0.001 HIS I 210 Details of bonding type rmsd covalent geometry : bond 0.00419 (31350) covalent geometry : angle 0.48895 (42550) hydrogen bonds : bond 0.03591 ( 976) hydrogen bonds : angle 3.74015 ( 2823) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 329 time to evaluate : 1.019 Fit side-chains REVERT: A 182 LYS cc_start: 0.8716 (mttm) cc_final: 0.8418 (mttp) REVERT: C 99 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7283 (mmm160) REVERT: E 99 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7055 (mmm160) REVERT: F 135 LEU cc_start: 0.6596 (OUTLIER) cc_final: 0.6206 (mp) REVERT: G 46 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8503 (mt) REVERT: G 81 ASP cc_start: 0.8441 (m-30) cc_final: 0.8132 (m-30) REVERT: G 99 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7132 (mmm160) REVERT: H 99 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.6607 (mmm160) REVERT: I 106 ASP cc_start: 0.7326 (m-30) cc_final: 0.6936 (m-30) REVERT: J 71 LYS cc_start: 0.8354 (mttt) cc_final: 0.8038 (mttt) REVERT: J 132 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8227 (mp) REVERT: M 108 ASN cc_start: 0.7710 (m110) cc_final: 0.7369 (m-40) REVERT: M 135 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7555 (mp) REVERT: M 182 LYS cc_start: 0.8497 (mttp) cc_final: 0.8139 (mttp) REVERT: M 183 MET cc_start: 0.8688 (mtm) cc_final: 0.8384 (mtm) REVERT: O 59 ASP cc_start: 0.6931 (OUTLIER) cc_final: 0.6602 (t0) REVERT: O 71 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7155 (mttt) REVERT: O 182 LYS cc_start: 0.8477 (mttm) cc_final: 0.8190 (mttm) REVERT: O 204 LYS cc_start: 0.8769 (mtmm) cc_final: 0.8514 (mtmt) REVERT: P 59 ASP cc_start: 0.6750 (OUTLIER) cc_final: 0.6275 (t0) REVERT: Q 47 ASN cc_start: 0.8895 (t0) cc_final: 0.8667 (t0) REVERT: R 152 TYR cc_start: 0.8933 (t80) cc_final: 0.8668 (t80) REVERT: T 38 ASP cc_start: 0.6779 (OUTLIER) cc_final: 0.6476 (m-30) REVERT: T 136 THR cc_start: 0.7358 (p) cc_final: 0.7076 (m) REVERT: V 81 ASP cc_start: 0.8252 (m-30) cc_final: 0.7614 (m-30) REVERT: X 102 TYR cc_start: 0.7950 (m-10) cc_final: 0.7680 (m-80) REVERT: X 183 MET cc_start: 0.8406 (mtm) cc_final: 0.8115 (mtm) outliers start: 139 outliers final: 89 residues processed: 437 average time/residue: 0.1658 time to fit residues: 120.9844 Evaluate side-chains 428 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 327 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 198 ILE Chi-restraints excluded: chain L residue 47 ASN Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 168 LEU Chi-restraints excluded: chain M residue 64 SER Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain M residue 156 SER Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 170 SER Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain N residue 47 ASN Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain O residue 47 ASN Chi-restraints excluded: chain O residue 59 ASP Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 151 VAL Chi-restraints excluded: chain P residue 59 ASP Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 207 MET Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 192 SER Chi-restraints excluded: chain S residue 47 ASN Chi-restraints excluded: chain S residue 59 ASP Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain T residue 38 ASP Chi-restraints excluded: chain T residue 47 ASN Chi-restraints excluded: chain T residue 131 GLU Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 83 LEU Chi-restraints excluded: chain U residue 86 SER Chi-restraints excluded: chain U residue 158 VAL Chi-restraints excluded: chain U residue 192 SER Chi-restraints excluded: chain V residue 77 GLN Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 183 MET Chi-restraints excluded: chain W residue 49 ASN Chi-restraints excluded: chain W residue 66 SER Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 207 MET Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 66 SER Chi-restraints excluded: chain X residue 86 SER Chi-restraints excluded: chain X residue 155 SER Chi-restraints excluded: chain X residue 207 MET Chi-restraints excluded: chain Z residue 198 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 234 optimal weight: 0.2980 chunk 279 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 276 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 308 optimal weight: 0.6980 chunk 147 optimal weight: 4.9990 chunk 235 optimal weight: 0.9980 chunk 354 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN J 104 GLN J 108 ASN P 108 ASN Q 108 ASN W 49 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.117820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.097158 restraints weight = 36559.941| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.59 r_work: 0.3229 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31350 Z= 0.140 Angle : 0.458 5.527 42550 Z= 0.259 Chirality : 0.044 0.167 4975 Planarity : 0.003 0.024 5525 Dihedral : 5.179 22.990 4402 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 3.91 % Allowed : 29.06 % Favored : 67.03 % 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 are not related in a simple way. whole: -1.37 (0.13), residues: 4275 helix: 2.22 (0.15), residues: 1175 sheet: -2.48 (0.14), residues: 1150 loop : -1.88 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 99 TYR 0.006 0.001 TYR R 102 PHE 0.014 0.001 PHE Z 205 TRP 0.010 0.001 TRP K 208 HIS 0.001 0.000 HIS M 210 Details of bonding type rmsd covalent geometry : bond 0.00332 (31350) covalent geometry : angle 0.45826 (42550) hydrogen bonds : bond 0.03290 ( 976) hydrogen bonds : angle 3.57269 ( 2823) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 328 time to evaluate : 0.958 Fit side-chains REVERT: A 182 LYS cc_start: 0.8719 (mttm) cc_final: 0.8463 (mttp) REVERT: B 135 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6333 (mt) REVERT: E 99 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7032 (mmm160) REVERT: F 135 LEU cc_start: 0.6646 (OUTLIER) cc_final: 0.6230 (mp) REVERT: G 46 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8479 (mt) REVERT: G 81 ASP cc_start: 0.8361 (m-30) cc_final: 0.7863 (m-30) REVERT: G 99 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7050 (mmm160) REVERT: H 99 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.6638 (mmm160) REVERT: I 106 ASP cc_start: 0.7266 (m-30) cc_final: 0.6929 (m-30) REVERT: J 71 LYS cc_start: 0.8341 (mttt) cc_final: 0.8018 (mttt) REVERT: J 132 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8200 (mp) REVERT: M 182 LYS cc_start: 0.8481 (mttp) cc_final: 0.8124 (mttp) REVERT: M 183 MET cc_start: 0.8620 (mtm) cc_final: 0.8251 (mtm) REVERT: N 134 LYS cc_start: 0.8022 (mttt) cc_final: 0.7816 (mtmt) REVERT: O 59 ASP cc_start: 0.6955 (OUTLIER) cc_final: 0.6588 (t0) REVERT: O 204 LYS cc_start: 0.8871 (mtmm) cc_final: 0.8636 (mtmt) REVERT: P 59 ASP cc_start: 0.6727 (OUTLIER) cc_final: 0.6283 (t0) REVERT: Q 47 ASN cc_start: 0.8879 (OUTLIER) cc_final: 0.8626 (t0) REVERT: R 99 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8121 (tpt170) REVERT: R 152 TYR cc_start: 0.8907 (t80) cc_final: 0.8685 (t80) REVERT: T 38 ASP cc_start: 0.6739 (OUTLIER) cc_final: 0.6445 (m-30) REVERT: T 136 THR cc_start: 0.7326 (p) cc_final: 0.7074 (m) REVERT: V 59 ASP cc_start: 0.6458 (OUTLIER) cc_final: 0.5750 (t0) REVERT: W 49 ASN cc_start: 0.8461 (OUTLIER) cc_final: 0.7780 (m110) REVERT: W 134 LYS cc_start: 0.8095 (mttt) cc_final: 0.7742 (mttt) REVERT: X 59 ASP cc_start: 0.6152 (OUTLIER) cc_final: 0.5748 (t0) REVERT: X 102 TYR cc_start: 0.7955 (m-10) cc_final: 0.7644 (m-80) REVERT: X 183 MET cc_start: 0.8428 (mtm) cc_final: 0.8118 (mtm) outliers start: 125 outliers final: 93 residues processed: 433 average time/residue: 0.1613 time to fit residues: 117.5127 Evaluate side-chains 425 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 317 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 198 ILE Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain L residue 71 LYS Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 168 LEU Chi-restraints excluded: chain M residue 64 SER Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain M residue 156 SER Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain N residue 47 ASN Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain O residue 47 ASN Chi-restraints excluded: chain O residue 59 ASP Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 151 VAL Chi-restraints excluded: chain P residue 59 ASP Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain P residue 120 THR Chi-restraints excluded: chain P residue 198 ILE Chi-restraints excluded: chain Q residue 47 ASN Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 207 MET Chi-restraints excluded: chain R residue 59 ASP Chi-restraints excluded: chain R residue 64 SER Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 99 ARG Chi-restraints excluded: chain R residue 192 SER Chi-restraints excluded: chain S residue 59 ASP Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain T residue 38 ASP Chi-restraints excluded: chain T residue 47 ASN Chi-restraints excluded: chain T residue 131 GLU Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 83 LEU Chi-restraints excluded: chain U residue 86 SER Chi-restraints excluded: chain U residue 158 VAL Chi-restraints excluded: chain U residue 192 SER Chi-restraints excluded: chain V residue 47 ASN Chi-restraints excluded: chain V residue 59 ASP Chi-restraints excluded: chain V residue 77 GLN Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 183 MET Chi-restraints excluded: chain W residue 47 ASN Chi-restraints excluded: chain W residue 49 ASN Chi-restraints excluded: chain W residue 66 SER Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 156 SER Chi-restraints excluded: chain W residue 207 MET Chi-restraints excluded: chain X residue 59 ASP Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 66 SER Chi-restraints excluded: chain X residue 86 SER Chi-restraints excluded: chain X residue 207 MET Chi-restraints excluded: chain Z residue 198 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 233 optimal weight: 3.9990 chunk 307 optimal weight: 4.9990 chunk 341 optimal weight: 4.9990 chunk 280 optimal weight: 7.9990 chunk 298 optimal weight: 4.9990 chunk 310 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 332 optimal weight: 4.9990 chunk 380 optimal weight: 6.9990 chunk 368 optimal weight: 0.0020 chunk 159 optimal weight: 6.9990 overall best weight: 2.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 108 ASN Q 108 ASN W 49 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.112179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.091740 restraints weight = 37612.575| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.61 r_work: 0.3145 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 31350 Z= 0.322 Angle : 0.584 6.479 42550 Z= 0.326 Chirality : 0.048 0.168 4975 Planarity : 0.003 0.026 5525 Dihedral : 5.797 23.435 4400 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.56 % Favored : 88.44 % Rotamer: Outliers : 4.91 % Allowed : 28.53 % Favored : 66.56 % 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 are not related in a simple way. whole: -1.70 (0.13), residues: 4275 helix: 1.86 (0.15), residues: 1175 sheet: -2.59 (0.15), residues: 1150 loop : -2.07 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 99 TYR 0.009 0.001 TYR R 102 PHE 0.016 0.002 PHE J 190 TRP 0.008 0.002 TRP X 208 HIS 0.002 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00767 (31350) covalent geometry : angle 0.58436 (42550) hydrogen bonds : bond 0.04208 ( 976) hydrogen bonds : angle 3.85333 ( 2823) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 348 time to evaluate : 0.983 Fit side-chains REVERT: A 182 LYS cc_start: 0.8731 (mttm) cc_final: 0.8489 (mttp) REVERT: B 99 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.6081 (mmm160) REVERT: B 135 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6532 (mt) REVERT: C 99 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7287 (mmm160) REVERT: D 99 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.6212 (mmm160) REVERT: E 99 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7133 (mmm160) REVERT: E 204 LYS cc_start: 0.8871 (mtmt) cc_final: 0.8617 (mtmm) REVERT: F 135 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6375 (mp) REVERT: G 46 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8608 (mt) REVERT: G 99 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7080 (mmm160) REVERT: H 99 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.6397 (mmm160) REVERT: H 172 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7953 (mt) REVERT: I 106 ASP cc_start: 0.7585 (m-30) cc_final: 0.7219 (m-30) REVERT: J 71 LYS cc_start: 0.8400 (mttt) cc_final: 0.8078 (mttt) REVERT: J 132 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8207 (mp) REVERT: M 135 LEU cc_start: 0.7838 (mp) cc_final: 0.7526 (mt) REVERT: M 182 LYS cc_start: 0.8638 (mttp) cc_final: 0.8285 (mttp) REVERT: O 59 ASP cc_start: 0.6920 (OUTLIER) cc_final: 0.6485 (t0) REVERT: O 71 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7229 (mttt) REVERT: O 81 ASP cc_start: 0.8204 (m-30) cc_final: 0.7791 (m-30) REVERT: O 204 LYS cc_start: 0.8741 (mtmm) cc_final: 0.8459 (mtmt) REVERT: P 59 ASP cc_start: 0.6887 (OUTLIER) cc_final: 0.6492 (t0) REVERT: P 207 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8480 (ptt) REVERT: Q 47 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8650 (t0) REVERT: R 99 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.6140 (mmm160) REVERT: T 38 ASP cc_start: 0.7023 (OUTLIER) cc_final: 0.6779 (t70) REVERT: X 38 ASP cc_start: 0.7288 (t70) cc_final: 0.6914 (m-30) REVERT: X 183 MET cc_start: 0.8637 (mtm) cc_final: 0.8330 (mtm) REVERT: Z 90 SER cc_start: 0.7860 (p) cc_final: 0.7594 (m) outliers start: 157 outliers final: 114 residues processed: 469 average time/residue: 0.1677 time to fit residues: 129.7344 Evaluate side-chains 468 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 336 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 183 MET Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 198 ILE Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain L residue 47 ASN Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 168 LEU Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 170 SER Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain N residue 47 ASN Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain O residue 47 ASN Chi-restraints excluded: chain O residue 59 ASP Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain O residue 151 VAL Chi-restraints excluded: chain P residue 59 ASP Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 120 THR Chi-restraints excluded: chain P residue 207 MET Chi-restraints excluded: chain Q residue 47 ASN Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 207 MET Chi-restraints excluded: chain R residue 59 ASP Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 99 ARG Chi-restraints excluded: chain R residue 192 SER Chi-restraints excluded: chain S residue 47 ASN Chi-restraints excluded: chain S residue 59 ASP Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain T residue 38 ASP Chi-restraints excluded: chain T residue 47 ASN Chi-restraints excluded: chain T residue 158 VAL Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 83 LEU Chi-restraints excluded: chain U residue 86 SER Chi-restraints excluded: chain U residue 158 VAL Chi-restraints excluded: chain U residue 176 VAL Chi-restraints excluded: chain U residue 192 SER Chi-restraints excluded: chain V residue 47 ASN Chi-restraints excluded: chain V residue 77 GLN Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 183 MET Chi-restraints excluded: chain V residue 187 THR Chi-restraints excluded: chain W residue 49 ASN Chi-restraints excluded: chain W residue 66 SER Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 156 SER Chi-restraints excluded: chain W residue 207 MET Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 66 SER Chi-restraints excluded: chain X residue 86 SER Chi-restraints excluded: chain X residue 155 SER Chi-restraints excluded: chain X residue 158 VAL Chi-restraints excluded: chain X residue 187 THR Chi-restraints excluded: chain X residue 207 MET Chi-restraints excluded: chain Z residue 47 ASN Chi-restraints excluded: chain Z residue 70 ILE Chi-restraints excluded: chain Z residue 81 ASP Chi-restraints excluded: chain Z residue 120 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 337 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 363 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 365 optimal weight: 10.0000 chunk 196 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 189 optimal weight: 0.9980 chunk 260 optimal weight: 0.5980 chunk 381 optimal weight: 4.9990 chunk 279 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 49 ASN M 108 ASN V 201 GLN W 49 ASN Z 49 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.116495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.095953 restraints weight = 36903.612| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.59 r_work: 0.3213 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 31350 Z= 0.150 Angle : 0.466 5.489 42550 Z= 0.263 Chirality : 0.044 0.155 4975 Planarity : 0.003 0.022 5525 Dihedral : 5.295 23.107 4400 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 4.50 % Allowed : 29.47 % Favored : 66.03 % 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 are not related in a simple way. whole: -1.41 (0.13), residues: 4275 helix: 2.24 (0.15), residues: 1175 sheet: -2.54 (0.14), residues: 1150 loop : -1.89 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 99 TYR 0.006 0.001 TYR R 102 PHE 0.013 0.001 PHE D 205 TRP 0.011 0.001 TRP U 208 HIS 0.001 0.000 HIS M 210 Details of bonding type rmsd covalent geometry : bond 0.00356 (31350) covalent geometry : angle 0.46635 (42550) hydrogen bonds : bond 0.03339 ( 976) hydrogen bonds : angle 3.58945 ( 2823) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 317 time to evaluate : 0.992 Fit side-chains REVERT: A 182 LYS cc_start: 0.8696 (mttm) cc_final: 0.8444 (mttp) REVERT: B 99 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.6038 (mmm160) REVERT: B 135 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6471 (mt) REVERT: C 99 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7253 (mmm160) REVERT: E 99 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.6945 (mmm160) REVERT: F 135 LEU cc_start: 0.6751 (OUTLIER) cc_final: 0.6336 (mp) REVERT: G 99 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7156 (mmm160) REVERT: H 99 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.6653 (mmm160) REVERT: J 71 LYS cc_start: 0.8354 (mttt) cc_final: 0.8019 (mttt) REVERT: J 132 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8209 (mp) REVERT: M 99 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.6292 (mmm160) REVERT: N 134 LYS cc_start: 0.8015 (mttt) cc_final: 0.7761 (mtmt) REVERT: O 59 ASP cc_start: 0.6962 (OUTLIER) cc_final: 0.6610 (t0) REVERT: O 71 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7200 (mttt) REVERT: O 99 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7969 (tpt170) REVERT: O 182 LYS cc_start: 0.8566 (mttp) cc_final: 0.8196 (mttm) REVERT: O 204 LYS cc_start: 0.8883 (mtmm) cc_final: 0.8622 (mtmt) REVERT: P 130 THR cc_start: 0.8128 (OUTLIER) cc_final: 0.7522 (p) REVERT: P 204 LYS cc_start: 0.9014 (mtmm) cc_final: 0.8794 (mtmt) REVERT: P 207 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8524 (ptt) REVERT: Q 47 ASN cc_start: 0.8896 (t0) cc_final: 0.8655 (t0) REVERT: R 99 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.6168 (mmm160) REVERT: R 152 TYR cc_start: 0.8950 (t80) cc_final: 0.8591 (t80) REVERT: R 196 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.8150 (m-40) REVERT: W 134 LYS cc_start: 0.8089 (mttt) cc_final: 0.7693 (mttt) REVERT: X 102 TYR cc_start: 0.7970 (m-10) cc_final: 0.7705 (m-80) REVERT: X 183 MET cc_start: 0.8591 (mtm) cc_final: 0.8329 (mtm) REVERT: Z 99 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7382 (mmm160) outliers start: 144 outliers final: 105 residues processed: 429 average time/residue: 0.1695 time to fit residues: 120.1791 Evaluate side-chains 433 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 311 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 198 ILE Chi-restraints excluded: chain L residue 47 ASN Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 168 LEU Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 99 ARG Chi-restraints excluded: chain M residue 156 SER Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 170 SER Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain N residue 47 ASN Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain O residue 47 ASN Chi-restraints excluded: chain O residue 59 ASP Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 99 ARG Chi-restraints excluded: chain O residue 151 VAL Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain P residue 130 THR Chi-restraints excluded: chain P residue 198 ILE Chi-restraints excluded: chain P residue 207 MET Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 168 LEU Chi-restraints excluded: chain Q residue 207 MET Chi-restraints excluded: chain R residue 59 ASP Chi-restraints excluded: chain R residue 64 SER Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 99 ARG Chi-restraints excluded: chain R residue 192 SER Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain S residue 59 ASP Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain T residue 47 ASN Chi-restraints excluded: chain T residue 131 GLU Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 83 LEU Chi-restraints excluded: chain U residue 86 SER Chi-restraints excluded: chain U residue 158 VAL Chi-restraints excluded: chain U residue 176 VAL Chi-restraints excluded: chain U residue 192 SER Chi-restraints excluded: chain V residue 77 GLN Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 183 MET Chi-restraints excluded: chain W residue 49 ASN Chi-restraints excluded: chain W residue 66 SER Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 156 SER Chi-restraints excluded: chain W residue 207 MET Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 66 SER Chi-restraints excluded: chain X residue 86 SER Chi-restraints excluded: chain X residue 158 VAL Chi-restraints excluded: chain X residue 207 MET Chi-restraints excluded: chain Z residue 47 ASN Chi-restraints excluded: chain Z residue 99 ARG Chi-restraints excluded: chain Z residue 120 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 128 optimal weight: 4.9990 chunk 189 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 420 optimal weight: 0.4980 chunk 226 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 49 ASN Z 49 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.112841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.092338 restraints weight = 37594.082| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.61 r_work: 0.3208 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 31350 Z= 0.273 Angle : 0.548 5.782 42550 Z= 0.307 Chirality : 0.046 0.169 4975 Planarity : 0.003 0.024 5525 Dihedral : 5.692 22.534 4400 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 5.03 % Allowed : 28.75 % Favored : 66.22 % 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 are not related in a simple way. whole: -1.60 (0.13), residues: 4275 helix: 1.89 (0.15), residues: 1200 sheet: -2.63 (0.15), residues: 1150 loop : -1.95 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 99 TYR 0.010 0.001 TYR R 102 PHE 0.014 0.002 PHE J 190 TRP 0.008 0.001 TRP X 208 HIS 0.001 0.001 HIS I 210 Details of bonding type rmsd covalent geometry : bond 0.00652 (31350) covalent geometry : angle 0.54841 (42550) hydrogen bonds : bond 0.03941 ( 976) hydrogen bonds : angle 3.75247 ( 2823) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 337 time to evaluate : 1.104 Fit side-chains REVERT: B 99 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.6044 (mmm160) REVERT: B 135 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6491 (mt) REVERT: C 99 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7315 (mmm160) REVERT: C 183 MET cc_start: 0.8793 (mtm) cc_final: 0.8339 (mtm) REVERT: E 99 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7077 (mmm160) REVERT: E 204 LYS cc_start: 0.8868 (mtmt) cc_final: 0.8616 (mtmm) REVERT: F 135 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6394 (mp) REVERT: G 99 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7111 (mmm160) REVERT: H 99 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.6436 (mmm160) REVERT: I 106 ASP cc_start: 0.7569 (m-30) cc_final: 0.7229 (m-30) REVERT: J 71 LYS cc_start: 0.8388 (mttt) cc_final: 0.8071 (mttt) REVERT: J 132 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8206 (mp) REVERT: M 99 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.6255 (mmm160) REVERT: M 135 LEU cc_start: 0.7773 (mp) cc_final: 0.7402 (mt) REVERT: M 182 LYS cc_start: 0.8621 (mttp) cc_final: 0.8354 (mttp) REVERT: O 59 ASP cc_start: 0.7002 (OUTLIER) cc_final: 0.6613 (t0) REVERT: O 71 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7257 (mttt) REVERT: O 182 LYS cc_start: 0.8627 (mttp) cc_final: 0.8414 (mttm) REVERT: O 204 LYS cc_start: 0.8800 (mtmm) cc_final: 0.8516 (mtmt) REVERT: P 99 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7652 (mmm160) REVERT: P 130 THR cc_start: 0.8129 (OUTLIER) cc_final: 0.7521 (p) REVERT: P 132 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.8028 (mt) REVERT: Q 47 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8661 (t0) REVERT: R 99 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.6121 (mmm160) REVERT: X 38 ASP cc_start: 0.7272 (t70) cc_final: 0.6933 (m-30) REVERT: X 77 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6344 (mm-40) REVERT: X 183 MET cc_start: 0.8654 (mtm) cc_final: 0.8329 (mtm) REVERT: Z 99 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7959 (tpt170) outliers start: 161 outliers final: 120 residues processed: 461 average time/residue: 0.1743 time to fit residues: 132.0963 Evaluate side-chains 467 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 329 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 207 MET Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 198 ILE Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain L residue 47 ASN Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 168 LEU Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 99 ARG Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain M residue 156 SER Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 170 SER Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain N residue 47 ASN Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain O residue 47 ASN Chi-restraints excluded: chain O residue 59 ASP Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 151 VAL Chi-restraints excluded: chain O residue 168 LEU Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain P residue 99 ARG Chi-restraints excluded: chain P residue 130 THR Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain P residue 198 ILE Chi-restraints excluded: chain Q residue 47 ASN Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 168 LEU Chi-restraints excluded: chain Q residue 207 MET Chi-restraints excluded: chain R residue 59 ASP Chi-restraints excluded: chain R residue 64 SER Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 99 ARG Chi-restraints excluded: chain R residue 192 SER Chi-restraints excluded: chain S residue 47 ASN Chi-restraints excluded: chain S residue 59 ASP Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain T residue 47 ASN Chi-restraints excluded: chain T residue 158 VAL Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 83 LEU Chi-restraints excluded: chain U residue 86 SER Chi-restraints excluded: chain U residue 158 VAL Chi-restraints excluded: chain U residue 176 VAL Chi-restraints excluded: chain U residue 192 SER Chi-restraints excluded: chain V residue 47 ASN Chi-restraints excluded: chain V residue 77 GLN Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 183 MET Chi-restraints excluded: chain W residue 49 ASN Chi-restraints excluded: chain W residue 66 SER Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 156 SER Chi-restraints excluded: chain W residue 207 MET Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 66 SER Chi-restraints excluded: chain X residue 77 GLN Chi-restraints excluded: chain X residue 86 SER Chi-restraints excluded: chain X residue 155 SER Chi-restraints excluded: chain X residue 158 VAL Chi-restraints excluded: chain X residue 172 LEU Chi-restraints excluded: chain X residue 207 MET Chi-restraints excluded: chain Z residue 47 ASN Chi-restraints excluded: chain Z residue 70 ILE Chi-restraints excluded: chain Z residue 99 ARG Chi-restraints excluded: chain Z residue 120 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 372 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 394 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 380 optimal weight: 4.9990 chunk 365 optimal weight: 9.9990 chunk 366 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 392 optimal weight: 1.9990 chunk 383 optimal weight: 0.5980 chunk 397 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 49 ASN Q 108 ASN W 49 ASN Z 49 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.114314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.093735 restraints weight = 37322.682| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.62 r_work: 0.3229 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 31350 Z= 0.211 Angle : 0.506 5.560 42550 Z= 0.284 Chirality : 0.045 0.164 4975 Planarity : 0.003 0.023 5525 Dihedral : 5.526 23.622 4400 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 4.78 % Allowed : 29.03 % Favored : 66.19 % 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 are not related in a simple way. whole: -1.52 (0.13), residues: 4275 helix: 2.12 (0.15), residues: 1175 sheet: -2.65 (0.14), residues: 1150 loop : -1.93 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 99 TYR 0.008 0.001 TYR R 102 PHE 0.013 0.002 PHE D 205 TRP 0.010 0.001 TRP U 208 HIS 0.001 0.000 HIS I 210 Details of bonding type rmsd covalent geometry : bond 0.00504 (31350) covalent geometry : angle 0.50596 (42550) hydrogen bonds : bond 0.03636 ( 976) hydrogen bonds : angle 3.69165 ( 2823) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 319 time to evaluate : 0.917 Fit side-chains REVERT: B 99 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.5950 (mmm160) REVERT: B 135 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6430 (mt) REVERT: C 99 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7264 (mmm160) REVERT: C 183 MET cc_start: 0.8795 (mtm) cc_final: 0.8255 (mtm) REVERT: E 99 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7069 (mmm160) REVERT: E 204 LYS cc_start: 0.8876 (mtmt) cc_final: 0.8626 (mtmm) REVERT: F 135 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6406 (mp) REVERT: G 99 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7147 (mmm160) REVERT: H 99 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.6610 (mmm160) REVERT: I 106 ASP cc_start: 0.7530 (m-30) cc_final: 0.7205 (m-30) REVERT: J 71 LYS cc_start: 0.8349 (mttt) cc_final: 0.7992 (mttt) REVERT: J 132 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8186 (mp) REVERT: M 99 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.6310 (mmm160) REVERT: M 135 LEU cc_start: 0.7723 (mp) cc_final: 0.7325 (mt) REVERT: M 182 LYS cc_start: 0.8570 (mttp) cc_final: 0.8310 (mttp) REVERT: N 134 LYS cc_start: 0.8017 (mttt) cc_final: 0.7739 (mtmt) REVERT: O 59 ASP cc_start: 0.6970 (OUTLIER) cc_final: 0.6623 (t0) REVERT: O 71 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7272 (mttt) REVERT: O 99 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7962 (tpt170) REVERT: O 182 LYS cc_start: 0.8596 (mttp) cc_final: 0.8372 (mttm) REVERT: O 204 LYS cc_start: 0.8829 (mtmm) cc_final: 0.8547 (mtmt) REVERT: P 99 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7740 (mmm160) REVERT: P 130 THR cc_start: 0.8113 (OUTLIER) cc_final: 0.7514 (p) REVERT: P 207 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8539 (ptt) REVERT: Q 47 ASN cc_start: 0.8872 (OUTLIER) cc_final: 0.8622 (t0) REVERT: R 99 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.6157 (mmm160) REVERT: W 134 LYS cc_start: 0.8038 (mttt) cc_final: 0.7776 (mttt) REVERT: W 183 MET cc_start: 0.8488 (mtt) cc_final: 0.8072 (mtt) REVERT: Z 99 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7299 (mmm160) outliers start: 153 outliers final: 123 residues processed: 432 average time/residue: 0.1767 time to fit residues: 124.8476 Evaluate side-chains 458 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 317 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 198 ILE Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain L residue 47 ASN Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 168 LEU Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 99 ARG Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain M residue 156 SER Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 170 SER Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain N residue 47 ASN Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain O residue 47 ASN Chi-restraints excluded: chain O residue 59 ASP Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 99 ARG Chi-restraints excluded: chain O residue 151 VAL Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain P residue 99 ARG Chi-restraints excluded: chain P residue 130 THR Chi-restraints excluded: chain P residue 198 ILE Chi-restraints excluded: chain P residue 207 MET Chi-restraints excluded: chain Q residue 47 ASN Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 158 VAL Chi-restraints excluded: chain Q residue 168 LEU Chi-restraints excluded: chain Q residue 207 MET Chi-restraints excluded: chain R residue 59 ASP Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 99 ARG Chi-restraints excluded: chain R residue 192 SER Chi-restraints excluded: chain S residue 47 ASN Chi-restraints excluded: chain S residue 59 ASP Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain T residue 47 ASN Chi-restraints excluded: chain T residue 131 GLU Chi-restraints excluded: chain T residue 158 VAL Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 83 LEU Chi-restraints excluded: chain U residue 86 SER Chi-restraints excluded: chain U residue 158 VAL Chi-restraints excluded: chain U residue 176 VAL Chi-restraints excluded: chain U residue 192 SER Chi-restraints excluded: chain V residue 47 ASN Chi-restraints excluded: chain V residue 66 SER Chi-restraints excluded: chain V residue 77 GLN Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 183 MET Chi-restraints excluded: chain W residue 49 ASN Chi-restraints excluded: chain W residue 66 SER Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 156 SER Chi-restraints excluded: chain W residue 207 MET Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 66 SER Chi-restraints excluded: chain X residue 86 SER Chi-restraints excluded: chain X residue 158 VAL Chi-restraints excluded: chain X residue 207 MET Chi-restraints excluded: chain Z residue 47 ASN Chi-restraints excluded: chain Z residue 81 ASP Chi-restraints excluded: chain Z residue 99 ARG Chi-restraints excluded: chain Z residue 120 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 83 optimal weight: 6.9990 chunk 391 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 309 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 242 optimal weight: 0.6980 chunk 67 optimal weight: 0.3980 chunk 282 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 216 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 49 ASN V 201 GLN W 49 ASN Z 49 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.116908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.096299 restraints weight = 36914.444| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.60 r_work: 0.3228 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31350 Z= 0.142 Angle : 0.457 5.241 42550 Z= 0.258 Chirality : 0.044 0.149 4975 Planarity : 0.003 0.023 5525 Dihedral : 5.227 21.969 4400 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 4.53 % Allowed : 29.09 % Favored : 66.38 % 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 are not related in a simple way. whole: -1.35 (0.14), residues: 4275 helix: 2.40 (0.15), residues: 1175 sheet: -2.51 (0.13), residues: 1500 loop : -1.63 (0.17), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG I 99 TYR 0.007 0.001 TYR E 102 PHE 0.012 0.001 PHE Z 205 TRP 0.011 0.001 TRP U 208 HIS 0.002 0.000 HIS Q 210 Details of bonding type rmsd covalent geometry : bond 0.00336 (31350) covalent geometry : angle 0.45719 (42550) hydrogen bonds : bond 0.03240 ( 976) hydrogen bonds : angle 3.52668 ( 2823) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 326 time to evaluate : 0.971 Fit side-chains REVERT: B 99 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.6142 (mmm160) REVERT: B 135 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6515 (mt) REVERT: B 204 LYS cc_start: 0.8888 (mtmm) cc_final: 0.8607 (mtmt) REVERT: C 99 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7224 (mmm160) REVERT: C 183 MET cc_start: 0.8724 (mtm) cc_final: 0.8194 (mtm) REVERT: E 99 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7069 (mmm160) REVERT: F 135 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6386 (mp) REVERT: G 99 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7070 (mmm160) REVERT: H 99 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.6504 (mmm160) REVERT: J 132 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8190 (mp) REVERT: M 99 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.6321 (mmm160) REVERT: N 134 LYS cc_start: 0.8002 (mttt) cc_final: 0.7762 (mtmt) REVERT: O 59 ASP cc_start: 0.6889 (OUTLIER) cc_final: 0.6581 (t0) REVERT: O 71 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7230 (mttt) REVERT: O 99 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7957 (tpt170) REVERT: O 182 LYS cc_start: 0.8569 (mttp) cc_final: 0.8347 (mttm) REVERT: O 204 LYS cc_start: 0.8856 (mtmm) cc_final: 0.8593 (mtmt) REVERT: P 130 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7622 (p) REVERT: P 132 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7882 (mt) REVERT: P 204 LYS cc_start: 0.9005 (mtmm) cc_final: 0.8778 (mtmt) REVERT: P 207 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8510 (ptt) REVERT: Q 47 ASN cc_start: 0.8855 (OUTLIER) cc_final: 0.8605 (t0) REVERT: R 99 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8107 (tpt170) REVERT: R 152 TYR cc_start: 0.8921 (t80) cc_final: 0.8573 (t80) REVERT: R 196 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.8157 (m-40) REVERT: W 134 LYS cc_start: 0.8056 (mttt) cc_final: 0.7700 (mttt) REVERT: Z 99 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7398 (mmm160) outliers start: 145 outliers final: 116 residues processed: 436 average time/residue: 0.1676 time to fit residues: 120.7006 Evaluate side-chains 454 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 319 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 198 ILE Chi-restraints excluded: chain L residue 47 ASN Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 168 LEU Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 99 ARG Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain M residue 156 SER Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 170 SER Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain N residue 47 ASN Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain O residue 47 ASN Chi-restraints excluded: chain O residue 59 ASP Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 99 ARG Chi-restraints excluded: chain O residue 151 VAL Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 130 THR Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain P residue 198 ILE Chi-restraints excluded: chain P residue 207 MET Chi-restraints excluded: chain Q residue 47 ASN Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 158 VAL Chi-restraints excluded: chain Q residue 168 LEU Chi-restraints excluded: chain Q residue 207 MET Chi-restraints excluded: chain R residue 59 ASP Chi-restraints excluded: chain R residue 64 SER Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 99 ARG Chi-restraints excluded: chain R residue 192 SER Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain S residue 59 ASP Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain T residue 47 ASN Chi-restraints excluded: chain T residue 158 VAL Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 83 LEU Chi-restraints excluded: chain U residue 86 SER Chi-restraints excluded: chain U residue 158 VAL Chi-restraints excluded: chain U residue 176 VAL Chi-restraints excluded: chain U residue 192 SER Chi-restraints excluded: chain V residue 47 ASN Chi-restraints excluded: chain V residue 77 GLN Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain W residue 49 ASN Chi-restraints excluded: chain W residue 66 SER Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 156 SER Chi-restraints excluded: chain W residue 207 MET Chi-restraints excluded: chain X residue 66 SER Chi-restraints excluded: chain X residue 78 MET Chi-restraints excluded: chain X residue 86 SER Chi-restraints excluded: chain X residue 155 SER Chi-restraints excluded: chain X residue 158 VAL Chi-restraints excluded: chain X residue 207 MET Chi-restraints excluded: chain Z residue 47 ASN Chi-restraints excluded: chain Z residue 81 ASP Chi-restraints excluded: chain Z residue 99 ARG Chi-restraints excluded: chain Z residue 120 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 179 optimal weight: 0.7980 chunk 231 optimal weight: 4.9990 chunk 359 optimal weight: 0.0980 chunk 315 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 320 optimal weight: 0.4980 chunk 393 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 163 optimal weight: 0.0470 chunk 19 optimal weight: 6.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 201 GLN E 49 ASN N 49 ASN W 49 ASN Z 49 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.117736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.097078 restraints weight = 36631.450| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.59 r_work: 0.3260 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31350 Z= 0.131 Angle : 0.447 5.113 42550 Z= 0.252 Chirality : 0.044 0.145 4975 Planarity : 0.003 0.024 5525 Dihedral : 5.104 21.492 4400 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 4.34 % Allowed : 29.28 % Favored : 66.38 % 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 are not related in a simple way. whole: -1.22 (0.14), residues: 4275 helix: 2.54 (0.15), residues: 1175 sheet: -2.47 (0.13), residues: 1500 loop : -1.56 (0.17), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 99 TYR 0.007 0.001 TYR R 102 PHE 0.012 0.001 PHE Z 205 TRP 0.010 0.001 TRP K 208 HIS 0.002 0.000 HIS M 210 Details of bonding type rmsd covalent geometry : bond 0.00310 (31350) covalent geometry : angle 0.44699 (42550) hydrogen bonds : bond 0.03160 ( 976) hydrogen bonds : angle 3.46331 ( 2823) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 321 time to evaluate : 1.031 Fit side-chains REVERT: B 99 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.6122 (mmm160) REVERT: B 135 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6512 (mt) REVERT: C 99 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8216 (mmm160) REVERT: C 183 MET cc_start: 0.8700 (mtm) cc_final: 0.8203 (mtm) REVERT: E 99 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.6999 (mmm160) REVERT: E 182 LYS cc_start: 0.8697 (mmtt) cc_final: 0.8266 (mttp) REVERT: F 135 LEU cc_start: 0.6793 (OUTLIER) cc_final: 0.6367 (mp) REVERT: G 99 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7057 (mmm160) REVERT: H 99 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.6646 (mmm160) REVERT: J 132 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8123 (mp) REVERT: M 99 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.6313 (mmm160) REVERT: M 182 LYS cc_start: 0.8503 (mttp) cc_final: 0.8150 (mttp) REVERT: N 134 LYS cc_start: 0.7957 (mttt) cc_final: 0.7718 (mtmt) REVERT: O 59 ASP cc_start: 0.6817 (OUTLIER) cc_final: 0.6502 (t0) REVERT: O 71 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7173 (mttt) REVERT: O 99 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7995 (tpt170) REVERT: O 182 LYS cc_start: 0.8568 (mttp) cc_final: 0.8186 (mttm) REVERT: O 204 LYS cc_start: 0.8838 (mtmm) cc_final: 0.8569 (mtmt) REVERT: P 130 THR cc_start: 0.8221 (OUTLIER) cc_final: 0.7645 (p) REVERT: P 132 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7810 (mt) REVERT: P 204 LYS cc_start: 0.9008 (mtmm) cc_final: 0.8776 (mtmt) REVERT: P 207 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8642 (ptm) REVERT: Q 47 ASN cc_start: 0.8852 (OUTLIER) cc_final: 0.8599 (t0) REVERT: R 99 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8102 (tpt170) REVERT: R 152 TYR cc_start: 0.8895 (t80) cc_final: 0.8581 (t80) REVERT: W 134 LYS cc_start: 0.8039 (mttt) cc_final: 0.7707 (mttt) REVERT: X 77 GLN cc_start: 0.6871 (OUTLIER) cc_final: 0.6277 (mm-40) REVERT: Z 99 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7380 (mmm160) outliers start: 139 outliers final: 112 residues processed: 427 average time/residue: 0.1684 time to fit residues: 119.3939 Evaluate side-chains 446 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 315 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 198 ILE Chi-restraints excluded: chain L residue 47 ASN Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 168 LEU Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 99 ARG Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain M residue 156 SER Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 170 SER Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain N residue 47 ASN Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain O residue 47 ASN Chi-restraints excluded: chain O residue 59 ASP Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 99 ARG Chi-restraints excluded: chain O residue 151 VAL Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 130 THR Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain P residue 198 ILE Chi-restraints excluded: chain P residue 207 MET Chi-restraints excluded: chain Q residue 47 ASN Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 158 VAL Chi-restraints excluded: chain Q residue 168 LEU Chi-restraints excluded: chain Q residue 207 MET Chi-restraints excluded: chain R residue 59 ASP Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 99 ARG Chi-restraints excluded: chain R residue 192 SER Chi-restraints excluded: chain S residue 59 ASP Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain T residue 47 ASN Chi-restraints excluded: chain T residue 131 GLU Chi-restraints excluded: chain T residue 158 VAL Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 83 LEU Chi-restraints excluded: chain U residue 86 SER Chi-restraints excluded: chain U residue 158 VAL Chi-restraints excluded: chain U residue 176 VAL Chi-restraints excluded: chain U residue 192 SER Chi-restraints excluded: chain V residue 47 ASN Chi-restraints excluded: chain V residue 77 GLN Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain W residue 49 ASN Chi-restraints excluded: chain W residue 66 SER Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 156 SER Chi-restraints excluded: chain W residue 207 MET Chi-restraints excluded: chain X residue 66 SER Chi-restraints excluded: chain X residue 77 GLN Chi-restraints excluded: chain X residue 78 MET Chi-restraints excluded: chain X residue 86 SER Chi-restraints excluded: chain X residue 155 SER Chi-restraints excluded: chain X residue 158 VAL Chi-restraints excluded: chain X residue 207 MET Chi-restraints excluded: chain Z residue 47 ASN Chi-restraints excluded: chain Z residue 99 ARG Chi-restraints excluded: chain Z residue 120 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 345 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 282 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 360 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 307 optimal weight: 3.9990 chunk 368 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 49 ASN Z 49 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.115129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.094481 restraints weight = 37291.483| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.62 r_work: 0.3202 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 31350 Z= 0.196 Angle : 0.491 5.288 42550 Z= 0.276 Chirality : 0.045 0.152 4975 Planarity : 0.003 0.024 5525 Dihedral : 5.392 22.098 4400 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 4.41 % Allowed : 29.28 % Favored : 66.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.14), residues: 4275 helix: 2.37 (0.15), residues: 1175 sheet: -2.55 (0.15), residues: 1150 loop : -1.81 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 99 TYR 0.009 0.001 TYR R 102 PHE 0.013 0.002 PHE Z 205 TRP 0.008 0.001 TRP K 208 HIS 0.001 0.000 HIS M 210 Details of bonding type rmsd covalent geometry : bond 0.00468 (31350) covalent geometry : angle 0.49073 (42550) hydrogen bonds : bond 0.03521 ( 976) hydrogen bonds : angle 3.57331 ( 2823) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6740.53 seconds wall clock time: 116 minutes 31.92 seconds (6991.92 seconds total)