Starting phenix.real_space_refine
on Sat Aug 23 00:22:02 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8hqe_34948/08_2025/8hqe_34948.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hqe_34948/08_2025/8hqe_34948.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hqe_34948/08_2025/8hqe_34948.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hqe_34948/08_2025/8hqe_34948.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hqe_34948/08_2025/8hqe_34948.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hqe_34948/08_2025/8hqe_34948.cif"
  }
  resolution = 2.97
  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=   0.040
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      63      5.16       5
     C    5649      2.51       5
     N    1517      2.21       5
     O    1674      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8903
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 2588
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2588
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "C"
      Number of atoms: 414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 414
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "H"
      Number of atoms: 1774
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1774
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "R"
      Number of atoms: 2440
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2440
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 6, 'TRANS': 300}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1687
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1687
          Classifications: {'peptide': 214}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 1, 'TRANS': 212}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 44
          Unresolved non-hydrogen angles: 52
          Unresolved non-hydrogen dihedrals: 40
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 23
  Time building chain proxies: 1.57, per 1000 atoms: 0.18
  Number of scatterers: 8903
  At special positions: 0
  Unit cell: (106.08, 121.68, 132.08, 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      63     16.00
     O    1674      8.00
     N    1517      7.00
     C    5649      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 147 " - pdb=" SG  CYS H 217 " distance=1.78
    Simple disulfide: pdb=" SG  CYS R 115 " - pdb=" SG  CYS R 186 " distance=2.03

  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: 0.63
  Conformation dependent library (CDL) restraints added in 371.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2148

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 12 sheets defined
      38.4% alpha, 19.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'B' and resid 2 through 26
      removed outlier: 3.688A  pdb=" N   LEU B   7 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   GLN B   9 " --> pdb=" O   ASP B   5 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   GLU B  10 " --> pdb=" O   GLN B   6 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   ALA B  21 " --> pdb=" O   GLN B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.858A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 10 through 22
      removed outlier: 4.349A  pdb=" N   LYS C  14 " --> pdb=" O   ALA C  10 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   VAL C  16 " --> pdb=" O   ALA C  12 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLN C  18 " --> pdb=" O   LYS C  14 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LEU C  19 " --> pdb=" O   LEU C  15 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 45
      removed outlier: 3.827A  pdb=" N   CYS C  41 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLU C  42 " --> pdb=" O   MET C  38 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ALA C  43 " --> pdb=" O   ALA C  39 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   HIS C  44 " --> pdb=" O   TYR C  40 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 38 through 71
      Proline residue:  R  58  - end of helix
    Processing helix  chain 'R' and resid 75 through 92
      removed outlier: 4.008A  pdb=" N   VAL R  79 " --> pdb=" O   ASN R  75 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   TYR R  80 " --> pdb=" O   VAL R  76 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   TYR R  91 " --> pdb=" O   CYS R  87 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 93 through 102
      removed outlier: 4.066A  pdb=" N   LEU R  97 " --> pdb=" O   GLY R  93 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   TRP R  98 " --> pdb=" O   THR R  94 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 112 through 145
    Processing helix  chain 'R' and resid 148 through 152
      removed outlier: 3.843A  pdb=" N   ARG R 151 " --> pdb=" O   LEU R 148 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLY R 152 " --> pdb=" O   GLU R 149 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 148 through 152'
    Processing helix  chain 'R' and resid 155 through 180
      removed outlier: 4.185A  pdb=" N   ALA R 159 " --> pdb=" O   ARG R 155 " (cutoff:3.500A)
      Proline residue:  R 176  - end of helix
    Processing helix  chain 'R' and resid 194 through 208
    Processing helix  chain 'R' and resid 208 through 228
      removed outlier: 3.680A  pdb=" N   LEU R 212 " --> pdb=" O   PHE R 208 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 233 through 272
      Proline residue:  R 257  - end of helix
    Processing helix  chain 'R' and resid 279 through 312
      Proline residue:  R 305  - end of helix
      removed outlier: 3.935A  pdb=" N   THR R 312 " --> pdb=" O   TYR R 308 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 312 through 331
    Processing helix  chain 'R' and resid 334 through 346
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 208 through 213
      removed outlier: 4.625A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 216
      No H-bonds generated for 'chain 'A' and resid 214 through 216'
    Processing helix  chain 'A' and resid 241 through 255
      removed outlier: 3.510A  pdb=" N   LYS A 248 " --> pdb=" O   HIS A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 278
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 312 through 317
      removed outlier: 4.387A  pdb=" N   THR A 316 " --> pdb=" O   LYS A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.563A  pdb=" N   VAL A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LYS A 345 " --> pdb=" O   ASP A 341 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 50
      removed outlier: 3.723A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   VAL B 327 " --> pdb=" O   TRP B 339 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.807A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 103 through 105
      removed outlier: 4.006A  pdb=" N   ILE B 123 " --> pdb=" O   ARG B 137 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 5.998A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.588A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.960A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.580A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.738A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ALA B 203 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 4.148A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.595A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.651A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.908A  pdb=" N   SER H  21 " --> pdb=" O   SER H   7 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   THR H  78 " --> pdb=" O   ASP H  73 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ASP H  73 " --> pdb=" O   THR H  78 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.626A  pdb=" N   TYR H  94 " --> pdb=" O   THR H 115 " (cutoff:3.500A)
      removed outlier: 7.359A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.978A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 128 through 130
      removed outlier: 3.609A  pdb=" N   PHE H 200 " --> pdb=" O   CYS H 147 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 182 through 183
      removed outlier: 6.826A  pdb=" N   TRP H 164 " --> pdb=" O   LEU H 176 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   TYR H 178 " --> pdb=" O   LEU H 162 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   LEU H 162 " --> pdb=" O   TYR H 178 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   TYR H 163 " --> pdb=" O   MET H 218 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 185 through 191
      removed outlier: 5.845A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.444A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 7.092A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 8.110A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 5.835A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)

    434 hydrogen bonds defined for protein.
    1254 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: 1.06

  Time building geometry restraints manager: 0.83 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.33: 2434
        1.33 -     1.45: 1728
        1.45 -     1.57: 4831
        1.57 -     1.69: 0
        1.69 -     1.81: 86
  Bond restraints: 9079
  Sorted by residual:
  bond pdb=" N   LEU C  19 "
       pdb=" CA  LEU C  19 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.030 1.23e-02 6.61e+03 6.14e+00
  bond pdb=" N   LEU A 310 "
       pdb=" CA  LEU A 310 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.20e-02 6.94e+03 5.82e+00
  bond pdb=" N   MET C  38 "
       pdb=" CA  MET C  38 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.26e-02 6.30e+03 5.54e+00
  bond pdb=" N   LYS R 239 "
       pdb=" CA  LYS R 239 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.19e-02 7.06e+03 5.39e+00
  bond pdb=" N   MET A 247 "
       pdb=" CA  MET A 247 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.030 1.28e-02 6.10e+03 5.38e+00
  ... (remaining 9074 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 11911
        1.99 -     3.98: 317
        3.98 -     5.98: 53
        5.98 -     7.97: 11
        7.97 -     9.96: 11
  Bond angle restraints: 12303
  Sorted by residual:
  angle pdb=" C   ILE H 126 "
        pdb=" CA  ILE H 126 "
        pdb=" CB  ILE H 126 "
      ideal   model   delta    sigma   weight residual
     111.23  102.28    8.95 1.08e+00 8.57e-01 6.87e+01
  angle pdb=" N   ILE H 126 "
        pdb=" CA  ILE H 126 "
        pdb=" C   ILE H 126 "
      ideal   model   delta    sigma   weight residual
     107.98  117.84   -9.86 1.51e+00 4.39e-01 4.26e+01
  angle pdb=" N   ARG R 103 "
        pdb=" CA  ARG R 103 "
        pdb=" C   ARG R 103 "
      ideal   model   delta    sigma   weight residual
     110.23  102.13    8.10 1.45e+00 4.76e-01 3.12e+01
  angle pdb=" N   VAL H 127 "
        pdb=" CA  VAL H 127 "
        pdb=" C   VAL H 127 "
      ideal   model   delta    sigma   weight residual
     109.30  116.00   -6.70 1.25e+00 6.40e-01 2.87e+01
  angle pdb=" C   ALA B 257 "
        pdb=" N   ASP B 258 "
        pdb=" CA  ASP B 258 "
      ideal   model   delta    sigma   weight residual
     121.54  130.74   -9.20 1.91e+00 2.74e-01 2.32e+01
  ... (remaining 12298 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 4767
       17.98 -    35.96: 474
       35.96 -    53.94: 112
       53.94 -    71.92: 12
       71.92 -    89.90: 13
  Dihedral angle restraints: 5378
    sinusoidal: 2048
      harmonic: 3330
  Sorted by residual:
  dihedral pdb=" CB  CYS R 115 "
           pdb=" SG  CYS R 115 "
           pdb=" SG  CYS R 186 "
           pdb=" CB  CYS R 186 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -145.16   59.16     1      1.00e+01 1.00e-02 4.68e+01
  dihedral pdb=" CB  CYS H 147 "
           pdb=" SG  CYS H 147 "
           pdb=" SG  CYS H 217 "
           pdb=" CB  CYS H 217 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  136.59  -43.59     1      1.00e+01 1.00e-02 2.65e+01
  dihedral pdb=" CA  PHE B 278 "
           pdb=" C   PHE B 278 "
           pdb=" N   SER B 279 "
           pdb=" CA  SER B 279 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.82   18.18     0      5.00e+00 4.00e-02 1.32e+01
  ... (remaining 5375 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1047
       0.052 -    0.105: 289
       0.105 -    0.157: 66
       0.157 -    0.210: 6
       0.210 -    0.262: 2
  Chirality restraints: 1410
  Sorted by residual:
  chirality pdb=" CB  VAL R  99 "
            pdb=" CA  VAL R  99 "
            pdb=" CG1 VAL R  99 "
            pdb=" CG2 VAL R  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.72e+00
  chirality pdb=" CA  ASP B 258 "
            pdb=" N   ASP B 258 "
            pdb=" C   ASP B 258 "
            pdb=" CB  ASP B 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CB  VAL R 253 "
            pdb=" CA  VAL R 253 "
            pdb=" CG1 VAL R 253 "
            pdb=" CG2 VAL R 253 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 8.05e-01
  ... (remaining 1407 not shown)

  Planarity restraints: 1555
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR H 223 "    0.056 5.00e-02 4.00e+02   8.48e-02 1.15e+01
        pdb=" N   PRO H 224 "   -0.147 5.00e-02 4.00e+02
        pdb=" CA  PRO H 224 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO H 224 "    0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA R 256 "    0.043 5.00e-02 4.00e+02   6.37e-02 6.50e+00
        pdb=" N   PRO R 257 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO R 257 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO R 257 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R  95 "    0.042 5.00e-02 4.00e+02   6.30e-02 6.36e+00
        pdb=" N   PRO R  96 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO R  96 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO R  96 "    0.035 5.00e-02 4.00e+02
  ... (remaining 1552 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 714
        2.74 -     3.28: 8933
        3.28 -     3.82: 15105
        3.82 -     4.36: 17064
        4.36 -     4.90: 29478
  Nonbonded interactions: 71294
  Sorted by model distance:
  nonbonded pdb=" O   VAL H 127 "
            pdb=" OG  SER H 150 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" O   VAL R 177 "
            pdb=" OG1 THR R 180 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" N   VAL H 127 "
            pdb=" OG  SER H 150 "
     model   vdw
     2.271 3.120
  nonbonded pdb=" OG  SER H 192 "
            pdb=" OG1 THR H 203 "
     model   vdw
     2.283 3.040
  ... (remaining 71289 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.470
  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:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.190
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:5.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
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      :  0.005   0.256   9082  Z= 0.254
  Angle     :  0.839   9.961  12309  Z= 0.466
  Chirality :  0.051   0.262   1410
  Planarity :  0.006   0.085   1555
  Dihedral  : 15.687  89.902   3221
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 18.75 %
    Favored  : 80.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.77 (0.23), residues: 1127
  helix: -0.92 (0.23), residues: 412
  sheet: -0.61 (0.32), residues: 266
  loop : -1.61 (0.28), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  32 
 TYR   0.017   0.002   TYR R  91 
 PHE   0.020   0.002   PHE A 323 
 TRP   0.012   0.001   TRP B 339 
 HIS   0.009   0.002   HIS R 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 9079)
  covalent geometry    : angle       0.83202 (12303)
  SS BOND              : bond        0.14759 (    3)
  SS BOND              : angle       4.88583 (    6)
  hydrogen bonds       : bond        0.20644 (  434)
  hydrogen bonds       : angle       8.35771 ( 1254)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 54
  time to evaluate  : 0.273 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 57
  average time/residue: 0.5560
  time to fit residues: 33.7014
Evaluate side-chains
  43 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 41
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  150 SER
Chi-restraints excluded: chain R residue  178 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    8.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 110 ASN
B 230 ASN
A 244 HIS
A 256 ASN
A 346 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2573 r_free = 0.2573 target = 0.039957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2342 r_free = 0.2342 target = 0.032490 restraints weight = 57728.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.2290 rms_B_bonded: 2.98
r_work: 0.2213 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9136
moved from start:          0.1324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   9082  Z= 0.182
  Angle     :  0.593   6.671  12309  Z= 0.320
  Chirality :  0.042   0.147   1410
  Planarity :  0.005   0.072   1555
  Dihedral  :  4.854  49.839   1246
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 19.90 %
    Favored  : 78.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.86 (0.25), residues: 1127
  helix:  0.36 (0.25), residues: 421
  sheet: -0.51 (0.33), residues: 261
  loop : -1.42 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  21 
 TYR   0.012   0.001   TYR H 178 
 PHE   0.015   0.001   PHE A 323 
 TRP   0.015   0.001   TRP B 169 
 HIS   0.006   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 9079)
  covalent geometry    : angle       0.59323 (12303)
  SS BOND              : bond        0.00589 (    3)
  SS BOND              : angle       0.88596 (    6)
  hydrogen bonds       : bond        0.04671 (  434)
  hydrogen bonds       : angle       5.63343 ( 1254)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 40
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
REVERT: R  228 GLN cc_start: 0.9613 (OUTLIER) cc_final: 0.9322 (pm20)
REVERT: A   14 GLU cc_start: 0.9324 (OUTLIER) cc_final: 0.9036 (tt0)
  outliers start: 17
  outliers final: 3
  residues processed: 55
  average time/residue: 0.5289
  time to fit residues: 30.9507
Evaluate side-chains
  43 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain R residue  178 PHE
Chi-restraints excluded: chain R residue  228 GLN
Chi-restraints excluded: chain R residue  335 VAL
Chi-restraints excluded: chain A residue   14 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 1 optimal weight:    7.9990
   chunk 30 optimal weight:    9.9990
   chunk 46 optimal weight:    4.9990
   chunk 42 optimal weight:    6.9990
   chunk 84 optimal weight:   10.0000
   chunk 80 optimal weight:    0.9980
   chunk 14 optimal weight:    9.9990
   chunk 88 optimal weight:    7.9990
   chunk 57 optimal weight:   10.0000
   chunk 81 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   overall best weight:    3.3586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2563 r_free = 0.2563 target = 0.039416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2323 r_free = 0.2323 target = 0.031901 restraints weight = 57427.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.2296 rms_B_bonded: 2.96
r_work: 0.2218 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9149
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   9082  Z= 0.173
  Angle     :  0.555   6.622  12309  Z= 0.297
  Chirality :  0.041   0.154   1410
  Planarity :  0.004   0.067   1555
  Dihedral  :  4.664  50.701   1245
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 19.79 %
    Favored  : 77.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.47 (0.25), residues: 1127
  helix:  0.86 (0.26), residues: 421
  sheet: -0.28 (0.33), residues: 253
  loop : -1.41 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  68 
 TYR   0.011   0.001   TYR H  94 
 PHE   0.013   0.001   PHE A 323 
 TRP   0.014   0.001   TRP B 169 
 HIS   0.006   0.001   HIS R 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 9079)
  covalent geometry    : angle       0.55505 (12303)
  SS BOND              : bond        0.00261 (    3)
  SS BOND              : angle       0.84490 (    6)
  hydrogen bonds       : bond        0.04238 (  434)
  hydrogen bonds       : angle       5.17445 ( 1254)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 40
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
REVERT: A  243 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8350 (mpp)
  outliers start: 26
  outliers final: 4
  residues processed: 62
  average time/residue: 0.5483
  time to fit residues: 36.1103
Evaluate side-chains
  43 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain R residue  178 PHE
Chi-restraints excluded: chain R residue  335 VAL
Chi-restraints excluded: chain A residue  243 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 10 optimal weight:    7.9990
   chunk 77 optimal weight:    9.9990
   chunk 54 optimal weight:    7.9990
   chunk 2 optimal weight:    0.0770
   chunk 67 optimal weight:    2.9990
   chunk 34 optimal weight:    6.9990
   chunk 108 optimal weight:    0.5980
   chunk 3 optimal weight:   10.0000
   chunk 1 optimal weight:    5.9990
   chunk 109 optimal weight:    6.9990
   chunk 28 optimal weight:    9.9990
   overall best weight:    3.3344

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2561 r_free = 0.2561 target = 0.039253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2318 r_free = 0.2318 target = 0.031696 restraints weight = 58056.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.2290 rms_B_bonded: 2.96
r_work: 0.2205 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9151
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   9082  Z= 0.172
  Angle     :  0.544   6.622  12309  Z= 0.291
  Chirality :  0.041   0.153   1410
  Planarity :  0.004   0.066   1555
  Dihedral  :  4.595  51.189   1245
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 20.21 %
    Favored  : 77.19 %
  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 aren not related in a simple way.
  whole: -0.30 (0.25), residues: 1127
  helix:  1.09 (0.26), residues: 421
  sheet: -0.35 (0.33), residues: 261
  loop : -1.32 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  68 
 TYR   0.010   0.001   TYR R  91 
 PHE   0.012   0.001   PHE R 141 
 TRP   0.010   0.001   TRP B 169 
 HIS   0.006   0.001   HIS R 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 9079)
  covalent geometry    : angle       0.54378 (12303)
  SS BOND              : bond        0.00273 (    3)
  SS BOND              : angle       0.89674 (    6)
  hydrogen bonds       : bond        0.04010 (  434)
  hydrogen bonds       : angle       5.02324 ( 1254)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 39
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  232 LYS cc_start: 0.9508 (tmmm) cc_final: 0.9298 (tmmm)
REVERT: R   89 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9281 (mm)
REVERT: A   14 GLU cc_start: 0.9368 (OUTLIER) cc_final: 0.9124 (tt0)
  outliers start: 25
  outliers final: 5
  residues processed: 61
  average time/residue: 0.5750
  time to fit residues: 37.5296
Evaluate side-chains
  46 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain R residue   89 LEU
Chi-restraints excluded: chain R residue  178 PHE
Chi-restraints excluded: chain R residue  335 VAL
Chi-restraints excluded: chain A residue   14 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 87 optimal weight:   20.0000
   chunk 101 optimal weight:   10.0000
   chunk 91 optimal weight:    0.3980
   chunk 82 optimal weight:    0.9990
   chunk 19 optimal weight:    9.9990
   chunk 13 optimal weight:    9.9990
   chunk 79 optimal weight:    3.9990
   chunk 90 optimal weight:    5.9990
   chunk 21 optimal weight:    9.9990
   chunk 58 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9980
   overall best weight:    2.4786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2576 r_free = 0.2576 target = 0.039613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2335 r_free = 0.2335 target = 0.032041 restraints weight = 57325.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.2306 rms_B_bonded: 2.95
r_work: 0.2228 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9143
moved from start:          0.2058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9082  Z= 0.142
  Angle     :  0.539   6.624  12309  Z= 0.286
  Chirality :  0.040   0.153   1410
  Planarity :  0.004   0.065   1555
  Dihedral  :  4.518  51.586   1245
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 21.15 %
    Favored  : 76.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.20 (0.25), residues: 1127
  helix:  1.20 (0.26), residues: 421
  sheet: -0.33 (0.32), residues: 260
  loop : -1.28 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  68 
 TYR   0.016   0.001   TYR R  91 
 PHE   0.012   0.001   PHE R 141 
 TRP   0.010   0.001   TRP B 169 
 HIS   0.006   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 9079)
  covalent geometry    : angle       0.53878 (12303)
  SS BOND              : bond        0.00225 (    3)
  SS BOND              : angle       0.88702 (    6)
  hydrogen bonds       : bond        0.03842 (  434)
  hydrogen bonds       : angle       4.87373 ( 1254)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 41
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
REVERT: C   13 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8601 (mpp-170)
REVERT: C   17 GLU cc_start: 0.9319 (mm-30) cc_final: 0.9080 (mm-30)
REVERT: C   20 LYS cc_start: 0.8852 (ptpp) cc_final: 0.8366 (ptpp)
REVERT: H  180 MET cc_start: 0.9699 (ttt) cc_final: 0.9497 (ptm)
REVERT: H  232 LYS cc_start: 0.9535 (tmmm) cc_final: 0.9296 (tmmm)
REVERT: R   89 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9243 (mm)
REVERT: A   14 GLU cc_start: 0.9344 (OUTLIER) cc_final: 0.9131 (tt0)
  outliers start: 26
  outliers final: 8
  residues processed: 66
  average time/residue: 0.5584
  time to fit residues: 39.2842
Evaluate side-chains
  51 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 40
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain C residue   13 ARG
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain R residue   89 LEU
Chi-restraints excluded: chain R residue   91 TYR
Chi-restraints excluded: chain R residue  178 PHE
Chi-restraints excluded: chain R residue  335 VAL
Chi-restraints excluded: chain A residue   14 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 103 optimal weight:    5.9990
   chunk 3 optimal weight:    8.9990
   chunk 20 optimal weight:    0.6980
   chunk 60 optimal weight:    5.9990
   chunk 76 optimal weight:    0.3980
   chunk 71 optimal weight:    6.9990
   chunk 21 optimal weight:   10.0000
   chunk 39 optimal weight:    5.9990
   chunk 110 optimal weight:    1.9990
   chunk 98 optimal weight:    9.9990
   overall best weight:    2.2186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2583 r_free = 0.2583 target = 0.039772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2342 r_free = 0.2342 target = 0.032150 restraints weight = 56811.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.2316 rms_B_bonded: 2.96
r_work: 0.2236 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9140
moved from start:          0.2167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9082  Z= 0.133
  Angle     :  0.545   7.437  12309  Z= 0.287
  Chirality :  0.041   0.157   1410
  Planarity :  0.004   0.065   1555
  Dihedral  :  4.458  52.026   1245
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 21.67 %
    Favored  : 76.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.26), residues: 1127
  helix:  1.26 (0.26), residues: 421
  sheet: -0.37 (0.32), residues: 260
  loop : -1.20 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 283 
 TYR   0.016   0.001   TYR R  91 
 PHE   0.012   0.001   PHE R 141 
 TRP   0.009   0.001   TRP B 169 
 HIS   0.006   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 9079)
  covalent geometry    : angle       0.54474 (12303)
  SS BOND              : bond        0.00225 (    3)
  SS BOND              : angle       0.83484 (    6)
  hydrogen bonds       : bond        0.03734 (  434)
  hydrogen bonds       : angle       4.80646 ( 1254)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 44
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
REVERT: H   46 GLU cc_start: 0.9443 (OUTLIER) cc_final: 0.9090 (pp20)
REVERT: H  180 MET cc_start: 0.9702 (OUTLIER) cc_final: 0.9485 (ptm)
REVERT: H  232 LYS cc_start: 0.9553 (tmmm) cc_final: 0.9306 (tmmm)
REVERT: R   89 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9256 (mm)
  outliers start: 21
  outliers final: 8
  residues processed: 63
  average time/residue: 0.6155
  time to fit residues: 41.1794
Evaluate side-chains
  51 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 40
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain H residue  180 MET
Chi-restraints excluded: chain R residue   89 LEU
Chi-restraints excluded: chain R residue   91 TYR
Chi-restraints excluded: chain R residue  178 PHE
Chi-restraints excluded: chain R residue  335 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 90 optimal weight:    9.9990
   chunk 94 optimal weight:    9.9990
   chunk 104 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 31 optimal weight:    8.9990
   chunk 5 optimal weight:    7.9990
   chunk 22 optimal weight:    8.9990
   chunk 49 optimal weight:    5.9990
   chunk 72 optimal weight:    4.9990
   chunk 105 optimal weight:    4.9990
   chunk 107 optimal weight:    0.9990
   overall best weight:    3.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C  18 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2564 r_free = 0.2564 target = 0.039160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2322 r_free = 0.2322 target = 0.031532 restraints weight = 57292.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.2294 rms_B_bonded: 2.94
r_work: 0.2211 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9153
moved from start:          0.2210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9082  Z= 0.182
  Angle     :  0.564   8.481  12309  Z= 0.297
  Chirality :  0.041   0.155   1410
  Planarity :  0.004   0.066   1555
  Dihedral  :  4.540  52.148   1245
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 21.98 %
    Favored  : 75.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.17 (0.26), residues: 1127
  helix:  1.23 (0.26), residues: 421
  sheet: -0.36 (0.32), residues: 260
  loop : -1.22 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 283 
 TYR   0.016   0.001   TYR R  91 
 PHE   0.013   0.001   PHE R 141 
 TRP   0.009   0.001   TRP B 169 
 HIS   0.006   0.001   HIS R 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 9079)
  covalent geometry    : angle       0.56413 (12303)
  SS BOND              : bond        0.00263 (    3)
  SS BOND              : angle       0.89555 (    6)
  hydrogen bonds       : bond        0.03865 (  434)
  hydrogen bonds       : angle       4.87705 ( 1254)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 40
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   46 GLU cc_start: 0.9456 (OUTLIER) cc_final: 0.9134 (pp20)
REVERT: H  232 LYS cc_start: 0.9524 (tmmm) cc_final: 0.9269 (tmmm)
REVERT: R   89 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9273 (mm)
  outliers start: 24
  outliers final: 9
  residues processed: 60
  average time/residue: 0.5306
  time to fit residues: 33.9355
Evaluate side-chains
  50 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 39
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain R residue   89 LEU
Chi-restraints excluded: chain R residue   91 TYR
Chi-restraints excluded: chain R residue  173 VAL
Chi-restraints excluded: chain R residue  178 PHE
Chi-restraints excluded: chain R residue  335 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 18 optimal weight:   10.0000
   chunk 109 optimal weight:   10.0000
   chunk 100 optimal weight:    0.2980
   chunk 53 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   chunk 96 optimal weight:    0.8980
   chunk 60 optimal weight:   10.0000
   chunk 42 optimal weight:    6.9990
   chunk 76 optimal weight:    2.9990
   chunk 49 optimal weight:    7.9990
   overall best weight:    2.0386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2590 r_free = 0.2590 target = 0.039872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2350 r_free = 0.2350 target = 0.032187 restraints weight = 56321.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.2323 rms_B_bonded: 2.94
r_work: 0.2241 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9138
moved from start:          0.2291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9082  Z= 0.128
  Angle     :  0.553   9.831  12309  Z= 0.289
  Chirality :  0.040   0.152   1410
  Planarity :  0.004   0.065   1555
  Dihedral  :  4.457  52.392   1245
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 23.02 %
    Favored  : 75.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.09 (0.26), residues: 1127
  helix:  1.31 (0.26), residues: 422
  sheet: -0.38 (0.32), residues: 260
  loop : -1.15 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  13 
 TYR   0.016   0.001   TYR R  91 
 PHE   0.012   0.001   PHE R 141 
 TRP   0.009   0.001   TRP B 169 
 HIS   0.006   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 9079)
  covalent geometry    : angle       0.55326 (12303)
  SS BOND              : bond        0.00230 (    3)
  SS BOND              : angle       0.82865 (    6)
  hydrogen bonds       : bond        0.03693 (  434)
  hydrogen bonds       : angle       4.76035 ( 1254)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 41
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   46 GLU cc_start: 0.9446 (OUTLIER) cc_final: 0.9084 (pp20)
REVERT: H  232 LYS cc_start: 0.9548 (tmmm) cc_final: 0.9295 (tmmm)
REVERT: R   89 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9266 (mm)
  outliers start: 15
  outliers final: 8
  residues processed: 56
  average time/residue: 0.5619
  time to fit residues: 33.5464
Evaluate side-chains
  50 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 40
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain R residue   89 LEU
Chi-restraints excluded: chain R residue   91 TYR
Chi-restraints excluded: chain R residue  178 PHE
Chi-restraints excluded: chain R residue  335 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 76 optimal weight:    6.9990
   chunk 95 optimal weight:    7.9990
   chunk 58 optimal weight:    1.9990
   chunk 111 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 100 optimal weight:    0.0980
   chunk 1 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 89 optimal weight:    5.9990
   chunk 43 optimal weight:    6.9990
   chunk 64 optimal weight:    3.9990
   overall best weight:    2.4188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2589 r_free = 0.2589 target = 0.039767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2352 r_free = 0.2352 target = 0.032180 restraints weight = 57472.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.2291 rms_B_bonded: 2.95
r_work: 0.2211 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9136
moved from start:          0.2319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9082  Z= 0.140
  Angle     :  0.562  11.380  12309  Z= 0.292
  Chirality :  0.041   0.152   1410
  Planarity :  0.004   0.066   1555
  Dihedral  :  4.438  52.679   1245
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 23.44 %
    Favored  : 75.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.26), residues: 1127
  helix:  1.32 (0.26), residues: 422
  sheet: -0.31 (0.32), residues: 265
  loop : -1.14 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  13 
 TYR   0.016   0.001   TYR R  91 
 PHE   0.012   0.001   PHE R 141 
 TRP   0.009   0.001   TRP B 169 
 HIS   0.006   0.001   HIS R 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 9079)
  covalent geometry    : angle       0.56164 (12303)
  SS BOND              : bond        0.00226 (    3)
  SS BOND              : angle       0.85507 (    6)
  hydrogen bonds       : bond        0.03700 (  434)
  hydrogen bonds       : angle       4.75743 ( 1254)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 41
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   46 GLU cc_start: 0.9441 (OUTLIER) cc_final: 0.9081 (pp20)
REVERT: H  232 LYS cc_start: 0.9534 (tmmm) cc_final: 0.9288 (tmmm)
REVERT: R   89 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9265 (mm)
  outliers start: 14
  outliers final: 7
  residues processed: 53
  average time/residue: 0.6996
  time to fit residues: 39.6976
Evaluate side-chains
  50 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain R residue   89 LEU
Chi-restraints excluded: chain R residue   91 TYR
Chi-restraints excluded: chain R residue  178 PHE
Chi-restraints excluded: chain R residue  335 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 67 optimal weight:    7.9990
   chunk 61 optimal weight:   10.0000
   chunk 102 optimal weight:    5.9990
   chunk 35 optimal weight:    8.9990
   chunk 83 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 91 optimal weight:   10.0000
   chunk 3 optimal weight:    0.0040
   chunk 104 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 69 optimal weight:    5.9990
   overall best weight:    4.0000

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C  44 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2564 r_free = 0.2564 target = 0.038942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2321 r_free = 0.2321 target = 0.031272 restraints weight = 56919.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.2294 rms_B_bonded: 2.92
r_work: 0.2214 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9156
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9082  Z= 0.199
  Angle     :  0.594  12.671  12309  Z= 0.308
  Chirality :  0.041   0.156   1410
  Planarity :  0.004   0.065   1555
  Dihedral  :  4.545  52.292   1245
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 23.65 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.09 (0.26), residues: 1127
  helix:  1.28 (0.26), residues: 421
  sheet: -0.30 (0.32), residues: 265
  loop : -1.18 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  68 
 TYR   0.017   0.001   TYR R  91 
 PHE   0.013   0.001   PHE R 141 
 TRP   0.008   0.001   TRP B 169 
 HIS   0.006   0.001   HIS R 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 9079)
  covalent geometry    : angle       0.59398 (12303)
  SS BOND              : bond        0.00278 (    3)
  SS BOND              : angle       0.90361 (    6)
  hydrogen bonds       : bond        0.03903 (  434)
  hydrogen bonds       : angle       4.86396 ( 1254)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 40
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   14 LYS cc_start: 0.9531 (pttm) cc_final: 0.9218 (pmtt)
REVERT: H   46 GLU cc_start: 0.9468 (OUTLIER) cc_final: 0.9137 (pp20)
REVERT: H  232 LYS cc_start: 0.9538 (tmmm) cc_final: 0.9278 (tmmm)
REVERT: R   89 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9263 (mm)
  outliers start: 13
  outliers final: 8
  residues processed: 52
  average time/residue: 0.6542
  time to fit residues: 36.4016
Evaluate side-chains
  50 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 40
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain R residue   89 LEU
Chi-restraints excluded: chain R residue   91 TYR
Chi-restraints excluded: chain R residue  173 VAL
Chi-restraints excluded: chain R residue  178 PHE
Chi-restraints excluded: chain R residue  335 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 100 optimal weight:    8.9990
   chunk 104 optimal weight:    3.9990
   chunk 43 optimal weight:    7.9990
   chunk 52 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0470
   chunk 74 optimal weight:    1.9990
   chunk 61 optimal weight:    5.9990
   chunk 29 optimal weight:    6.9990
   chunk 48 optimal weight:    0.0060
   chunk 9 optimal weight:    6.9990
   chunk 72 optimal weight:    4.9990
   overall best weight:    2.2100

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2589 r_free = 0.2589 target = 0.039793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2349 r_free = 0.2349 target = 0.032175 restraints weight = 56301.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.2322 rms_B_bonded: 2.93
r_work: 0.2237 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9135
moved from start:          0.2378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9082  Z= 0.133
  Angle     :  0.576  11.853  12309  Z= 0.298
  Chirality :  0.041   0.153   1410
  Planarity :  0.004   0.065   1555
  Dihedral  :  4.470  52.728   1245
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 23.75 %
    Favored  : 75.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.04 (0.26), residues: 1127
  helix:  1.30 (0.26), residues: 422
  sheet: -0.32 (0.32), residues: 265
  loop : -1.10 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 283 
 TYR   0.015   0.001   TYR R  91 
 PHE   0.012   0.001   PHE R 141 
 TRP   0.009   0.001   TRP B 169 
 HIS   0.006   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 9079)
  covalent geometry    : angle       0.57637 (12303)
  SS BOND              : bond        0.00262 (    3)
  SS BOND              : angle       0.79058 (    6)
  hydrogen bonds       : bond        0.03698 (  434)
  hydrogen bonds       : angle       4.75147 ( 1254)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2257.13 seconds
wall clock time: 39 minutes 30.10 seconds (2370.10 seconds total)