Starting phenix.real_space_refine
on Sun Apr  5 01:31:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9p7z_71358/04_2026/9p7z_71358.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9p7z_71358/04_2026/9p7z_71358.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9p7z_71358/04_2026/9p7z_71358.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9p7z_71358/04_2026/9p7z_71358.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9p7z_71358/04_2026/9p7z_71358.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9p7z_71358/04_2026/9p7z_71358.cif"
  }
  resolution = 2.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.032
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      51      5.16       5
     C    4374      2.51       5
     N    1161      2.21       5
     O    1243      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6829
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "R"
      Number of atoms: 2286
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 297, 2286
          Classifications: {'peptide': 297}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 287}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 81
          Unresolved non-hydrogen angles: 100
          Unresolved non-hydrogen dihedrals: 65
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 4, 'GLU:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 58
    Chain: "L"
      Number of atoms: 58
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 58
          Classifications: {'peptide': 6}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 4}
    Chain: "A"
      Number of atoms: 1640
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1640
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 34}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 119
          Unresolved non-hydrogen angles: 142
          Unresolved non-hydrogen dihedrals: 96
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 64
    Chain: "B"
      Number of atoms: 2473
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2473
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 128
          Unresolved non-hydrogen angles: 157
          Unresolved non-hydrogen dihedrals: 99
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3, 'GLN:plan1': 5, 'ARG:plan': 7, 'ASN:plan1': 3}
          Unresolved non-hydrogen planarities: 97
    Chain: "C"
      Number of atoms: 372
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 372
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 4, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 20
  Time building chain proxies: 1.66, per 1000 atoms: 0.24
  Number of scatterers: 6829
  At special positions: 0
  Unit cell: (89.856, 95.68, 125.632, 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      51     16.00
     O    1243      8.00
     N    1161      7.00
     C    4374      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 141 " - pdb=" SG  CYS R 224 " 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: 0.58
  Conformation dependent library (CDL) restraints added in 279.2 milliseconds
  

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1726

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 9 sheets defined
      47.6% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'R' and resid 59 through 90
    Processing helix  chain 'R' and resid 100 through 127
      removed outlier: 3.986A  pdb=" N   HIS R 104 " --> pdb=" O   THR R 100 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   MET R 120 " --> pdb=" O   LEU R 116 " (cutoff:3.500A)
      Proline residue:  R 121  - end of helix
    Processing helix  chain 'R' and resid 136 through 172
    Processing helix  chain 'R' and resid 172 through 179
    Processing helix  chain 'R' and resid 181 through 201
    Processing helix  chain 'R' and resid 201 through 206
      removed outlier: 4.058A  pdb=" N   PHE R 205 " --> pdb=" O   VAL R 201 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 218 through 220
      No H-bonds generated for 'chain 'R' and resid 218 through 220'
    Processing helix  chain 'R' and resid 229 through 245
    Processing helix  chain 'R' and resid 245 through 273
    Processing helix  chain 'R' and resid 295 through 329
      Proline residue:  R 318  - end of helix
      removed outlier: 3.804A  pdb=" N   CYS R 327 " --> pdb=" O   ARG R 323 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ILE R 329 " --> pdb=" O   MET R 325 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 330 through 334
    Processing helix  chain 'R' and resid 335 through 364
      removed outlier: 3.725A  pdb=" N   HIS R 343 " --> pdb=" O   TYR R 339 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   SER R 357 " --> pdb=" O   PHE R 353 " (cutoff:3.500A)
      Proline residue:  R 361  - end of helix
    Processing helix  chain 'R' and resid 369 through 374
      removed outlier: 4.403A  pdb=" N   HIS R 373 " --> pdb=" O   ALA R 369 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ILE R 374 " --> pdb=" O   ASN R 370 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 369 through 374'
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.817A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 56
      removed outlier: 3.573A  pdb=" N   ILE A  56 " --> pdb=" O   GLN A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.420A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.724A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.702A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 3.547A  pdb=" N   ALA A 299 " --> pdb=" O   THR A 295 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 11 through 24
      removed outlier: 3.543A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing sheet with id=AA1, first strand: chain 'R' and resid 207 through 211
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191
      removed outlier: 3.595A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.553A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.442A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.630A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.009A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.247A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.498A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.983A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.036A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.085A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.193A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.590A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.003A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.875A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.292A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.444A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.695A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.691A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ASP B 303 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    403 hydrogen bonds defined for protein.
    1161 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: 1.05

  Time building geometry restraints manager: 0.78 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1825
        1.33 -     1.45: 1279
        1.45 -     1.57: 3794
        1.57 -     1.69: 0
        1.69 -     1.81: 74
  Bond restraints: 6972
  Sorted by residual:
  bond pdb=" N   ILE L  12 "
       pdb=" CA  ILE L  12 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.19e-02 7.06e+03 9.13e+00
  bond pdb=" N   TYR L  11 "
       pdb=" CA  TYR L  11 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.034 1.37e-02 5.33e+03 6.33e+00
  bond pdb=" N   ARG L   9 "
       pdb=" CA  ARG L   9 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.55e-02 4.16e+03 4.22e+00
  bond pdb=" C   VAL R 201 "
       pdb=" N   PRO R 202 "
    ideal  model  delta    sigma   weight residual
    1.335  1.359 -0.024 1.19e-02 7.06e+03 4.06e+00
  bond pdb=" N   ARG L   8 "
       pdb=" CA  ARG L   8 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.90e-02 2.77e+03 2.53e+00
  ... (remaining 6967 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 9277
        1.61 -     3.21: 188
        3.21 -     4.82: 23
        4.82 -     6.42: 4
        6.42 -     8.03: 2
  Bond angle restraints: 9494
  Sorted by residual:
  angle pdb=" N   ASP A 315 "
        pdb=" CA  ASP A 315 "
        pdb=" C   ASP A 315 "
      ideal   model   delta    sigma   weight residual
     114.75  109.89    4.86 1.26e+00 6.30e-01 1.49e+01
  angle pdb=" N   TYR L  11 "
        pdb=" CA  TYR L  11 "
        pdb=" C   TYR L  11 "
      ideal   model   delta    sigma   weight residual
     113.72  109.11    4.61 1.30e+00 5.92e-01 1.26e+01
  angle pdb=" N   VAL B  90 "
        pdb=" CA  VAL B  90 "
        pdb=" C   VAL B  90 "
      ideal   model   delta    sigma   weight residual
     111.81  109.39    2.42 8.60e-01 1.35e+00 7.95e+00
  angle pdb=" CB  MET B  61 "
        pdb=" CG  MET B  61 "
        pdb=" SD  MET B  61 "
      ideal   model   delta    sigma   weight residual
     112.70  120.73   -8.03 3.00e+00 1.11e-01 7.16e+00
  angle pdb=" CA  MET B  61 "
        pdb=" CB  MET B  61 "
        pdb=" CG  MET B  61 "
      ideal   model   delta    sigma   weight residual
     114.10  119.39   -5.29 2.00e+00 2.50e-01 7.00e+00
  ... (remaining 9489 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 3670
       17.83 -    35.65: 301
       35.65 -    53.48: 78
       53.48 -    71.31: 21
       71.31 -    89.13: 7
  Dihedral angle restraints: 4077
    sinusoidal: 1417
      harmonic: 2660
  Sorted by residual:
  dihedral pdb=" CB  CYS R 141 "
           pdb=" SG  CYS R 141 "
           pdb=" SG  CYS R 224 "
           pdb=" CB  CYS R 224 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -174.82   88.82     1      1.00e+01 1.00e-02 9.40e+01
  dihedral pdb=" CG  ARG B 219 "
           pdb=" CD  ARG B 219 "
           pdb=" NE  ARG B 219 "
           pdb=" CZ  ARG B 219 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -39.94  -50.06     2      1.50e+01 4.44e-03 1.25e+01
  dihedral pdb=" CA  TRP B  82 "
           pdb=" C   TRP B  82 "
           pdb=" N   ASP B  83 "
           pdb=" CA  ASP B  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.47   17.53     0      5.00e+00 4.00e-02 1.23e+01
  ... (remaining 4074 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 744
       0.036 -    0.073: 273
       0.073 -    0.109: 76
       0.109 -    0.145: 28
       0.145 -    0.182: 2
  Chirality restraints: 1123
  Sorted by residual:
  chirality pdb=" CA  LEU L  13 "
            pdb=" N   LEU L  13 "
            pdb=" C   LEU L  13 "
            pdb=" CB  LEU L  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.25e-01
  chirality pdb=" CA  ILE L  12 "
            pdb=" N   ILE L  12 "
            pdb=" C   ILE L  12 "
            pdb=" CB  ILE L  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.02e-01
  chirality pdb=" CA  MET R 120 "
            pdb=" N   MET R 120 "
            pdb=" C   MET R 120 "
            pdb=" CB  MET R 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.16e-01
  ... (remaining 1120 not shown)

  Planarity restraints: 1194
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG L   9 "   -0.171 9.50e-02 1.11e+02   7.69e-02 3.64e+00
        pdb=" NE  ARG L   9 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG L   9 "    0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG L   9 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG L   9 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.026 5.00e-02 4.00e+02   4.03e-02 2.59e+00
        pdb=" N   PRO B 236 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 201 "   -0.023 5.00e-02 4.00e+02   3.54e-02 2.00e+00
        pdb=" N   PRO R 202 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO R 202 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO R 202 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 1191 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.82: 2056
        2.82 -     3.34: 6348
        3.34 -     3.86: 11832
        3.86 -     4.38: 13440
        4.38 -     4.90: 23260
  Nonbonded interactions: 56936
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 290 "
            pdb=" O   SER A 293 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" NE2 GLN B 220 "
            pdb=" OD1 ASP B 258 "
     model   vdw
     2.317 3.120
  nonbonded pdb=" OD1 ASP A 251 "
            pdb=" ND2 ASN A 255 "
     model   vdw
     2.325 3.120
  nonbonded pdb=" NH1 ARG R 142 "
            pdb=" O   LEU R 204 "
     model   vdw
     2.329 3.120
  nonbonded pdb=" OG1 THR B 321 "
            pdb=" OD1 ASP B 323 "
     model   vdw
     2.361 3.040
  ... (remaining 56931 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:             1.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.120
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
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      :  0.003   0.036   6973  Z= 0.158
  Angle     :  0.559   8.028   9496  Z= 0.329
  Chirality :  0.043   0.182   1123
  Planarity :  0.005   0.077   1194
  Dihedral  : 15.233  89.133   2348
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.69 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 16.76 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  2.12 (0.29), residues: 893
  helix:  3.32 (0.25), residues: 388
  sheet:  1.07 (0.38), residues: 179
  loop : -0.90 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 219 
 TYR   0.012   0.001   TYR R 145 
 PHE   0.014   0.002   PHE B 151 
 TRP   0.013   0.002   TRP B  63 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 6972)
  covalent geometry    : angle       0.55899 ( 9494)
  SS BOND              : bond        0.00400 (    1)
  SS BOND              : angle       1.19480 (    2)
  hydrogen bonds       : bond        0.11371 (  403)
  hydrogen bonds       : angle       5.27320 ( 1161)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.251 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 101
  average time/residue: 0.7706
  time to fit residues: 80.9043
Evaluate side-chains
  100 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   13 LEU
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  331 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
R 126 ASN
R 172 HIS
A 269 ASN
A 311 ASN
B 259 GLN
B 266 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.194846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.154656 restraints weight = 5738.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3794 rms_B_bonded: 1.40
r_work: 0.3619 rms_B_bonded: 1.68 restraints_weight: 0.5000
r_work: 0.3522 rms_B_bonded: 2.68 restraints_weight: 0.2500
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.0738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6973  Z= 0.168
  Angle     :  0.568   7.338   9496  Z= 0.316
  Chirality :  0.044   0.160   1123
  Planarity :  0.005   0.057   1194
  Dihedral  :  4.868  41.331    976
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.02 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 14.29 %
    Favored  : 83.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  1.89 (0.28), residues: 893
  helix:  3.07 (0.25), residues: 395
  sheet:  1.06 (0.39), residues: 162
  loop : -0.98 (0.32), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 219 
 TYR   0.015   0.002   TYR R 145 
 PHE   0.017   0.002   PHE B 151 
 TRP   0.015   0.002   TRP B  63 
 HIS   0.005   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 6972)
  covalent geometry    : angle       0.56803 ( 9494)
  SS BOND              : bond        0.00507 (    1)
  SS BOND              : angle       1.47209 (    2)
  hydrogen bonds       : bond        0.06247 (  403)
  hydrogen bonds       : angle       4.72605 ( 1161)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.232 
Fit side-chains
REVERT: R  333 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7130 (mt0)
  outliers start: 18
  outliers final: 7
  residues processed: 110
  average time/residue: 0.7084
  time to fit residues: 81.2977
Evaluate side-chains
  104 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  232 THR
Chi-restraints excluded: chain R residue  333 GLN
Chi-restraints excluded: chain R residue  356 SER
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  324 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 75 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 85 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   chunk 36 optimal weight:    8.9990
   chunk 83 optimal weight:    9.9990
   chunk 10 optimal weight:    3.9990
   chunk 22 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 71 optimal weight:    1.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
R 126 ASN
A 269 ASN
B 266 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.193869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.153822 restraints weight = 5689.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3789 rms_B_bonded: 1.32
r_work: 0.3597 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.3505 rms_B_bonded: 2.79 restraints_weight: 0.2500
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.0863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6973  Z= 0.177
  Angle     :  0.578   7.734   9496  Z= 0.321
  Chirality :  0.045   0.157   1123
  Planarity :  0.005   0.061   1194
  Dihedral  :  4.862  41.882    972
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.02 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 14.14 %
    Favored  : 83.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  1.74 (0.28), residues: 893
  helix:  2.92 (0.25), residues: 395
  sheet:  0.94 (0.39), residues: 164
  loop : -1.00 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 219 
 TYR   0.014   0.002   TYR R 145 
 PHE   0.017   0.002   PHE B 151 
 TRP   0.015   0.002   TRP B  63 
 HIS   0.006   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 6972)
  covalent geometry    : angle       0.57748 ( 9494)
  SS BOND              : bond        0.00535 (    1)
  SS BOND              : angle       1.67208 (    2)
  hydrogen bonds       : bond        0.06375 (  403)
  hydrogen bonds       : angle       4.72224 ( 1161)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.257 
Fit side-chains
REVERT: R  103 TYR cc_start: 0.7829 (m-80) cc_final: 0.7493 (m-80)
REVERT: R  333 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7144 (mt0)
REVERT: A  294 ASN cc_start: 0.6774 (OUTLIER) cc_final: 0.6308 (t0)
REVERT: A  315 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6867 (p0)
REVERT: B  256 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7562 (mtp180)
  outliers start: 19
  outliers final: 7
  residues processed: 107
  average time/residue: 0.7631
  time to fit residues: 84.9769
Evaluate side-chains
  106 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  333 GLN
Chi-restraints excluded: chain R residue  356 SER
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  256 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 4 optimal weight:    9.9990
   chunk 50 optimal weight:    7.9990
   chunk 45 optimal weight:    1.9990
   chunk 3 optimal weight:    8.9990
   chunk 35 optimal weight:    0.7980
   chunk 28 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9980
   chunk 86 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
R 102 HIS
R 126 ASN
A 269 ASN
B 266 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.193687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.153320 restraints weight = 5787.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3786 rms_B_bonded: 1.22
r_work: 0.3607 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3513 rms_B_bonded: 2.68 restraints_weight: 0.2500
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.0968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6973  Z= 0.178
  Angle     :  0.581   7.676   9496  Z= 0.323
  Chirality :  0.045   0.158   1123
  Planarity :  0.005   0.061   1194
  Dihedral  :  4.906  41.893    972
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.14 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 13.56 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  1.74 (0.28), residues: 893
  helix:  2.91 (0.25), residues: 395
  sheet:  0.98 (0.39), residues: 164
  loop : -1.01 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 219 
 TYR   0.012   0.002   TYR R 145 
 PHE   0.017   0.002   PHE B 151 
 TRP   0.015   0.002   TRP B  63 
 HIS   0.006   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 6972)
  covalent geometry    : angle       0.58111 ( 9494)
  SS BOND              : bond        0.00479 (    1)
  SS BOND              : angle       1.55624 (    2)
  hydrogen bonds       : bond        0.06361 (  403)
  hydrogen bonds       : angle       4.69782 ( 1161)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.276 
Fit side-chains
REVERT: R  103 TYR cc_start: 0.7821 (m-80) cc_final: 0.7392 (m-80)
REVERT: R  333 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7109 (mt0)
REVERT: A  294 ASN cc_start: 0.6763 (OUTLIER) cc_final: 0.6294 (t0)
REVERT: A  315 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.6892 (p0)
REVERT: B  137 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8188 (tpp-160)
REVERT: B  256 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7538 (mtp180)
  outliers start: 22
  outliers final: 8
  residues processed: 110
  average time/residue: 0.7446
  time to fit residues: 85.3207
Evaluate side-chains
  109 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  295 VAL
Chi-restraints excluded: chain R residue  333 GLN
Chi-restraints excluded: chain R residue  356 SER
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  256 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 77 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 43 optimal weight:   10.0000
   chunk 26 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   chunk 63 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
R 104 HIS
R 126 ASN
A 269 ASN
B 266 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.195133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.150842 restraints weight = 5804.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3761 rms_B_bonded: 1.36
r_work: 0.3592 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3494 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.0947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6973  Z= 0.148
  Angle     :  0.535   7.838   9496  Z= 0.297
  Chirality :  0.043   0.145   1123
  Planarity :  0.004   0.046   1194
  Dihedral  :  4.721  40.862    972
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.80 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 14.29 %
    Favored  : 82.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  1.87 (0.28), residues: 893
  helix:  3.09 (0.25), residues: 394
  sheet:  1.05 (0.38), residues: 174
  loop : -1.10 (0.33), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 219 
 TYR   0.012   0.002   TYR R 319 
 PHE   0.016   0.002   PHE B 151 
 TRP   0.013   0.002   TRP B  63 
 HIS   0.004   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6972)
  covalent geometry    : angle       0.53497 ( 9494)
  SS BOND              : bond        0.00414 (    1)
  SS BOND              : angle       1.34979 (    2)
  hydrogen bonds       : bond        0.05735 (  403)
  hydrogen bonds       : angle       4.56168 ( 1161)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.280 
Fit side-chains
REVERT: R  103 TYR cc_start: 0.7848 (m-80) cc_final: 0.7422 (m-80)
REVERT: R  333 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7129 (mt0)
REVERT: A  294 ASN cc_start: 0.6783 (OUTLIER) cc_final: 0.6332 (t0)
REVERT: A  315 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.6862 (p0)
REVERT: B  256 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7528 (mtp180)
  outliers start: 19
  outliers final: 11
  residues processed: 108
  average time/residue: 0.7268
  time to fit residues: 81.7036
Evaluate side-chains
  109 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  201 VAL
Chi-restraints excluded: chain R residue  232 THR
Chi-restraints excluded: chain R residue  295 VAL
Chi-restraints excluded: chain R residue  333 GLN
Chi-restraints excluded: chain R residue  355 VAL
Chi-restraints excluded: chain R residue  356 SER
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  256 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    0.0970
   chunk 12 optimal weight:    0.9990
   chunk 48 optimal weight:    8.9990
   chunk 70 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0770
   chunk 86 optimal weight:    3.9990
   chunk 21 optimal weight:    8.9990
   chunk 30 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 8 optimal weight:    0.5980
   chunk 87 optimal weight:    0.0570
   overall best weight:    0.3656

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

Flipped N/Q/H residues before XYZ refinement:
R 126 ASN
A 269 ASN
B 266 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.199500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.158380 restraints weight = 5869.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3852 rms_B_bonded: 1.35
r_work: 0.3720 rms_B_bonded: 1.52 restraints_weight: 0.5000
r_work: 0.3626 rms_B_bonded: 2.44 restraints_weight: 0.2500
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.1092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6973  Z= 0.101
  Angle     :  0.447   6.929   9496  Z= 0.246
  Chirality :  0.040   0.134   1123
  Planarity :  0.004   0.045   1194
  Dihedral  :  4.156  37.060    972
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.58 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 15.45 %
    Favored  : 82.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  2.17 (0.28), residues: 893
  helix:  3.41 (0.25), residues: 394
  sheet:  1.08 (0.37), residues: 178
  loop : -1.01 (0.33), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 219 
 TYR   0.013   0.001   TYR R 319 
 PHE   0.013   0.001   PHE A 189 
 TRP   0.011   0.001   TRP B 169 
 HIS   0.001   0.000   HIS R 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00190 ( 6972)
  covalent geometry    : angle       0.44690 ( 9494)
  SS BOND              : bond        0.00314 (    1)
  SS BOND              : angle       0.82432 (    2)
  hydrogen bonds       : bond        0.04241 (  403)
  hydrogen bonds       : angle       4.23165 ( 1161)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.264 
Fit side-chains
REVERT: R  103 TYR cc_start: 0.7756 (m-80) cc_final: 0.7334 (m-80)
REVERT: R  306 ARG cc_start: 0.7623 (mtm180) cc_final: 0.7332 (mtt180)
REVERT: A  294 ASN cc_start: 0.6795 (OUTLIER) cc_final: 0.6360 (t0)
REVERT: B  137 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8008 (tpp-160)
REVERT: B  217 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.8079 (ppp)
REVERT: B  256 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7419 (mtp180)
REVERT: C   32 LYS cc_start: 0.7564 (tptp) cc_final: 0.7348 (tttm)
  outliers start: 17
  outliers final: 7
  residues processed: 109
  average time/residue: 0.7558
  time to fit residues: 85.6393
Evaluate side-chains
  105 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  232 THR
Chi-restraints excluded: chain R residue  355 VAL
Chi-restraints excluded: chain R residue  356 SER
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  256 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 70 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 74 optimal weight:    0.0980
   chunk 26 optimal weight:    4.9990
   chunk 25 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
R 126 ASN
A 269 ASN
A 306 GLN
B 266 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.196192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.153332 restraints weight = 5728.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3781 rms_B_bonded: 1.44
r_work: 0.3624 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3525 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.1000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6973  Z= 0.131
  Angle     :  0.505   6.899   9496  Z= 0.279
  Chirality :  0.042   0.142   1123
  Planarity :  0.004   0.046   1194
  Dihedral  :  4.459  38.281    972
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.91 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 15.74 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  2.10 (0.28), residues: 893
  helix:  3.33 (0.25), residues: 394
  sheet:  1.15 (0.38), residues: 174
  loop : -1.05 (0.33), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 219 
 TYR   0.011   0.001   TYR R 145 
 PHE   0.015   0.002   PHE B 151 
 TRP   0.013   0.002   TRP B  82 
 HIS   0.003   0.001   HIS R 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 6972)
  covalent geometry    : angle       0.50460 ( 9494)
  SS BOND              : bond        0.00390 (    1)
  SS BOND              : angle       1.10367 (    2)
  hydrogen bonds       : bond        0.05251 (  403)
  hydrogen bonds       : angle       4.40780 ( 1161)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.266 
Fit side-chains
REVERT: R  103 TYR cc_start: 0.7800 (m-80) cc_final: 0.7332 (m-80)
REVERT: R  306 ARG cc_start: 0.7674 (mtm180) cc_final: 0.7359 (mtt180)
REVERT: A  294 ASN cc_start: 0.6798 (OUTLIER) cc_final: 0.6349 (t0)
REVERT: B  137 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8173 (tpp-160)
REVERT: B  217 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8138 (ppp)
REVERT: B  256 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7471 (mtp180)
  outliers start: 16
  outliers final: 10
  residues processed: 102
  average time/residue: 0.7736
  time to fit residues: 82.1396
Evaluate side-chains
  107 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  201 VAL
Chi-restraints excluded: chain R residue  225 THR
Chi-restraints excluded: chain R residue  232 THR
Chi-restraints excluded: chain R residue  355 VAL
Chi-restraints excluded: chain R residue  356 SER
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  256 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 8 optimal weight:    0.6980
   chunk 61 optimal weight:    0.6980
   chunk 60 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 79 optimal weight:    5.9990
   chunk 84 optimal weight:   10.0000
   chunk 54 optimal weight:    0.4980
   chunk 39 optimal weight:   10.0000
   chunk 62 optimal weight:    0.5980
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
R 126 ASN
A 306 GLN
B 266 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.197718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.156623 restraints weight = 5831.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.3828 rms_B_bonded: 1.28
r_work: 0.3646 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3552 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.1056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6973  Z= 0.112
  Angle     :  0.474   7.510   9496  Z= 0.260
  Chirality :  0.041   0.136   1123
  Planarity :  0.004   0.045   1194
  Dihedral  :  4.266  35.231    972
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.13 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 15.16 %
    Favored  : 82.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  2.16 (0.28), residues: 893
  helix:  3.40 (0.25), residues: 394
  sheet:  1.10 (0.37), residues: 178
  loop : -1.03 (0.33), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 219 
 TYR   0.012   0.001   TYR R 319 
 PHE   0.013   0.001   PHE A 189 
 TRP   0.011   0.002   TRP B  82 
 HIS   0.002   0.001   HIS R 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 6972)
  covalent geometry    : angle       0.47357 ( 9494)
  SS BOND              : bond        0.00328 (    1)
  SS BOND              : angle       0.85362 (    2)
  hydrogen bonds       : bond        0.04679 (  403)
  hydrogen bonds       : angle       4.28887 ( 1161)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.196 
Fit side-chains
REVERT: R  103 TYR cc_start: 0.7841 (m-80) cc_final: 0.7398 (m-80)
REVERT: R  306 ARG cc_start: 0.7688 (mtm180) cc_final: 0.7384 (mtt180)
REVERT: A  294 ASN cc_start: 0.6822 (OUTLIER) cc_final: 0.6366 (t0)
REVERT: B  137 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8108 (tpp-160)
REVERT: B  217 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8146 (ppp)
REVERT: B  256 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7463 (mtp180)
  outliers start: 19
  outliers final: 9
  residues processed: 102
  average time/residue: 0.7474
  time to fit residues: 79.2953
Evaluate side-chains
  104 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  201 VAL
Chi-restraints excluded: chain R residue  232 THR
Chi-restraints excluded: chain R residue  355 VAL
Chi-restraints excluded: chain R residue  356 SER
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  256 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 78 optimal weight:    7.9990
   chunk 34 optimal weight:    0.0050
   chunk 22 optimal weight:    7.9990
   chunk 19 optimal weight:    0.8980
   chunk 83 optimal weight:   10.0000
   chunk 14 optimal weight:    0.9990
   chunk 33 optimal weight:    6.9990
   chunk 4 optimal weight:   10.0000
   chunk 16 optimal weight:    4.9990
   chunk 9 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.7800

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

Flipped N/Q/H residues before XYZ refinement:
R 126 ASN
B 266 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.194154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.154277 restraints weight = 5780.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.3804 rms_B_bonded: 1.20
r_work: 0.3619 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.3526 rms_B_bonded: 2.59 restraints_weight: 0.2500
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.1137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6973  Z= 0.179
  Angle     :  0.586   8.822   9496  Z= 0.322
  Chirality :  0.045   0.159   1123
  Planarity :  0.005   0.058   1194
  Dihedral  :  4.837  40.728    972
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.25 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 15.74 %
    Favored  : 82.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  1.90 (0.28), residues: 893
  helix:  3.12 (0.25), residues: 394
  sheet:  1.09 (0.40), residues: 162
  loop : -1.02 (0.32), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 219 
 TYR   0.012   0.002   TYR R 145 
 PHE   0.018   0.002   PHE B 151 
 TRP   0.021   0.002   TRP R 316 
 HIS   0.005   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 6972)
  covalent geometry    : angle       0.58532 ( 9494)
  SS BOND              : bond        0.00386 (    1)
  SS BOND              : angle       1.58952 (    2)
  hydrogen bonds       : bond        0.06296 (  403)
  hydrogen bonds       : angle       4.63318 ( 1161)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.256 
Fit side-chains
REVERT: A  294 ASN cc_start: 0.6810 (OUTLIER) cc_final: 0.6328 (t0)
REVERT: B  137 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8216 (tpp-160)
REVERT: B  217 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8172 (ppp)
REVERT: B  256 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7572 (mtp180)
  outliers start: 15
  outliers final: 9
  residues processed: 101
  average time/residue: 0.7714
  time to fit residues: 81.0729
Evaluate side-chains
  105 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  201 VAL
Chi-restraints excluded: chain R residue  225 THR
Chi-restraints excluded: chain R residue  232 THR
Chi-restraints excluded: chain R residue  356 SER
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  256 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 70 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 77 optimal weight:    0.4980
   chunk 81 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 34 optimal weight:    7.9990
   chunk 19 optimal weight:    0.7980
   chunk 39 optimal weight:    9.9990
   chunk 49 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
R 126 ASN
A 306 GLN
B 266 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.196726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.156372 restraints weight = 5790.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.3827 rms_B_bonded: 1.28
r_work: 0.3641 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.3544 rms_B_bonded: 2.81 restraints_weight: 0.2500
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.1063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6973  Z= 0.121
  Angle     :  0.496   8.957   9496  Z= 0.271
  Chirality :  0.042   0.138   1123
  Planarity :  0.004   0.045   1194
  Dihedral  :  4.434  35.976    972
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.35 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 15.74 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  2.07 (0.28), residues: 893
  helix:  3.31 (0.25), residues: 394
  sheet:  1.13 (0.38), residues: 174
  loop : -1.07 (0.33), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 219 
 TYR   0.012   0.001   TYR R 319 
 PHE   0.013   0.001   PHE A 189 
 TRP   0.013   0.002   TRP R 316 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 6972)
  covalent geometry    : angle       0.49589 ( 9494)
  SS BOND              : bond        0.00273 (    1)
  SS BOND              : angle       0.99795 (    2)
  hydrogen bonds       : bond        0.04960 (  403)
  hydrogen bonds       : angle       4.37662 ( 1161)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.256 
Fit side-chains
REVERT: R  103 TYR cc_start: 0.7823 (m-80) cc_final: 0.7288 (m-80)
REVERT: R  306 ARG cc_start: 0.7700 (mtm180) cc_final: 0.7404 (mtt180)
REVERT: A  294 ASN cc_start: 0.6784 (OUTLIER) cc_final: 0.6332 (t0)
REVERT: B  137 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8092 (tpp-160)
REVERT: B  217 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.8103 (ppp)
REVERT: B  256 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7507 (mtp180)
  outliers start: 14
  outliers final: 8
  residues processed: 101
  average time/residue: 0.7498
  time to fit residues: 78.9663
Evaluate side-chains
  103 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  201 VAL
Chi-restraints excluded: chain R residue  232 THR
Chi-restraints excluded: chain R residue  356 SER
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  256 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 41 optimal weight:    0.4980
   chunk 52 optimal weight:    5.9990
   chunk 72 optimal weight:    0.2980
   chunk 45 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0020
   chunk 31 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.4988

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

Flipped N/Q/H residues before XYZ refinement:
R 126 ASN
A 306 GLN
B 266 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.198618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.158600 restraints weight = 5818.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.3842 rms_B_bonded: 1.25
r_work: 0.3704 rms_B_bonded: 1.50 restraints_weight: 0.5000
r_work: 0.3604 rms_B_bonded: 2.42 restraints_weight: 0.2500
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.1194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6973  Z= 0.105
  Angle     :  0.466   8.828   9496  Z= 0.254
  Chirality :  0.041   0.134   1123
  Planarity :  0.004   0.045   1194
  Dihedral  :  4.178  34.497    972
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.69 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 16.18 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  2.22 (0.28), residues: 893
  helix:  3.55 (0.25), residues: 388
  sheet:  1.08 (0.37), residues: 179
  loop : -1.01 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 219 
 TYR   0.012   0.001   TYR R 319 
 PHE   0.012   0.001   PHE A 189 
 TRP   0.010   0.002   TRP B  82 
 HIS   0.002   0.001   HIS R 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00200 ( 6972)
  covalent geometry    : angle       0.46612 ( 9494)
  SS BOND              : bond        0.00241 (    1)
  SS BOND              : angle       0.82065 (    2)
  hydrogen bonds       : bond        0.04359 (  403)
  hydrogen bonds       : angle       4.22718 ( 1161)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4410.30 seconds
wall clock time: 75 minutes 26.79 seconds (4526.79 seconds total)