Starting phenix.real_space_refine
on Sun Apr  5 00:11:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9p88_71368/04_2026/9p88_71368.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9p88_71368/04_2026/9p88_71368.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9p88_71368/04_2026/9p88_71368.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9p88_71368/04_2026/9p88_71368.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9p88_71368/04_2026/9p88_71368.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9p88_71368/04_2026/9p88_71368.cif"
  }
  resolution = 2.9
  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=   0.036
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      36      5.16       5
     C    4068      2.51       5
     N    1084      2.21       5
     O    1113      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-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6301
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 2429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2429
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 55}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 179
          Unresolved non-hydrogen angles: 226
          Unresolved non-hydrogen dihedrals: 134
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 9, 'GLN:plan1': 6, 'ARG:plan': 7, 'ASN:plan1': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 132
    Chain: "G"
      Number of atoms: 362
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 362
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 67
          Unresolved non-hydrogen angles: 80
          Unresolved non-hydrogen dihedrals: 54
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 32
    Chain: "A"
      Number of atoms: 1465
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1465
          Classifications: {'peptide': 219}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 95}
          Link IDs: {'PTRANS': 5, 'TRANS': 213}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 365
          Unresolved non-hydrogen angles: 454
          Unresolved non-hydrogen dihedrals: 292
          Unresolved non-hydrogen chiralities: 17
          Planarities with less than four sites: {'GLU:plan': 16, 'ARG:plan': 13, 'ASN:plan1': 8, 'GLN:plan1': 6, 'ASP:plan': 13, 'HIS:plan': 2, 'TYR:plan': 4}
          Unresolved non-hydrogen planarities: 254
    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: "R"
      Number of atoms: 1987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 1987
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 101}
          Link IDs: {'PTRANS': 10, 'TRANS': 277}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 325
          Unresolved non-hydrogen angles: 413
          Unresolved non-hydrogen dihedrals: 254
          Unresolved non-hydrogen chiralities: 41
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 5, 'ASN:plan1': 5, 'TYR:plan': 1, 'PHE:plan': 2, 'ARG:plan': 10, 'GLN:plan1': 6, 'HIS:plan': 5}
          Unresolved non-hydrogen planarities: 164
  Time building chain proxies: 1.31, per 1000 atoms: 0.21
  Number of scatterers: 6301
  At special positions: 0
  Unit cell: (76.544, 99.008, 126.464, 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      36     16.00
     O    1113      8.00
     N    1084      7.00
     C    4068      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: 0.52
  Conformation dependent library (CDL) restraints added in 350.5 milliseconds
  

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1728

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 9 sheets defined
      49.6% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'B' and resid 2 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 8 through 24
      removed outlier: 3.589A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.805A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'A' and resid 15 through 38
      removed outlier: 4.120A  pdb=" N   ARG A  38 " --> pdb=" O   ARG A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 63
    Processing helix  chain 'A' and resid 212 through 221
      removed outlier: 4.991A  pdb=" N   ILE A 217 " --> pdb=" O   ARG A 214 " (cutoff:3.500A)
      removed outlier: 5.796A  pdb=" N   HIS A 218 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 235
      No H-bonds generated for 'chain 'A' and resid 233 through 235'
    Processing helix  chain 'A' and resid 246 through 261
      removed outlier: 3.665A  pdb=" N   GLU A 250 " --> pdb=" O   ASN A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 265
    Processing helix  chain 'A' and resid 275 through 286
    Processing helix  chain 'A' and resid 287 through 291
    Processing helix  chain 'A' and resid 301 through 316
    Processing helix  chain 'A' and resid 335 through 356
    Processing helix  chain 'R' and resid 59 through 90
    Processing helix  chain 'R' and resid 99 through 118
    Processing helix  chain 'R' and resid 119 through 129
      removed outlier: 3.516A  pdb=" N   ILE R 128 " --> pdb=" O   LEU R 124 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 137 through 172
    Processing helix  chain 'R' and resid 172 through 179
    Processing helix  chain 'R' and resid 181 through 206
      Proline residue:  R 202  - end of helix
    Processing helix  chain 'R' and resid 229 through 245
    Processing helix  chain 'R' and resid 245 through 270
    Processing helix  chain 'R' and resid 293 through 329
      Proline residue:  R 318  - end of helix
    Processing helix  chain 'R' and resid 335 through 368
      removed outlier: 3.896A  pdb=" N   SER R 357 " --> pdb=" O   PHE R 353 " (cutoff:3.500A)
      Proline residue:  R 361  - end of helix
      removed outlier: 4.427A  pdb=" N   TYR R 364 " --> pdb=" O   ASN R 360 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 368 through 374
    Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.724A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.694A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.952A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.900A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.035A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.116A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.173A  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: 6.647A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.064A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.833A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.843A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (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: 4.388A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.461A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.542A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.848A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.924A  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: 3.647A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 190 through 195
      removed outlier: 3.660A  pdb=" N   SER A 225 " --> pdb=" O   LYS A  41 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   ILE A 226 " --> pdb=" O   ILE A 270 " (cutoff:3.500A)
      removed outlier: 7.381A  pdb=" N   PHE A 272 " --> pdb=" O   ILE A 226 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   PHE A 228 " --> pdb=" O   PHE A 272 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   ASN A 274 " --> pdb=" O   PHE A 228 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   VAL A 230 " --> pdb=" O   ASN A 274 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 207 through 210

    423 hydrogen bonds defined for protein.
    1224 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: 0.94

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1021
        1.32 -     1.44: 1752
        1.44 -     1.57: 3608
        1.57 -     1.69: 0
        1.69 -     1.81: 51
  Bond restraints: 6432
  Sorted by residual:
  bond pdb=" N   TYR A 356 "
       pdb=" CA  TYR A 356 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.036 1.18e-02 7.18e+03 9.42e+00
  bond pdb=" N   ILE A 259 "
       pdb=" CA  ILE A 259 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 1.19e-02 7.06e+03 8.23e+00
  bond pdb=" N   SER A 320 "
       pdb=" CA  SER A 320 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.033 1.17e-02 7.31e+03 8.04e+00
  bond pdb=" N   TYR A 285 "
       pdb=" CA  TYR A 285 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.14e-02 7.69e+03 7.89e+00
  bond pdb=" N   ASN A 274 "
       pdb=" CA  ASN A 274 "
    ideal  model  delta    sigma   weight residual
    1.452  1.488 -0.035 1.25e-02 6.40e+03 7.84e+00
  ... (remaining 6427 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 8320
        1.51 -     3.02: 436
        3.02 -     4.53: 45
        4.53 -     6.04: 6
        6.04 -     7.56: 4
  Bond angle restraints: 8811
  Sorted by residual:
  angle pdb=" N   TYR A 356 "
        pdb=" CA  TYR A 356 "
        pdb=" C   TYR A 356 "
      ideal   model   delta    sigma   weight residual
     112.72  108.29    4.43 1.14e+00 7.69e-01 1.51e+01
  angle pdb=" N   TYR L  11 "
        pdb=" CA  TYR L  11 "
        pdb=" C   TYR L  11 "
      ideal   model   delta    sigma   weight residual
     113.88  109.40    4.48 1.23e+00 6.61e-01 1.33e+01
  angle pdb=" N   ASP A 296 "
        pdb=" CA  ASP A 296 "
        pdb=" C   ASP A 296 "
      ideal   model   delta    sigma   weight residual
     113.72  109.03    4.69 1.30e+00 5.92e-01 1.30e+01
  angle pdb=" C   TYR A 356 "
        pdb=" CA  TYR A 356 "
        pdb=" CB  TYR A 356 "
      ideal   model   delta    sigma   weight residual
     110.94  116.86   -5.92 1.65e+00 3.67e-01 1.29e+01
  angle pdb=" CA  ASN A 357 "
        pdb=" C   ASN A 357 "
        pdb=" O   ASN A 357 "
      ideal   model   delta    sigma   weight residual
     121.84  117.80    4.04 1.16e+00 7.43e-01 1.21e+01
  ... (remaining 8806 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.52: 3351
       16.52 -    33.04: 278
       33.04 -    49.56: 75
       49.56 -    66.07: 18
       66.07 -    82.59: 3
  Dihedral angle restraints: 3725
    sinusoidal: 1071
      harmonic: 2654
  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
      93.00   49.39   43.61     1      1.00e+01 1.00e-02 2.65e+01
  dihedral pdb=" CG  ARG B  19 "
           pdb=" CD  ARG B  19 "
           pdb=" NE  ARG B  19 "
           pdb=" CZ  ARG B  19 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   40.99   49.01     2      1.50e+01 4.44e-03 1.22e+01
  dihedral pdb=" CA  PHE B 151 "
           pdb=" C   PHE B 151 "
           pdb=" N   LEU B 152 "
           pdb=" CA  LEU B 152 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.50   16.50     0      5.00e+00 4.00e-02 1.09e+01
  ... (remaining 3722 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 705
       0.043 -    0.085: 241
       0.085 -    0.128: 91
       0.128 -    0.170: 23
       0.170 -    0.213: 9
  Chirality restraints: 1069
  Sorted by residual:
  chirality pdb=" CA  ILE A 190 "
            pdb=" N   ILE A 190 "
            pdb=" C   ILE A 190 "
            pdb=" CB  ILE A 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CA  ILE A 323 "
            pdb=" N   ILE A 323 "
            pdb=" C   ILE A 323 "
            pdb=" CB  ILE A 323 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CA  ILE A 270 "
            pdb=" N   ILE A 270 "
            pdb=" C   ILE A 270 "
            pdb=" CB  ILE A 270 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 1.00e+00
  ... (remaining 1066 not shown)

  Planarity restraints: 1121
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG L   8 "    0.303 9.50e-02 1.11e+02   1.36e-01 1.13e+01
        pdb=" NE  ARG L   8 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG L   8 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG L   8 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG L   8 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 201 "   -0.040 5.00e-02 4.00e+02   5.97e-02 5.69e+00
        pdb=" N   PRO R 202 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO R 202 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO R 202 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  55 "    0.013 2.00e-02 2.50e+03   1.63e-02 4.66e+00
        pdb=" CG  PHE A  55 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  55 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  55 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  55 "    0.029 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  55 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  55 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1118 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 583
        2.74 -     3.28: 6207
        3.28 -     3.82: 10992
        3.82 -     4.36: 12124
        4.36 -     4.90: 21852
  Nonbonded interactions: 51758
  Sorted by model distance:
  nonbonded pdb=" OG  SER R 107 "
            pdb=" OD1 ASN R 158 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" O   PHE R 345 "
            pdb=" OG1 THR R 349 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.336 3.040
  nonbonded pdb=" OG1 THR B  34 "
            pdb=" O   LEU B 300 "
     model   vdw
     2.354 3.040
  nonbonded pdb=" O   TRP R 193 "
            pdb=" OG  SER R 196 "
     model   vdw
     2.369 3.040
  ... (remaining 51753 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:             1.380
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.270
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:6.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
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   0.052   6433  Z= 0.359
  Angle     :  0.720   7.555   8813  Z= 0.493
  Chirality :  0.052   0.213   1069
  Planarity :  0.006   0.136   1121
  Dihedral  : 14.457  82.593   1994
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 21.08 %
    Favored  : 77.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.42 (0.28), residues: 888
  helix:  2.82 (0.24), residues: 406
  sheet:  0.04 (0.37), residues: 175
  loop : -1.15 (0.33), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  19 
 TYR   0.016   0.001   TYR R 339 
 PHE   0.029   0.002   PHE A  55 
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00530 ( 6432)
  covalent geometry    : angle       0.72001 ( 8811)
  SS BOND              : bond        0.00258 (    1)
  SS BOND              : angle       1.36557 (    2)
  hydrogen bonds       : bond        0.12421 (  423)
  hydrogen bonds       : angle       5.63395 ( 1224)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.224 
Fit side-chains
REVERT: B  228 ASP cc_start: 0.7877 (m-30) cc_final: 0.7391 (m-30)
REVERT: B  234 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.7117 (t80)
  outliers start: 5
  outliers final: 3
  residues processed: 102
  average time/residue: 0.4290
  time to fit residues: 46.4828
Evaluate side-chains
  89 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 85
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue  141 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0870
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    9.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:   30.0000
   overall best weight:    1.8166

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

Flipped N/Q/H residues before XYZ refinement:
R 343 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.202275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.164940 restraints weight = 6699.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.3779 rms_B_bonded: 1.42
r_work: 0.3460 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.1004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   6433  Z= 0.203
  Angle     :  0.612   8.402   8813  Z= 0.329
  Chirality :  0.045   0.203   1069
  Planarity :  0.005   0.044   1121
  Dihedral  :  5.471  57.322    962
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  5.42 %
    Allowed  : 16.05 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.50 (0.28), residues: 888
  helix:  2.98 (0.24), residues: 409
  sheet: -0.17 (0.37), residues: 188
  loop : -1.17 (0.34), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  19 
 TYR   0.017   0.002   TYR A 356 
 PHE   0.025   0.002   PHE B 151 
 TRP   0.012   0.002   TRP B  63 
 HIS   0.004   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 ( 6432)
  covalent geometry    : angle       0.61197 ( 8811)
  SS BOND              : bond        0.00283 (    1)
  SS BOND              : angle       0.80412 (    2)
  hydrogen bonds       : bond        0.05315 (  423)
  hydrogen bonds       : angle       4.74013 ( 1224)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 96
  time to evaluate  : 0.166 
Fit side-chains
REVERT: B  228 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7781 (m-30)
REVERT: B  234 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.7353 (t80)
REVERT: B  318 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8532 (pp)
REVERT: B  338 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7625 (mm)
REVERT: A  356 TYR cc_start: 0.6472 (OUTLIER) cc_final: 0.5468 (p90)
REVERT: R   87 THR cc_start: 0.8000 (m) cc_final: 0.7726 (p)
REVERT: R  371 PHE cc_start: 0.5409 (t80) cc_final: 0.4879 (t80)
  outliers start: 28
  outliers final: 12
  residues processed: 115
  average time/residue: 0.4063
  time to fit residues: 49.7160
Evaluate side-chains
  111 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  221 GLU
Chi-restraints excluded: chain A residue  248 MET
Chi-restraints excluded: chain A residue  275 LYS
Chi-restraints excluded: chain A residue  333 ASP
Chi-restraints excluded: chain A residue  356 TYR
Chi-restraints excluded: chain R residue   56 VAL
Chi-restraints excluded: chain R residue  117 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 80 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 73 optimal weight:    9.9990
   chunk 69 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 75 optimal weight:   30.0000
   chunk 74 optimal weight:    0.6980
   chunk 52 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.204639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.172700 restraints weight = 6691.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.3880 rms_B_bonded: 1.26
r_work: 0.3562 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.1256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6433  Z= 0.133
  Angle     :  0.517   6.014   8813  Z= 0.280
  Chirality :  0.042   0.167   1069
  Planarity :  0.004   0.044   1121
  Dihedral  :  5.175  56.300    961
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 17.60 %
    Favored  : 78.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.69 (0.29), residues: 888
  helix:  3.16 (0.24), residues: 409
  sheet: -0.12 (0.37), residues: 186
  loop : -1.07 (0.34), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  19 
 TYR   0.014   0.001   TYR A 356 
 PHE   0.017   0.001   PHE B 151 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6432)
  covalent geometry    : angle       0.51632 ( 8811)
  SS BOND              : bond        0.00319 (    1)
  SS BOND              : angle       1.47957 (    2)
  hydrogen bonds       : bond        0.04382 (  423)
  hydrogen bonds       : angle       4.41850 ( 1224)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.186 
Fit side-chains
REVERT: B  234 PHE cc_start: 0.8429 (OUTLIER) cc_final: 0.7410 (t80)
REVERT: R   87 THR cc_start: 0.8056 (m) cc_final: 0.7814 (p)
REVERT: R  357 SER cc_start: 0.8380 (p) cc_final: 0.7846 (m)
REVERT: R  371 PHE cc_start: 0.5046 (t80) cc_final: 0.4766 (t80)
  outliers start: 18
  outliers final: 9
  residues processed: 109
  average time/residue: 0.4084
  time to fit residues: 47.3552
Evaluate side-chains
  105 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  221 GLU
Chi-restraints excluded: chain A residue  248 MET
Chi-restraints excluded: chain A residue  333 ASP
Chi-restraints excluded: chain R residue   56 VAL
Chi-restraints excluded: chain R residue  141 CYS
Chi-restraints excluded: chain R residue  338 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 78 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0370
   chunk 84 optimal weight:    1.9990
   chunk 62 optimal weight:   10.0000
   chunk 31 optimal weight:    0.7980
   chunk 3 optimal weight:    6.9990
   chunk 82 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.7260

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

Flipped N/Q/H residues before XYZ refinement:
** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.205180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.173110 restraints weight = 6716.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3886 rms_B_bonded: 1.30
r_work: 0.3516 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.1470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6433  Z= 0.121
  Angle     :  0.493   5.398   8813  Z= 0.268
  Chirality :  0.042   0.178   1069
  Planarity :  0.004   0.046   1121
  Dihedral  :  4.480  55.054    957
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 17.60 %
    Favored  : 77.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.92 (0.29), residues: 888
  helix:  3.33 (0.24), residues: 409
  sheet:  0.07 (0.38), residues: 182
  loop : -0.99 (0.35), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  19 
 TYR   0.021   0.001   TYR R 153 
 PHE   0.016   0.001   PHE B 151 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 6432)
  covalent geometry    : angle       0.49231 ( 8811)
  SS BOND              : bond        0.00338 (    1)
  SS BOND              : angle       1.33804 (    2)
  hydrogen bonds       : bond        0.04063 (  423)
  hydrogen bonds       : angle       4.21953 ( 1224)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 97
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
REVERT: B  234 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.7364 (t80)
REVERT: A  356 TYR cc_start: 0.6454 (OUTLIER) cc_final: 0.5252 (p90)
REVERT: R  357 SER cc_start: 0.8329 (p) cc_final: 0.7810 (m)
REVERT: R  371 PHE cc_start: 0.5183 (t80) cc_final: 0.4945 (t80)
  outliers start: 27
  outliers final: 14
  residues processed: 114
  average time/residue: 0.4018
  time to fit residues: 48.8646
Evaluate side-chains
  112 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  221 GLU
Chi-restraints excluded: chain A residue  248 MET
Chi-restraints excluded: chain A residue  275 LYS
Chi-restraints excluded: chain A residue  333 ASP
Chi-restraints excluded: chain A residue  356 TYR
Chi-restraints excluded: chain R residue   56 VAL
Chi-restraints excluded: chain R residue  141 CYS
Chi-restraints excluded: chain R residue  338 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 79 optimal weight:    6.9990
   chunk 60 optimal weight:   20.0000
   chunk 61 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0870
   chunk 10 optimal weight:    0.5980
   chunk 38 optimal weight:   10.0000
   chunk 34 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.6958

-------------------------------------------------------------------------------
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 = 0.4217 r_free = 0.4217 target = 0.205381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.171073 restraints weight = 6789.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.3866 rms_B_bonded: 1.32
r_work: 0.3565 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.1607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6433  Z= 0.118
  Angle     :  0.488   5.359   8813  Z= 0.265
  Chirality :  0.042   0.202   1069
  Planarity :  0.004   0.049   1121
  Dihedral  :  4.443  54.541    957
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 19.92 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.99 (0.29), residues: 888
  helix:  3.40 (0.24), residues: 409
  sheet:  0.10 (0.38), residues: 182
  loop : -0.97 (0.35), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  19 
 TYR   0.014   0.001   TYR A 356 
 PHE   0.015   0.001   PHE B 151 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 6432)
  covalent geometry    : angle       0.48817 ( 8811)
  SS BOND              : bond        0.00256 (    1)
  SS BOND              : angle       1.08568 (    2)
  hydrogen bonds       : bond        0.03940 (  423)
  hydrogen bonds       : angle       4.16475 ( 1224)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
REVERT: B  234 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.7370 (t80)
REVERT: A  356 TYR cc_start: 0.6345 (OUTLIER) cc_final: 0.5234 (p90)
REVERT: R   87 THR cc_start: 0.8059 (m) cc_final: 0.7775 (p)
REVERT: R  357 SER cc_start: 0.8302 (p) cc_final: 0.7764 (m)
REVERT: R  371 PHE cc_start: 0.5023 (t80) cc_final: 0.4779 (t80)
  outliers start: 19
  outliers final: 12
  residues processed: 109
  average time/residue: 0.4192
  time to fit residues: 48.6017
Evaluate side-chains
  110 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  221 GLU
Chi-restraints excluded: chain A residue  248 MET
Chi-restraints excluded: chain A residue  275 LYS
Chi-restraints excluded: chain A residue  333 ASP
Chi-restraints excluded: chain A residue  356 TYR
Chi-restraints excluded: chain R residue   56 VAL
Chi-restraints excluded: chain R residue  141 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 38 optimal weight:   10.0000
   chunk 22 optimal weight:    3.9990
   chunk 67 optimal weight:   10.0000
   chunk 76 optimal weight:    0.7980
   chunk 58 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 46 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.9386

-------------------------------------------------------------------------------
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 = 0.4173 r_free = 0.4173 target = 0.200736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.165916 restraints weight = 6740.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.3809 rms_B_bonded: 1.31
r_work: 0.3499 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.1796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   6433  Z= 0.207
  Angle     :  0.609   8.455   8813  Z= 0.326
  Chirality :  0.047   0.295   1069
  Planarity :  0.005   0.055   1121
  Dihedral  :  4.883  51.782    957
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 19.34 %
    Favored  : 76.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.74 (0.29), residues: 888
  helix:  3.13 (0.24), residues: 410
  sheet:  0.02 (0.38), residues: 183
  loop : -1.04 (0.34), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  19 
 TYR   0.019   0.002   TYR A 356 
 PHE   0.028   0.002   PHE B 151 
 TRP   0.012   0.002   TRP B  63 
 HIS   0.005   0.001   HIS R 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 ( 6432)
  covalent geometry    : angle       0.60883 ( 8811)
  SS BOND              : bond        0.00439 (    1)
  SS BOND              : angle       1.35137 (    2)
  hydrogen bonds       : bond        0.05061 (  423)
  hydrogen bonds       : angle       4.46934 ( 1224)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 94
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
REVERT: B  228 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7780 (m-30)
REVERT: B  234 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.7383 (t80)
REVERT: A  356 TYR cc_start: 0.6290 (OUTLIER) cc_final: 0.5355 (p90)
REVERT: R  357 SER cc_start: 0.8475 (OUTLIER) cc_final: 0.7965 (m)
  outliers start: 23
  outliers final: 11
  residues processed: 106
  average time/residue: 0.4055
  time to fit residues: 45.7985
Evaluate side-chains
  108 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  221 GLU
Chi-restraints excluded: chain A residue  275 LYS
Chi-restraints excluded: chain A residue  333 ASP
Chi-restraints excluded: chain A residue  356 TYR
Chi-restraints excluded: chain R residue   56 VAL
Chi-restraints excluded: chain R residue  141 CYS
Chi-restraints excluded: chain R residue  338 LEU
Chi-restraints excluded: chain R residue  357 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 71 optimal weight:   10.0000
   chunk 83 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0000
   chunk 31 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   chunk 67 optimal weight:    9.9990
   chunk 64 optimal weight:    0.7980
   chunk 52 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.6784

-------------------------------------------------------------------------------
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 = 0.4209 r_free = 0.4209 target = 0.204654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.168106 restraints weight = 6717.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3832 rms_B_bonded: 1.30
r_work: 0.3502 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.1838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6433  Z= 0.122
  Angle     :  0.520   7.071   8813  Z= 0.278
  Chirality :  0.043   0.280   1069
  Planarity :  0.004   0.045   1121
  Dihedral  :  4.581  53.463    957
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 20.70 %
    Favored  : 75.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.94 (0.29), residues: 888
  helix:  3.38 (0.24), residues: 409
  sheet:  0.06 (0.38), residues: 182
  loop : -1.02 (0.34), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  19 
 TYR   0.012   0.001   TYR A 356 
 PHE   0.015   0.001   PHE B 151 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 6432)
  covalent geometry    : angle       0.51990 ( 8811)
  SS BOND              : bond        0.00244 (    1)
  SS BOND              : angle       1.15014 (    2)
  hydrogen bonds       : bond        0.04097 (  423)
  hydrogen bonds       : angle       4.22804 ( 1224)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
REVERT: B  234 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7436 (t80)
REVERT: A  249 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6822 (mp0)
REVERT: A  292 PHE cc_start: 0.7016 (m-10) cc_final: 0.6709 (m-10)
REVERT: R   87 THR cc_start: 0.7934 (m) cc_final: 0.7627 (p)
REVERT: R  357 SER cc_start: 0.8319 (OUTLIER) cc_final: 0.7852 (m)
REVERT: R  371 PHE cc_start: 0.5197 (t80) cc_final: 0.4723 (t80)
  outliers start: 19
  outliers final: 9
  residues processed: 105
  average time/residue: 0.4123
  time to fit residues: 46.1740
Evaluate side-chains
  102 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  249 GLU
Chi-restraints excluded: chain A residue  275 LYS
Chi-restraints excluded: chain R residue   56 VAL
Chi-restraints excluded: chain R residue  141 CYS
Chi-restraints excluded: chain R residue  357 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 50 optimal weight:    0.8980
   chunk 71 optimal weight:   40.0000
   chunk 70 optimal weight:    0.9990
   chunk 56 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0050
   chunk 66 optimal weight:   10.0000
   chunk 40 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.6796

-------------------------------------------------------------------------------
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 = 0.4213 r_free = 0.4213 target = 0.205044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.169386 restraints weight = 6695.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3840 rms_B_bonded: 1.15
r_work: 0.3527 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3391 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.1904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6433  Z= 0.121
  Angle     :  0.517   6.400   8813  Z= 0.276
  Chirality :  0.042   0.243   1069
  Planarity :  0.004   0.051   1121
  Dihedral  :  4.512  53.445    957
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 21.66 %
    Favored  : 75.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.98 (0.29), residues: 888
  helix:  3.41 (0.24), residues: 409
  sheet:  0.06 (0.38), residues: 182
  loop : -0.97 (0.35), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  19 
 TYR   0.037   0.001   TYR A 356 
 PHE   0.016   0.001   PHE B 151 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.002   0.001   HIS R 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 6432)
  covalent geometry    : angle       0.51643 ( 8811)
  SS BOND              : bond        0.00225 (    1)
  SS BOND              : angle       1.06020 (    2)
  hydrogen bonds       : bond        0.03974 (  423)
  hydrogen bonds       : angle       4.16389 ( 1224)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
REVERT: B  234 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.7441 (t80)
REVERT: A  249 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.6849 (mp0)
REVERT: R   87 THR cc_start: 0.7827 (m) cc_final: 0.7469 (p)
REVERT: R  357 SER cc_start: 0.8240 (OUTLIER) cc_final: 0.7774 (m)
REVERT: R  371 PHE cc_start: 0.5303 (t80) cc_final: 0.4669 (t80)
  outliers start: 15
  outliers final: 8
  residues processed: 102
  average time/residue: 0.4156
  time to fit residues: 45.2788
Evaluate side-chains
  103 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  249 GLU
Chi-restraints excluded: chain A residue  275 LYS
Chi-restraints excluded: chain R residue  141 CYS
Chi-restraints excluded: chain R residue  357 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 38 optimal weight:   10.0000
   chunk 5 optimal weight:    0.7980
   chunk 42 optimal weight:    0.5980
   chunk 79 optimal weight:    0.0030
   chunk 35 optimal weight:    0.9980
   chunk 50 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   chunk 55 optimal weight:    0.7980
   chunk 73 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.5590

-------------------------------------------------------------------------------
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 = 0.4223 r_free = 0.4223 target = 0.205986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.169682 restraints weight = 6774.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3819 rms_B_bonded: 1.40
r_work: 0.3510 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.2008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6433  Z= 0.114
  Angle     :  0.517   7.579   8813  Z= 0.274
  Chirality :  0.042   0.212   1069
  Planarity :  0.004   0.050   1121
  Dihedral  :  4.468  53.813    957
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 22.24 %
    Favored  : 75.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.05 (0.29), residues: 888
  helix:  3.46 (0.24), residues: 409
  sheet:  0.23 (0.39), residues: 177
  loop : -1.01 (0.34), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  19 
 TYR   0.031   0.001   TYR A 356 
 PHE   0.014   0.001   PHE B 151 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.002   0.000   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 6432)
  covalent geometry    : angle       0.51660 ( 8811)
  SS BOND              : bond        0.00200 (    1)
  SS BOND              : angle       1.03699 (    2)
  hydrogen bonds       : bond        0.03807 (  423)
  hydrogen bonds       : angle       4.10538 ( 1224)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
REVERT: B  234 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.7352 (t80)
REVERT: A  249 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6822 (mp0)
REVERT: R   87 THR cc_start: 0.8030 (m) cc_final: 0.7737 (p)
REVERT: R  357 SER cc_start: 0.8253 (p) cc_final: 0.7766 (m)
REVERT: R  371 PHE cc_start: 0.5111 (t80) cc_final: 0.4671 (t80)
  outliers start: 12
  outliers final: 8
  residues processed: 103
  average time/residue: 0.4170
  time to fit residues: 45.7606
Evaluate side-chains
  101 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  249 GLU
Chi-restraints excluded: chain A residue  275 LYS
Chi-restraints excluded: chain R residue  141 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 37 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 41 optimal weight:    0.1980
   chunk 14 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 84 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 38 optimal weight:    8.9990
   chunk 9 optimal weight:    0.5980
   chunk 60 optimal weight:    9.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.205441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.170384 restraints weight = 6644.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3852 rms_B_bonded: 1.30
r_work: 0.3543 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6433  Z= 0.122
  Angle     :  0.528   6.827   8813  Z= 0.280
  Chirality :  0.042   0.183   1069
  Planarity :  0.004   0.050   1121
  Dihedral  :  4.539  53.592    957
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 23.40 %
    Favored  : 74.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.07 (0.29), residues: 888
  helix:  3.48 (0.24), residues: 409
  sheet:  0.22 (0.39), residues: 177
  loop : -1.00 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  19 
 TYR   0.033   0.001   TYR A 356 
 PHE   0.016   0.001   PHE B 151 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.002   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 6432)
  covalent geometry    : angle       0.52734 ( 8811)
  SS BOND              : bond        0.00205 (    1)
  SS BOND              : angle       1.00549 (    2)
  hydrogen bonds       : bond        0.03887 (  423)
  hydrogen bonds       : angle       4.13271 ( 1224)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
REVERT: B  234 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.7451 (t80)
REVERT: A  202 ARG cc_start: 0.8336 (mmt-90) cc_final: 0.8079 (mmt180)
REVERT: A  249 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6874 (mp0)
REVERT: R   87 THR cc_start: 0.8026 (m) cc_final: 0.7759 (p)
REVERT: R  357 SER cc_start: 0.8284 (p) cc_final: 0.7797 (m)
REVERT: R  371 PHE cc_start: 0.5172 (t80) cc_final: 0.4691 (t80)
  outliers start: 12
  outliers final: 8
  residues processed: 100
  average time/residue: 0.4190
  time to fit residues: 44.4980
Evaluate side-chains
  97 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  249 GLU
Chi-restraints excluded: chain A residue  275 LYS
Chi-restraints excluded: chain R residue  141 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 0 optimal weight:   50.0000
   chunk 22 optimal weight:    0.0020
   chunk 3 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0170
   chunk 65 optimal weight:   10.0000
   chunk 9 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   chunk 7 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   overall best weight:    1.6032

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

Flipped N/Q/H residues before XYZ refinement:
** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.201923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.166768 restraints weight = 6707.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3808 rms_B_bonded: 1.30
r_work: 0.3508 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6433  Z= 0.181
  Angle     :  0.611  10.984   8813  Z= 0.322
  Chirality :  0.045   0.189   1069
  Planarity :  0.004   0.056   1121
  Dihedral  :  4.866  51.576    957
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 22.63 %
    Favored  : 74.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.80 (0.29), residues: 888
  helix:  3.25 (0.24), residues: 410
  sheet: -0.09 (0.38), residues: 183
  loop : -1.02 (0.35), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  19 
 TYR   0.031   0.002   TYR A 356 
 PHE   0.025   0.002   PHE B 151 
 TRP   0.011   0.002   TRP B  63 
 HIS   0.003   0.001   HIS R 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 6432)
  covalent geometry    : angle       0.61110 ( 8811)
  SS BOND              : bond        0.00338 (    1)
  SS BOND              : angle       1.14960 (    2)
  hydrogen bonds       : bond        0.04729 (  423)
  hydrogen bonds       : angle       4.39438 ( 1224)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1897.73 seconds
wall clock time: 32 minutes 59.23 seconds (1979.23 seconds total)