Starting phenix.real_space_refine
on Wed Feb  4 06:18:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j4r_61136/02_2026/9j4r_61136.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j4r_61136/02_2026/9j4r_61136.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.09
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j4r_61136/02_2026/9j4r_61136.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j4r_61136/02_2026/9j4r_61136.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j4r_61136/02_2026/9j4r_61136.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j4r_61136/02_2026/9j4r_61136.cif"
  }
  resolution = 3.09
  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=  -0.002 sd=   0.111
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      15      5.16       5
     C    5792      2.51       5
     N    1575      2.21       5
     O    1552      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8934
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3742
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 490, 3742
          Classifications: {'peptide': 490}
          Link IDs: {'PTRANS': 37, 'TRANS': 452}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2596
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2596
          Classifications: {'peptide': 340}
          Link IDs: {'PTRANS': 24, 'TRANS': 315}
    Chain: "C"
      Number of atoms: 2596
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2596
          Classifications: {'peptide': 340}
          Link IDs: {'PTRANS': 24, 'TRANS': 315}
  Time building chain proxies: 2.51, per 1000 atoms: 0.28
  Number of scatterers: 8934
  At special positions: 0
  Unit cell: (96.2577, 85.2282, 134.36, 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      15     16.00
     O    1552      8.00
     N    1575      7.00
     C    5792      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.79
  Conformation dependent library (CDL) restraints added in 387.7 milliseconds
  

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2094

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 8 sheets defined
      55.2% alpha, 16.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 38
      removed outlier: 3.662A  pdb=" N   TYR A  32 " --> pdb=" O   LEU A  28 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LEU A  33 " --> pdb=" O   PRO A  29 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   GLY A  34 " --> pdb=" O   VAL A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 50
    Processing helix  chain 'A' and resid 52 through 85
      removed outlier: 3.545A  pdb=" N   GLU A  56 " --> pdb=" O   PRO A  52 " (cutoff:3.500A)
      Proline residue:  A  78  - end of helix
    Processing helix  chain 'A' and resid 90 through 100
    Processing helix  chain 'A' and resid 101 through 104
    Processing helix  chain 'A' and resid 105 through 116
    Processing helix  chain 'A' and resid 129 through 156
      Proline residue:  A 144  - end of helix
    Processing helix  chain 'A' and resid 158 through 168
      removed outlier: 3.855A  pdb=" N   GLU A 162 " --> pdb=" O   ASP A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 179
    Processing helix  chain 'A' and resid 179 through 202
      removed outlier: 3.801A  pdb=" N   GLN A 183 " --> pdb=" O   VAL A 179 " (cutoff:3.500A)
      Proline residue:  A 186  - end of helix
    Processing helix  chain 'A' and resid 203 through 209
    Processing helix  chain 'A' and resid 213 through 223
    Processing helix  chain 'A' and resid 227 through 256
    Processing helix  chain 'A' and resid 263 through 267
      removed outlier: 4.095A  pdb=" N   ARG A 267 " --> pdb=" O   GLY A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 285
    Processing helix  chain 'A' and resid 286 through 293
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 305 through 307
      No H-bonds generated for 'chain 'A' and resid 305 through 307'
    Processing helix  chain 'A' and resid 308 through 310
      No H-bonds generated for 'chain 'A' and resid 308 through 310'
    Processing helix  chain 'A' and resid 311 through 347
      removed outlier: 3.543A  pdb=" N   ALA A 316 " --> pdb=" O   THR A 312 " (cutoff:3.500A)
      Proline residue:  A 328  - end of helix
      Proline residue:  A 339  - end of helix
    Processing helix  chain 'A' and resid 349 through 365
    Processing helix  chain 'A' and resid 366 through 381
    Processing helix  chain 'A' and resid 382 through 386
    Processing helix  chain 'A' and resid 388 through 400
      removed outlier: 3.751A  pdb=" N   LEU A 392 " --> pdb=" O   THR A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 415
      Proline residue:  A 407  - end of helix
      removed outlier: 3.518A  pdb=" N   VAL A 415 " --> pdb=" O   ALA A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 427
      removed outlier: 3.858A  pdb=" N   GLU A 420 " --> pdb=" O   PRO A 416 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLY A 427 " --> pdb=" O   ALA A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 438
    Processing helix  chain 'A' and resid 438 through 459
      removed outlier: 4.080A  pdb=" N   ARG A 444 " --> pdb=" O   PRO A 440 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LYS A 459 " --> pdb=" O   ILE A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 468
    Processing helix  chain 'A' and resid 474 through 485
    Processing helix  chain 'A' and resid 487 through 516
      Proline residue:  A 493  - end of helix
    Processing helix  chain 'B' and resid 44 through 53
    Processing helix  chain 'B' and resid 74 through 79
      removed outlier: 3.506A  pdb=" N   ARG B  78 " --> pdb=" O   PRO B  74 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   GLY B  79 " --> pdb=" O   PRO B  75 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 74 through 79'
    Processing helix  chain 'B' and resid 94 through 100
    Processing helix  chain 'B' and resid 101 through 103
      No H-bonds generated for 'chain 'B' and resid 101 through 103'
    Processing helix  chain 'B' and resid 107 through 120
    Processing helix  chain 'B' and resid 133 through 147
      removed outlier: 3.586A  pdb=" N   GLN B 138 " --> pdb=" O   GLY B 134 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   ARG B 139 " --> pdb=" O   GLY B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 181
    Processing helix  chain 'B' and resid 191 through 199
      removed outlier: 3.541A  pdb=" N   ALA B 195 " --> pdb=" O   ASP B 191 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   SER B 197 " --> pdb=" O   GLU B 193 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 222
    Processing helix  chain 'B' and resid 225 through 232
    Processing helix  chain 'B' and resid 269 through 271
      No H-bonds generated for 'chain 'B' and resid 269 through 271'
    Processing helix  chain 'C' and resid 44 through 53
      removed outlier: 3.511A  pdb=" N   LEU C  48 " --> pdb=" O   GLY C  44 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 78
      removed outlier: 3.745A  pdb=" N   ARG C  78 " --> pdb=" O   PRO C  75 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 96 through 102
      removed outlier: 4.372A  pdb=" N   GLY C 102 " --> pdb=" O   ASN C  98 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 108 through 119
      removed outlier: 3.775A  pdb=" N   ALA C 112 " --> pdb=" O   ARG C 108 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 128 through 132
      removed outlier: 3.500A  pdb=" N   LEU C 132 " --> pdb=" O   PRO C 129 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 133 through 147
    Processing helix  chain 'C' and resid 158 through 162
      removed outlier: 4.268A  pdb=" N   SER C 161 " --> pdb=" O   PRO C 158 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 163 through 182
      removed outlier: 4.572A  pdb=" N   ALA C 168 " --> pdb=" O   ALA C 164 " (cutoff:3.500A)
      removed outlier: 4.524A  pdb=" N   ALA C 169 " --> pdb=" O   GLY C 165 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   GLU C 172 " --> pdb=" O   ALA C 168 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 191 through 198
      removed outlier: 3.584A  pdb=" N   ALA C 195 " --> pdb=" O   ASP C 191 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 215 through 222
    Processing helix  chain 'C' and resid 225 through 233
    Processing helix  chain 'C' and resid 269 through 271
      No H-bonds generated for 'chain 'C' and resid 269 through 271'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 22 through 28
      removed outlier: 5.936A  pdb=" N   ARG B  23 " --> pdb=" O   LYS B  14 " (cutoff:3.500A)
      removed outlier: 7.949A  pdb=" N   LYS B  14 " --> pdb=" O   ARG B  23 " (cutoff:3.500A)
      removed outlier: 7.634A  pdb=" N   LEU B  27 " --> pdb=" O   LYS B  10 " (cutoff:3.500A)
      removed outlier: 5.365A  pdb=" N   LYS B  10 " --> pdb=" O   LEU B  27 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   ILE B  12 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   ALA B  60 " --> pdb=" O   ILE B  12 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 81 through 83
      removed outlier: 3.993A  pdb=" N   GLN B 212 " --> pdb=" O   VAL B 204 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   ARG B 206 " --> pdb=" O   ILE B 210 " (cutoff:3.500A)
      removed outlier: 5.272A  pdb=" N   ILE B 210 " --> pdb=" O   ARG B 206 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 336 through 338
      removed outlier: 3.760A  pdb=" N   VAL B 336 " --> pdb=" O   SER B 267 " (cutoff:3.500A)
      removed outlier: 4.714A  pdb=" N   LEU B 265 " --> pdb=" O   LEU B 338 " (cutoff:3.500A)
      removed outlier: 11.015A  pdb=" N   LEU B 256 " --> pdb=" O   GLU B 248 " (cutoff:3.500A)
      removed outlier: 11.068A  pdb=" N   GLU B 248 " --> pdb=" O   LEU B 256 " (cutoff:3.500A)
      removed outlier: 8.990A  pdb=" N   GLU B 258 " --> pdb=" O   TYR B 246 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   TYR B 246 " --> pdb=" O   GLU B 258 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 273 through 276
      removed outlier: 6.500A  pdb=" N   ARG B 299 " --> pdb=" O   VAL B 287 " (cutoff:3.500A)
      removed outlier: 4.624A  pdb=" N   ARG B 289 " --> pdb=" O   THR B 297 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   THR B 297 " --> pdb=" O   ARG B 289 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 19 through 28
      removed outlier: 3.755A  pdb=" N   LEU C  19 " --> pdb=" O   PHE C  16 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   LYS C  14 " --> pdb=" O   VAL C  21 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   ARG C  23 " --> pdb=" O   ILE C  12 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   ILE C  12 " --> pdb=" O   ARG C  23 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   VAL C  25 " --> pdb=" O   LYS C  10 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   LYS C  10 " --> pdb=" O   VAL C  25 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   LEU C  27 " --> pdb=" O   GLU C   8 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   GLU C   8 " --> pdb=" O   LEU C  27 " (cutoff:3.500A)
      removed outlier: 4.744A  pdb=" N   ILE C  12 " --> pdb=" O   ALA C  60 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   ALA C  60 " --> pdb=" O   ILE C  12 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 81 through 83
      removed outlier: 6.478A  pdb=" N   GLY C  81 " --> pdb=" O   LEU C 154 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   ASP C 156 " --> pdb=" O   GLY C  81 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   VAL C  83 " --> pdb=" O   ASP C 156 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   GLN C 212 " --> pdb=" O   VAL C 204 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   ARG C 206 " --> pdb=" O   ILE C 210 " (cutoff:3.500A)
      removed outlier: 5.258A  pdb=" N   ILE C 210 " --> pdb=" O   ARG C 206 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 252 through 255
      removed outlier: 4.313A  pdb=" N   LEU C 265 " --> pdb=" O   LEU C 338 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 276
      removed outlier: 6.676A  pdb=" N   ARG C 299 " --> pdb=" O   VAL C 287 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   ARG C 289 " --> pdb=" O   THR C 297 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   THR C 297 " --> pdb=" O   ARG C 289 " (cutoff:3.500A)

    499 hydrogen bonds defined for protein.
    1440 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: 1.54

  Time building geometry restraints manager: 1.07 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2955
        1.34 -     1.46: 1420
        1.46 -     1.57: 4728
        1.57 -     1.69: 0
        1.69 -     1.81: 24
  Bond restraints: 9127
  Sorted by residual:
  bond pdb=" C   LEU A  28 "
       pdb=" N   PRO A  29 "
    ideal  model  delta    sigma   weight residual
    1.334  1.361 -0.027 2.34e-02 1.83e+03 1.37e+00
  bond pdb=" CG  PRO B 263 "
       pdb=" CD  PRO B 263 "
    ideal  model  delta    sigma   weight residual
    1.503  1.540 -0.037 3.40e-02 8.65e+02 1.16e+00
  bond pdb=" CB  PRO C 239 "
       pdb=" CG  PRO C 239 "
    ideal  model  delta    sigma   weight residual
    1.492  1.544 -0.052 5.00e-02 4.00e+02 1.10e+00
  bond pdb=" C   LEU A 100 "
       pdb=" N   PRO A 101 "
    ideal  model  delta    sigma   weight residual
    1.334  1.357 -0.023 2.34e-02 1.83e+03 9.83e-01
  bond pdb=" C   LEU A 461 "
       pdb=" N   PRO A 462 "
    ideal  model  delta    sigma   weight residual
    1.334  1.357 -0.023 2.34e-02 1.83e+03 9.80e-01
  ... (remaining 9122 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 12147
        1.62 -     3.24: 210
        3.24 -     4.86: 41
        4.86 -     6.48: 9
        6.48 -     8.10: 2
  Bond angle restraints: 12409
  Sorted by residual:
  angle pdb=" C   ASP B  86 "
        pdb=" N   TYR B  87 "
        pdb=" CA  TYR B  87 "
      ideal   model   delta    sigma   weight residual
     121.54  126.33   -4.79 1.91e+00 2.74e-01 6.28e+00
  angle pdb=" CA  TYR A 143 "
        pdb=" C   TYR A 143 "
        pdb=" N   PRO A 144 "
      ideal   model   delta    sigma   weight residual
     118.44  122.29   -3.85 1.59e+00 3.96e-01 5.85e+00
  angle pdb=" C   SER A 257 "
        pdb=" N   LEU A 258 "
        pdb=" CA  LEU A 258 "
      ideal   model   delta    sigma   weight residual
     121.54  126.01   -4.47 1.91e+00 2.74e-01 5.47e+00
  angle pdb=" CA  LEU A 258 "
        pdb=" CB  LEU A 258 "
        pdb=" CG  LEU A 258 "
      ideal   model   delta    sigma   weight residual
     116.30  124.40   -8.10 3.50e+00 8.16e-02 5.35e+00
  angle pdb=" C   ASP C  86 "
        pdb=" N   TYR C  87 "
        pdb=" CA  TYR C  87 "
      ideal   model   delta    sigma   weight residual
     121.54  125.82   -4.28 1.91e+00 2.74e-01 5.02e+00
  ... (remaining 12404 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.68: 5051
       17.68 -    35.35: 365
       35.35 -    53.03: 50
       53.03 -    70.71: 12
       70.71 -    88.38: 6
  Dihedral angle restraints: 5484
    sinusoidal: 2193
      harmonic: 3291
  Sorted by residual:
  dihedral pdb=" CA  ALA C  95 "
           pdb=" C   ALA C  95 "
           pdb=" N   LEU C  96 "
           pdb=" CA  LEU C  96 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.54   16.46     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" CA  ASP A 202 "
           pdb=" CB  ASP A 202 "
           pdb=" CG  ASP A 202 "
           pdb=" OD1 ASP A 202 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.52   56.52     1      2.00e+01 2.50e-03 1.08e+01
  dihedral pdb=" CA  LEU C 238 "
           pdb=" C   LEU C 238 "
           pdb=" N   PRO C 239 "
           pdb=" CA  PRO C 239 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.74   16.26     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 5481 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 874
       0.027 -    0.054: 362
       0.054 -    0.082: 95
       0.082 -    0.109: 88
       0.109 -    0.136: 21
  Chirality restraints: 1440
  Sorted by residual:
  chirality pdb=" CA  ILE A 365 "
            pdb=" N   ILE A 365 "
            pdb=" C   ILE A 365 "
            pdb=" CB  ILE A 365 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.63e-01
  chirality pdb=" CA  ILE B  80 "
            pdb=" N   ILE B  80 "
            pdb=" C   ILE B  80 "
            pdb=" CB  ILE B  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.79e-01
  chirality pdb=" CB  ILE A 455 "
            pdb=" CA  ILE A 455 "
            pdb=" CG1 ILE A 455 "
            pdb=" CG2 ILE A 455 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.52    0.12 2.00e-01 2.50e+01 3.78e-01
  ... (remaining 1437 not shown)

  Planarity restraints: 1604
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 238 "    0.074 5.00e-02 4.00e+02   1.11e-01 1.98e+01
        pdb=" N   PRO C 239 "   -0.192 5.00e-02 4.00e+02
        pdb=" CA  PRO C 239 "    0.059 5.00e-02 4.00e+02
        pdb=" CD  PRO C 239 "    0.060 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 262 "   -0.040 5.00e-02 4.00e+02   6.04e-02 5.85e+00
        pdb=" N   PRO B 263 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO B 263 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 263 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 100 "    0.035 5.00e-02 4.00e+02   5.39e-02 4.66e+00
        pdb=" N   PRO A 101 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 101 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 101 "    0.030 5.00e-02 4.00e+02
  ... (remaining 1601 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 607
        2.74 -     3.28: 8457
        3.28 -     3.82: 14423
        3.82 -     4.36: 17315
        4.36 -     4.90: 31177
  Nonbonded interactions: 71979
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 138 "
            pdb=" OG1 THR A 142 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" O   GLY C 105 "
            pdb=" NH1 ARG C 108 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" OG1 THR B 189 "
            pdb=" OE1 GLU B 194 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" NH1 ARG C 175 "
            pdb=" O   PHE C 198 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" NH2 ARG C 234 "
            pdb=" OE1 GLN C 314 "
     model   vdw
     2.286 3.120
  ... (remaining 71974 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
}

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:             1.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.420
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7076
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   0.052   9127  Z= 0.131
  Angle     :  0.571   8.095  12409  Z= 0.276
  Chirality :  0.039   0.136   1440
  Planarity :  0.006   0.111   1604
  Dihedral  : 12.474  88.384   3390
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.25), residues: 1162
  helix:  1.58 (0.22), residues: 576
  sheet:  0.16 (0.39), residues: 171
  loop : -1.26 (0.29), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 108 
 TYR   0.013   0.001   TYR A 230 
 PHE   0.014   0.001   PHE A 377 
 TRP   0.013   0.001   TRP A 443 
 HIS   0.002   0.000   HIS A 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 9127)
  covalent geometry    : angle       0.57102 (12409)
  hydrogen bonds       : bond        0.12941 (  499)
  hydrogen bonds       : angle       5.43020 ( 1440)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.331 
Fit side-chains
REVERT: A   84 THR cc_start: 0.7451 (m) cc_final: 0.7209 (m)
REVERT: A  222 TYR cc_start: 0.7965 (t80) cc_final: 0.7700 (t80)
REVERT: A  363 TYR cc_start: 0.7069 (t80) cc_final: 0.6731 (t80)
REVERT: B  246 TYR cc_start: 0.7001 (p90) cc_final: 0.6377 (p90)
REVERT: B  301 ARG cc_start: 0.7369 (ttm110) cc_final: 0.6554 (ttp80)
REVERT: C   77 LYS cc_start: 0.7705 (mmmt) cc_final: 0.7156 (mtmt)
REVERT: C  136 GLN cc_start: 0.7487 (mt0) cc_final: 0.7152 (mt0)
REVERT: C  205 MET cc_start: 0.8082 (mtp) cc_final: 0.7604 (mtp)
REVERT: C  285 GLU cc_start: 0.6701 (mt-10) cc_final: 0.5943 (pt0)
REVERT: C  301 ARG cc_start: 0.6757 (ttp80) cc_final: 0.5926 (ttm-80)
REVERT: C  322 LYS cc_start: 0.7308 (tptt) cc_final: 0.6872 (mmtm)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.1465
  time to fit residues: 22.2721
Evaluate side-chains
  85 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9990
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 125 GLN
C 283 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.153515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.119477 restraints weight = 9878.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 1.70
r_work: 0.3079 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2934 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.0874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9127  Z= 0.150
  Angle     :  0.576   6.127  12409  Z= 0.277
  Chirality :  0.040   0.140   1440
  Planarity :  0.006   0.077   1604
  Dihedral  :  3.876  16.253   1299
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  5.62 %
    Favored  : 93.39 %
  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:  0.72 (0.25), residues: 1162
  helix:  1.72 (0.22), residues: 585
  sheet:  0.05 (0.39), residues: 180
  loop : -1.21 (0.30), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 201 
 TYR   0.013   0.001   TYR A 230 
 PHE   0.010   0.001   PHE A 214 
 TRP   0.012   0.001   TRP A 443 
 HIS   0.002   0.001   HIS B 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 9127)
  covalent geometry    : angle       0.57617 (12409)
  hydrogen bonds       : bond        0.03650 (  499)
  hydrogen bonds       : angle       4.49584 ( 1440)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.393 
Fit side-chains
REVERT: A   84 THR cc_start: 0.8119 (m) cc_final: 0.7864 (m)
REVERT: A  353 ARG cc_start: 0.7519 (mtm110) cc_final: 0.7147 (mtm110)
REVERT: B  246 TYR cc_start: 0.7430 (p90) cc_final: 0.7076 (p90)
REVERT: B  301 ARG cc_start: 0.7861 (ttm110) cc_final: 0.7361 (ttp80)
REVERT: C   56 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7879 (mt-10)
REVERT: C  205 MET cc_start: 0.8230 (mtp) cc_final: 0.7893 (mtp)
REVERT: C  222 ARG cc_start: 0.8241 (mmt90) cc_final: 0.7825 (tpp80)
REVERT: C  285 GLU cc_start: 0.7734 (mt-10) cc_final: 0.6978 (pt0)
REVERT: C  322 LYS cc_start: 0.7718 (tptt) cc_final: 0.7396 (mmtm)
  outliers start: 9
  outliers final: 6
  residues processed: 99
  average time/residue: 0.1449
  time to fit residues: 18.3855
Evaluate side-chains
  97 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain C residue   56 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 16 optimal weight:    0.2980
   chunk 51 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   chunk 108 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 75 optimal weight:    0.6980
   chunk 90 optimal weight:    1.9990
   chunk 109 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
C 125 GLN
C 136 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.178595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.148140 restraints weight = 9322.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 1.69
r_work: 0.3264 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.1045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9127  Z= 0.122
  Angle     :  0.532   5.672  12409  Z= 0.256
  Chirality :  0.038   0.137   1440
  Planarity :  0.005   0.065   1604
  Dihedral  :  3.771  16.599   1299
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  6.83 %
    Favored  : 92.29 %
  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:  0.85 (0.25), residues: 1162
  helix:  1.87 (0.22), residues: 584
  sheet:  0.12 (0.39), residues: 180
  loop : -1.21 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 301 
 TYR   0.010   0.001   TYR A  32 
 PHE   0.009   0.001   PHE B 227 
 TRP   0.013   0.001   TRP A 443 
 HIS   0.001   0.000   HIS A 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 9127)
  covalent geometry    : angle       0.53218 (12409)
  hydrogen bonds       : bond        0.03314 (  499)
  hydrogen bonds       : angle       4.31647 ( 1440)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 91
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A   84 THR cc_start: 0.8195 (m) cc_final: 0.7939 (m)
REVERT: B  243 ARG cc_start: 0.7524 (mtp85) cc_final: 0.7234 (mtp180)
REVERT: B  246 TYR cc_start: 0.7563 (p90) cc_final: 0.7330 (p90)
REVERT: B  253 ARG cc_start: 0.8154 (ttm170) cc_final: 0.7903 (mtp180)
REVERT: B  301 ARG cc_start: 0.7963 (ttm110) cc_final: 0.7515 (ttp80)
REVERT: C  222 ARG cc_start: 0.8418 (mmt90) cc_final: 0.7996 (tpp80)
REVERT: C  285 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7125 (pt0)
REVERT: C  322 LYS cc_start: 0.7675 (tptt) cc_final: 0.7457 (mmtm)
  outliers start: 8
  outliers final: 5
  residues processed: 94
  average time/residue: 0.1345
  time to fit residues: 16.4130
Evaluate side-chains
  92 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 87
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  225 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   chunk 80 optimal weight:    2.9990
   chunk 64 optimal weight:    0.5980
   chunk 90 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 104 optimal weight:    0.0570
   chunk 53 optimal weight:    0.9990
   chunk 100 optimal weight:    0.5980
   chunk 93 optimal weight:    2.9990
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
C 137 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.175636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.147387 restraints weight = 9468.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.3569 rms_B_bonded: 1.46
r_work: 0.3352 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.1192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9127  Z= 0.117
  Angle     :  0.522   5.644  12409  Z= 0.250
  Chirality :  0.038   0.136   1440
  Planarity :  0.005   0.056   1604
  Dihedral  :  3.702  16.175   1299
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  8.26 %
    Favored  : 90.64 %
  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:  0.94 (0.25), residues: 1162
  helix:  1.97 (0.22), residues: 584
  sheet:  0.14 (0.39), residues: 180
  loop : -1.20 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 353 
 TYR   0.009   0.001   TYR A  32 
 PHE   0.015   0.001   PHE B 124 
 TRP   0.012   0.001   TRP A 443 
 HIS   0.001   0.000   HIS A 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 9127)
  covalent geometry    : angle       0.52166 (12409)
  hydrogen bonds       : bond        0.03121 (  499)
  hydrogen bonds       : angle       4.19174 ( 1440)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.339 
Fit side-chains
REVERT: A   84 THR cc_start: 0.8200 (m) cc_final: 0.7949 (m)
REVERT: B  253 ARG cc_start: 0.8092 (ttm170) cc_final: 0.7841 (mtp180)
REVERT: B  301 ARG cc_start: 0.8025 (ttm110) cc_final: 0.7610 (ttp80)
REVERT: C   56 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7725 (mt-10)
REVERT: C  222 ARG cc_start: 0.8376 (mmt90) cc_final: 0.7970 (tpp80)
REVERT: C  285 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7075 (pt0)
REVERT: C  290 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7408 (mt-10)
  outliers start: 10
  outliers final: 8
  residues processed: 96
  average time/residue: 0.1292
  time to fit residues: 16.2982
Evaluate side-chains
  92 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain C residue  215 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 108 optimal weight:    6.9990
   chunk 85 optimal weight:    2.9990
   chunk 48 optimal weight:    7.9990
   chunk 38 optimal weight:    0.5980
   chunk 110 optimal weight:    2.9990
   chunk 98 optimal weight:    0.4980
   chunk 35 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9980
   chunk 93 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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 = 0.3956 r_free = 0.3956 target = 0.175144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.145669 restraints weight = 9469.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 1.61
r_work: 0.3318 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.1338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   9127  Z= 0.191
  Angle     :  0.601   5.772  12409  Z= 0.286
  Chirality :  0.041   0.168   1440
  Planarity :  0.006   0.055   1604
  Dihedral  :  3.934  16.247   1299
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  :  9.36 %
    Favored  : 89.43 %
  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:  0.62 (0.25), residues: 1162
  helix:  1.67 (0.22), residues: 585
  sheet:  0.05 (0.38), residues: 182
  loop : -1.35 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 353 
 TYR   0.016   0.002   TYR A  32 
 PHE   0.016   0.002   PHE A 214 
 TRP   0.012   0.001   TRP A 443 
 HIS   0.002   0.001   HIS C  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 ( 9127)
  covalent geometry    : angle       0.60143 (12409)
  hydrogen bonds       : bond        0.03822 (  499)
  hydrogen bonds       : angle       4.39663 ( 1440)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.353 
Fit side-chains
REVERT: A   84 THR cc_start: 0.8252 (m) cc_final: 0.7973 (m)
REVERT: B  253 ARG cc_start: 0.8087 (ttm170) cc_final: 0.7813 (mtp180)
REVERT: B  301 ARG cc_start: 0.8051 (ttm110) cc_final: 0.7615 (ttp80)
REVERT: C   56 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7672 (mt-10)
REVERT: C  222 ARG cc_start: 0.8433 (mmt90) cc_final: 0.8006 (tpp80)
REVERT: C  285 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7191 (pt0)
  outliers start: 11
  outliers final: 9
  residues processed: 102
  average time/residue: 0.1266
  time to fit residues: 17.0414
Evaluate side-chains
  99 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  232 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 54 optimal weight:    0.4980
   chunk 112 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0470
   chunk 99 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 108 optimal weight:    2.9990
   chunk 63 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   overall best weight:    0.5678

-------------------------------------------------------------------------------
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 = 0.3980 r_free = 0.3980 target = 0.177445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.147622 restraints weight = 9394.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 1.78
r_work: 0.3355 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.1388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9127  Z= 0.122
  Angle     :  0.539   5.590  12409  Z= 0.260
  Chirality :  0.038   0.136   1440
  Planarity :  0.005   0.052   1604
  Dihedral  :  3.815  16.519   1299
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 10.79 %
    Favored  : 87.89 %
  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:  0.79 (0.25), residues: 1162
  helix:  1.87 (0.22), residues: 584
  sheet:  0.19 (0.40), residues: 163
  loop : -1.35 (0.29), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 353 
 TYR   0.011   0.001   TYR A  32 
 PHE   0.009   0.001   PHE B 227 
 TRP   0.014   0.001   TRP A 443 
 HIS   0.002   0.000   HIS A 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 9127)
  covalent geometry    : angle       0.53937 (12409)
  hydrogen bonds       : bond        0.03206 (  499)
  hydrogen bonds       : angle       4.24232 ( 1440)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 THR cc_start: 0.8224 (m) cc_final: 0.7942 (m)
REVERT: B  301 ARG cc_start: 0.8008 (ttm110) cc_final: 0.7580 (ttp80)
REVERT: C   56 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7701 (mt-10)
REVERT: C  136 GLN cc_start: 0.8142 (mt0) cc_final: 0.7864 (mt0)
REVERT: C  222 ARG cc_start: 0.8394 (mmt90) cc_final: 0.7994 (tpp80)
REVERT: C  285 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7169 (pt0)
  outliers start: 12
  outliers final: 6
  residues processed: 95
  average time/residue: 0.1339
  time to fit residues: 16.6908
Evaluate side-chains
  91 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain C residue   56 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0970
   chunk 17 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0170
   chunk 82 optimal weight:    0.5980
   chunk 42 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   chunk 91 optimal weight:    2.9990
   chunk 72 optimal weight:    0.6980
   overall best weight:    0.4016

-------------------------------------------------------------------------------
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 = 0.3971 r_free = 0.3971 target = 0.176877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 85)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.148865 restraints weight = 9473.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3624 rms_B_bonded: 1.53
r_work: 0.3402 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.1451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9127  Z= 0.105
  Angle     :  0.515   5.572  12409  Z= 0.248
  Chirality :  0.038   0.133   1440
  Planarity :  0.005   0.051   1604
  Dihedral  :  3.668  16.228   1299
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  : 11.45 %
    Favored  : 87.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.25), residues: 1162
  helix:  2.05 (0.22), residues: 584
  sheet:  0.14 (0.39), residues: 180
  loop : -1.20 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 353 
 TYR   0.008   0.001   TYR A  32 
 PHE   0.008   0.001   PHE A 494 
 TRP   0.014   0.001   TRP A 443 
 HIS   0.001   0.000   HIS A 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 9127)
  covalent geometry    : angle       0.51509 (12409)
  hydrogen bonds       : bond        0.02884 (  499)
  hydrogen bonds       : angle       4.08686 ( 1440)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 THR cc_start: 0.8177 (m) cc_final: 0.7863 (m)
REVERT: A  222 TYR cc_start: 0.8647 (t80) cc_final: 0.8319 (t80)
REVERT: B  301 ARG cc_start: 0.8034 (ttm110) cc_final: 0.7597 (ttp80)
REVERT: C   56 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7742 (mt-10)
REVERT: C  136 GLN cc_start: 0.8163 (mt0) cc_final: 0.7911 (mt0)
REVERT: C  222 ARG cc_start: 0.8362 (mmt90) cc_final: 0.7965 (tpp80)
REVERT: C  285 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7107 (pt0)
  outliers start: 7
  outliers final: 6
  residues processed: 91
  average time/residue: 0.1331
  time to fit residues: 15.7148
Evaluate side-chains
  86 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 79
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain C residue  215 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 87 optimal weight:    0.6980
   chunk 82 optimal weight:    3.9990
   chunk 104 optimal weight:    0.5980
   chunk 96 optimal weight:    0.9990
   chunk 81 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   chunk 24 optimal weight:    0.4980
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3985 r_free = 0.3985 target = 0.177950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.148905 restraints weight = 9384.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 1.76
r_work: 0.3351 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.1504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9127  Z= 0.130
  Angle     :  0.541   5.917  12409  Z= 0.259
  Chirality :  0.039   0.138   1440
  Planarity :  0.005   0.051   1604
  Dihedral  :  3.720  15.918   1299
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 11.67 %
    Favored  : 87.44 %
  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:  0.95 (0.25), residues: 1162
  helix:  1.99 (0.22), residues: 584
  sheet:  0.13 (0.38), residues: 182
  loop : -1.21 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 353 
 TYR   0.011   0.001   TYR A  32 
 PHE   0.009   0.001   PHE A 214 
 TRP   0.012   0.001   TRP A 443 
 HIS   0.001   0.000   HIS A 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 9127)
  covalent geometry    : angle       0.54087 (12409)
  hydrogen bonds       : bond        0.03132 (  499)
  hydrogen bonds       : angle       4.12893 ( 1440)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 THR cc_start: 0.8209 (m) cc_final: 0.7893 (m)
REVERT: B  301 ARG cc_start: 0.8035 (ttm110) cc_final: 0.7592 (ttp80)
REVERT: C   56 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7716 (mt-10)
REVERT: C  136 GLN cc_start: 0.8229 (mt0) cc_final: 0.7984 (mt0)
REVERT: C  222 ARG cc_start: 0.8400 (mmt90) cc_final: 0.7979 (tpp80)
REVERT: C  285 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7055 (pt0)
  outliers start: 8
  outliers final: 7
  residues processed: 89
  average time/residue: 0.1323
  time to fit residues: 15.1838
Evaluate side-chains
  91 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain C residue  215 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 83 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   chunk 46 optimal weight:    0.5980
   chunk 106 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0570
   chunk 32 optimal weight:    0.9980
   chunk 3 optimal weight:    0.4980
   chunk 26 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0970
   chunk 98 optimal weight:    0.0980
   overall best weight:    0.2696

-------------------------------------------------------------------------------
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 = 0.3995 r_free = 0.3995 target = 0.178846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.150833 restraints weight = 9383.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 1.48
r_work: 0.3397 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.1590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9127  Z= 0.096
  Angle     :  0.502   5.771  12409  Z= 0.242
  Chirality :  0.037   0.131   1440
  Planarity :  0.005   0.050   1604
  Dihedral  :  3.568  17.052   1299
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  : 11.89 %
    Favored  : 87.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.25), residues: 1162
  helix:  2.16 (0.22), residues: 585
  sheet:  0.20 (0.39), residues: 180
  loop : -1.11 (0.30), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 353 
 TYR   0.008   0.001   TYR A 143 
 PHE   0.007   0.001   PHE B 227 
 TRP   0.015   0.001   TRP A 443 
 HIS   0.001   0.000   HIS C 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 9127)
  covalent geometry    : angle       0.50190 (12409)
  hydrogen bonds       : bond        0.02683 (  499)
  hydrogen bonds       : angle       3.97615 ( 1440)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 THR cc_start: 0.8150 (m) cc_final: 0.7874 (m)
REVERT: A  222 TYR cc_start: 0.8652 (t80) cc_final: 0.8331 (t80)
REVERT: A  357 ARG cc_start: 0.7284 (mmp-170) cc_final: 0.7011 (mmp80)
REVERT: B  301 ARG cc_start: 0.8040 (ttm110) cc_final: 0.7615 (ttp80)
REVERT: C   56 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7745 (mt-10)
REVERT: C  222 ARG cc_start: 0.8370 (mmt90) cc_final: 0.7963 (tpp80)
REVERT: C  285 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7091 (pt0)
REVERT: C  290 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7491 (mt-10)
  outliers start: 7
  outliers final: 6
  residues processed: 94
  average time/residue: 0.1279
  time to fit residues: 15.7389
Evaluate side-chains
  91 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain C residue  215 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 99 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 15 optimal weight:    0.4980
   chunk 57 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
C 136 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.178057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.149227 restraints weight = 9440.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 1.67
r_work: 0.3450 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3313 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.1565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9127  Z= 0.138
  Angle     :  0.558   6.565  12409  Z= 0.265
  Chirality :  0.039   0.139   1440
  Planarity :  0.005   0.056   1604
  Dihedral  :  3.698  16.082   1299
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 12.00 %
    Favored  : 87.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.25), residues: 1162
  helix:  2.01 (0.22), residues: 585
  sheet:  0.17 (0.38), residues: 182
  loop : -1.15 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 353 
 TYR   0.012   0.001   TYR A  32 
 PHE   0.010   0.001   PHE A 214 
 TRP   0.010   0.001   TRP A 443 
 HIS   0.002   0.000   HIS A 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 9127)
  covalent geometry    : angle       0.55751 (12409)
  hydrogen bonds       : bond        0.03148 (  499)
  hydrogen bonds       : angle       4.10509 ( 1440)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 THR cc_start: 0.8215 (m) cc_final: 0.7961 (m)
REVERT: A  357 ARG cc_start: 0.7361 (mmp-170) cc_final: 0.7084 (mmp80)
REVERT: B  301 ARG cc_start: 0.8100 (ttm110) cc_final: 0.7628 (ttp80)
REVERT: C   56 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7895 (mt-10)
REVERT: C  136 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.8003 (mt0)
REVERT: C  222 ARG cc_start: 0.8455 (mmt90) cc_final: 0.8025 (tpp80)
REVERT: C  285 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7166 (pt0)
  outliers start: 9
  outliers final: 7
  residues processed: 90
  average time/residue: 0.1356
  time to fit residues: 15.8197
Evaluate side-chains
  93 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain C residue  136 GLN
Chi-restraints excluded: chain C residue  215 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 89 optimal weight:    0.0470
   chunk 105 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 53 optimal weight:    0.6980
   chunk 106 optimal weight:    0.9990
   chunk 115 optimal weight:    0.0030
   chunk 97 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.4488

-------------------------------------------------------------------------------
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 = 0.3978 r_free = 0.3978 target = 0.177181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.150465 restraints weight = 9337.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.3674 rms_B_bonded: 1.46
r_work: 0.3489 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3353 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9127  Z= 0.110
  Angle     :  0.529   7.230  12409  Z= 0.254
  Chirality :  0.038   0.135   1440
  Planarity :  0.005   0.050   1604
  Dihedral  :  3.655  16.319   1299
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 12.00 %
    Favored  : 87.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.25), residues: 1162
  helix:  2.06 (0.22), residues: 585
  sheet:  0.20 (0.39), residues: 180
  loop : -1.12 (0.30), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 353 
 TYR   0.010   0.001   TYR A  32 
 PHE   0.008   0.001   PHE B 227 
 TRP   0.013   0.001   TRP A 443 
 HIS   0.001   0.000   HIS A 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 9127)
  covalent geometry    : angle       0.52917 (12409)
  hydrogen bonds       : bond        0.02919 (  499)
  hydrogen bonds       : angle       4.06889 ( 1440)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2145.98 seconds
wall clock time: 37 minutes 32.11 seconds (2252.11 seconds total)